https://wiki.lhep.unibe.ch/api.php?action=feedcontributions&feedformat=atom&user=Nsallin 2026-05-14T09:59:20Z User contributions MediaWiki 1.43.8 https://wiki.lhep.unibe.ch/index.php?title=Get_Started&diff=958 2026-05-12T15:13:45Z

<p>Nsallin: </p> <hr /> <div>Welcome in the neutrino group, on this page you will find information about how to get access to the resources necessary to work and some useful tips to get started. The first requirement is to get a ''UNIBE email account'', please ask the LHEP secretary if you don't have one yet.<br /> <br /> = Slack =<br /> Slack is a very practical tool to exchange with other collaborators. We have a dedicated workspace for LHEP people and there is a DUNE collaboration one.<br /> <br /> === LHEP Slack ===<br /> To obtain an access to the LHEP Slack workspace, simply ask someone already in the workplace to add you. How to add a person: Under ''home'' you can click on the title of the workspace, which open a scroll-down menu. Then click on ''invite people to join...'' and provide the email address of the person you want to add.<br /> <br /> === DUNE Slack ===<br /> To get added to the DUNE workspace, write to ''dune-slack@fnal.gov'' to request access.<br /> <br /> = FNAL =<br /> <br /> == FNAL Account ==<br /> A Fermilab account is needed to get access to some DUNE ressources and to the Fermilab site. To request the account please follow these [https://get-connected.fnal.gov/users-affiliates-access/ instructions]. To get the on-site access visit the [[Access to Fermilab]] page<br /> <br /> == FNAL Mailing list ==<br /> A lot of information are transmitted through the Fermilab mailing list. Here are the instruction to subscribe to the desired one: [https://listserv.fnal.gov/users.asp FNAL Mailing list]<br /> <br /> <br /> = NERSC =<br /> The ''National Energy Research Scientific Computing Center'' (NERSC) is a US computing facility with dedicated DUNE resources. Most of the data are accessible from there and the infrastructure allows to run demanding jobs. The [https://docs.nersc.gov/getting-started/ get started] page will give you addidtional information (including how ot create an account). The associated Jupyter hub can be accessed under [https://jupyter.nersc.gov/hub/login?next=%2Fhub%2Fhome Jupyter@NERSC]<br /> <br /> = DUNE Github =<br /> Most to the code scripts are stored on the DUNE Github under the ''ndlar-flow'' project. Information to join it can be found one the [[Ndlar-flow]] page.<br /> <br /> = LHEP =<br /> Some ressources are also available directly from LHEP.<br /> <br /> === Mailing list ===<br /> There are also several lhep mailing lists, you can see more information [https://listserv.unibe.ch/mailman/listinfo here]. The general LHEP mailing list is ''lhep'' and the neutrino group one is ''lhep-neutrino'' (Note that for shady reasons we are currently using ''lhep-newprojects'' as our group one)<br /> <br /> === Servers ===<br /> 2 Servers are available, neutrino01 and neutrino02 under the address &lt;code&gt;neutrino0X.lhep.unibe.ch&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === Google Drive ===<br /> A lot of documents are available on our common google drive under the username &lt;code&gt;argoncube@gmail.com&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === ELOG ===<br /> The LHEP [https://elog.lhep.unibe.ch ELOG] is used to store diverse information. Ask somebody from the LHEP IT to be added.<br /> <br /> === Github ===<br /> An LHEP neutrino Github is also available [https://github.com/LHEP-neutrino here]. Ask one of the owner to be added.<br /> <br /> = CERN account =<br /> The CERN account allows you to access computing ressources and on-site access. To request it, ask Michele to fill the relevant form and follow the procedure detailed in the email resulting from the access request.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Get_Started&diff=957 2026-05-12T15:13:27Z

<p>Nsallin: </p> <hr /> <div>Welcome in the neutrino group, on this page you will find information about how to get access to the resources necessary to work and some useful tips to get started. The first requirement is to get a ''UNIBE email account'', please ask the LHEP secretary if you don't have one yet.<br /> <br /> = Slack =<br /> Slack is a very practical tool to exchange with other collaborators. We have a dedicated workspace for LHEP people and there is a DUNE collaboration one.<br /> <br /> === LHEP Slack ===<br /> To obtain an access to the LHEP Slack workspace, simply ask someone already in the workplace to add you. How to add a person: Under ''home'' you can click on the title of the workspace, which open a scroll-down menu. Then click on ''invite people to join...'' and provide the email address of the person you want to add.<br /> <br /> === DUNE Slack ===<br /> To get added to the DUNE workspace, write to ''dune-slack@fnal.gov'' to request access.<br /> <br /> = FNAL =<br /> <br /> == FNAL Account ==<br /> A Fermilab account is needed to get access to some DUNE ressources and to the Fermilab site. To request the account please follow these [https://get-connected.fnal.gov/users-affiliates-access/ instructions]. To get the on-site access visit the [[Access to Fermilab]] page<br /> <br /> == FNAL Mailing list ==<br /> A lot of information are transmitted through the Fermilab mailing list. Here are the instruction to subscribe to the desired one:[https://listserv.fnal.gov/users.asp FNAL Mailing list]<br /> <br /> <br /> = NERSC =<br /> The ''National Energy Research Scientific Computing Center'' (NERSC) is a US computing facility with dedicated DUNE resources. Most of the data are accessible from there and the infrastructure allows to run demanding jobs. The [https://docs.nersc.gov/getting-started/ get started] page will give you addidtional information (including how ot create an account). The associated Jupyter hub can be accessed under [https://jupyter.nersc.gov/hub/login?next=%2Fhub%2Fhome Jupyter@NERSC]<br /> <br /> = DUNE Github =<br /> Most to the code scripts are stored on the DUNE Github under the ''ndlar-flow'' project. Information to join it can be found one the [[Ndlar-flow]] page.<br /> <br /> = LHEP =<br /> Some ressources are also available directly from LHEP.<br /> <br /> === Mailing list ===<br /> There are also several lhep mailing lists, you can see more information [https://listserv.unibe.ch/mailman/listinfo here]. The general LHEP mailing list is ''lhep'' and the neutrino group one is ''lhep-neutrino'' (Note that for shady reasons we are currently using ''lhep-newprojects'' as our group one)<br /> <br /> === Servers ===<br /> 2 Servers are available, neutrino01 and neutrino02 under the address &lt;code&gt;neutrino0X.lhep.unibe.ch&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === Google Drive ===<br /> A lot of documents are available on our common google drive under the username &lt;code&gt;argoncube@gmail.com&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === ELOG ===<br /> The LHEP [https://elog.lhep.unibe.ch ELOG] is used to store diverse information. Ask somebody from the LHEP IT to be added.<br /> <br /> === Github ===<br /> An LHEP neutrino Github is also available [https://github.com/LHEP-neutrino here]. Ask one of the owner to be added.<br /> <br /> = CERN account =<br /> The CERN account allows you to access computing ressources and on-site access. To request it, ask Michele to fill the relevant form and follow the procedure detailed in the email resulting from the access request.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=956 2026-05-12T14:35:02Z

<p>Nsallin: /* Useful links */</p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == Group meeting ==<br /> Once a week we have the group meeting where the current activities of the group members are presented and discussed. The agenda can be found on [https://indico.global/category/1448/ indico]. If you present something, please update you slides on the agenda to archive your work and future references. Note that to upload your slides you will need to create an account, this can be done through the cern account or the Switch edi-ID (UNIBE account).<br /> <br /> == ND-LAr ==<br /> [https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]<br /> [https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository. See the FSD data chapter for a short introduction.<br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> A short introduction to 2x2 and FSD data can be found on the [[Setup to process FSD data on neutrino01]] page.<br /> <br /> == 2x2 ==<br /> <br /> === Shifting ===<br /> The instructions to shift from the Bern ROC machine are listed [[Bern ROC shifting station|here]].<br /> <br /> == ArCLight ==<br /> <br /> === Production ===<br /> Documentation of the production can be found [[Production of ArCLights|here]].<br /> <br /> === QC/QA ===<br /> Documentation for the quality control can be found [[ACL Quality Control|here]]<br /> <br /> == Tutorials ==<br /> Here are regrouped a few, hopefully soon many, tutorials.<br /> <br /> === Git repo ===<br /> How to set up a (or many) [[Git repository]].<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://indico.global/category/1448/ Group Meeting Agenda]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://www.reiseplattform.unibe.ch/before_you_start/index_eng.html UNIBE travel platform]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=955 2026-05-12T14:22:49Z

<p>Nsallin: </p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == Group meeting ==<br /> Once a week we have the group meeting where the current activities of the group members are presented and discussed. The agenda can be found on [https://indico.global/category/1448/ indico]. If you present something, please update you slides on the agenda to archive your work and future references. Note that to upload your slides you will need to create an account, this can be done through the cern account or the Switch edi-ID (UNIBE account).<br /> <br /> == ND-LAr ==<br /> [https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]<br /> [https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository. See the FSD data chapter for a short introduction.<br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> A short introduction to 2x2 and FSD data can be found on the [[Setup to process FSD data on neutrino01]] page.<br /> <br /> == 2x2 ==<br /> <br /> === Shifting ===<br /> The instructions to shift from the Bern ROC machine are listed [[Bern ROC shifting station|here]].<br /> <br /> == ArCLight ==<br /> <br /> === Production ===<br /> Documentation of the production can be found [[Production of ArCLights|here]].<br /> <br /> === QC/QA ===<br /> Documentation for the quality control can be found [[ACL Quality Control|here]]<br /> <br /> == Tutorials ==<br /> Here are regrouped a few, hopefully soon many, tutorials.<br /> <br /> === Git repo ===<br /> How to set up a (or many) [[Git repository]].<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://www.reiseplattform.unibe.ch/before_you_start/index_eng.html UNIBE travel platform]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=954 2026-05-12T14:21:54Z

<p>Nsallin: add group meeting section</p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == Group meeting ==<br /> Once a week we have the group meeting where the current activities of the group members are presented and discussed. The agenda can be found on [indico https://indico.global/category/1448/]. If you present something, please update you slides on the agenda to archive your work and future references. Note that to upload your slides you will need to create an account, this can be done through the cern account or the Switch edi-ID (UNIBE account).<br /> <br /> == ND-LAr ==<br /> [[https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]] &lt;br&gt;<br /> [[https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]] &lt;br&gt;<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository. See the FSD data chapter for a short introduction.<br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> A short introduction to 2x2 and FSD data can be found on the [[Setup to process FSD data on neutrino01]] page.<br /> <br /> == 2x2 ==<br /> <br /> === Shifting ===<br /> The instructions to shift from the Bern ROC machine are listed [[Bern ROC shifting station|here]].<br /> <br /> == ArCLight ==<br /> <br /> === Production ===<br /> Documentation of the production can be found [[Production of ArCLights|here]].<br /> <br /> === QC/QA ===<br /> Documentation for the quality control can be found [[ACL Quality Control|here]]<br /> <br /> == Tutorials ==<br /> Here are regrouped a few, hopefully soon many, tutorials.<br /> <br /> === Git repo ===<br /> How to set up a (or many) [[Git repository]].<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://www.reiseplattform.unibe.ch/before_you_start/index_eng.html UNIBE travel platform]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=File:TRAVELING_REIMBURSEMENT.pdf&diff=948 2026-04-30T11:39:43Z

<p>Nsallin: Nsallin uploaded a new version of File:TRAVELING REIMBURSEMENT.pdf</p> <hr /> <div>The form to submit a reimbursement request</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Get_Started&diff=947 2026-04-14T15:20:12Z

<p>Nsallin: </p> <hr /> <div>Welcome in the neutrino group, on this page you will find information about how to get access to the resources necessary to work and some useful tips to get started. The first requirement is to get a ''UNIBE email account'', please ask the LHEP secretary if you don't have one yet.<br /> <br /> = Slack =<br /> Slack is a very practical tool to exchange with other collaborators. We have a dedicated workspace for LHEP people and there is a DUNE collaboration one.<br /> <br /> === LHEP Slack ===<br /> To obtain an access to the LHEP Slack workspace, simply ask someone already in the workplace to add you. How to add a person: Under ''home'' you can click on the title of the workspace, which open a scroll-down menu. Then click on ''invite people to join...'' and provide the email address of the person you want to add.<br /> <br /> === DUNE Slack ===<br /> To get added to the DUNE workspace, write to ''dune-slack@fnal.gov'' to request access.<br /> <br /> = FNAL =<br /> <br /> == FNAL Account ==<br /> A Fermilab account is needed to get access to some DUNE ressources and to the Fermilab site. To request the account please follow these [https://get-connected.fnal.gov/users-affiliates-access/ instructions]. To get the on-site access visit the [[Access to Fermilab]] page<br /> <br /> == FNAL Mailing list ==<br /> A lot of information are transmitted through the Fermilab mailing list. Here are the instcruction to suscribe<br /> <br /> <br /> = NERSC =<br /> The ''National Energy Research Scientific Computing Center'' (NERSC) is a US computing facility with dedicated DUNE resources. Most of the data are accessible from there and the infrastructure allows to run demanding jobs. The [https://docs.nersc.gov/getting-started/ get started] page will give you addidtional information (including how ot create an account). The associated Jupyter hub can be accessed under [https://jupyter.nersc.gov/hub/login?next=%2Fhub%2Fhome Jupyter@NERSC]<br /> <br /> = DUNE Github =<br /> Most to the code scripts are stored on the DUNE Github under the ''ndlar-flow'' project. Information to join it can be found one the [[Ndlar-flow]] page.<br /> <br /> = LHEP =<br /> Some ressources are also available directly from LHEP.<br /> <br /> === Mailing list ===<br /> There are also several lhep mailing lists, you can see more information [https://listserv.unibe.ch/mailman/listinfo here]. The general LHEP mailing list is ''lhep'' and the neutrino group one is ''lhep-neutrino'' (Note that for shady reasons we are currently using ''lhep-newprojects'' as our group one)<br /> <br /> === Servers ===<br /> 2 Servers are available, neutrino01 and neutrino02 under the address &lt;code&gt;neutrino0X.lhep.unibe.ch&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === Google Drive ===<br /> A lot of documents are available on our common google drive under the username &lt;code&gt;argoncube@gmail.com&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === ELOG ===<br /> The LHEP [https://elog.lhep.unibe.ch ELOG] is used to store diverse information. Ask somebody from the LHEP IT to be added.<br /> <br /> === Github ===<br /> An LHEP neutrino Github is also available [https://github.com/LHEP-neutrino here]. Ask one of the owner to be added.<br /> <br /> = CERN account =<br /> The CERN account allows you to access computing ressources and on-site access. To request it, ask Michele to fill the relevant form and follow the procedure detailed in the email resulting from the access request.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Get_Started&diff=946 2026-04-14T15:18:00Z

<p>Nsallin: </p> <hr /> <div>Welcome in the neutrino group, on this page you will find information about how to get access to the resources necessary to work and some useful tips to get started. The first requirement is to get a ''UNIBE email account'', please ask the LHEP secretary if you don't have one yet.<br /> <br /> = Slack =<br /> Slack is a very practical tool to exchange with other collaborators. We have a dedicated workspace for LHEP people and there is a DUNE collaboration one.<br /> <br /> === LHEP Slack ===<br /> To obtain an access to the LHEP Slack workspace, simply ask someone already in the workplace to add you. How to add a person: Under ''home'' you can click on the title of the workspace, which open a scroll-down menu. Then click on ''invite people to join...'' and provide the email address of the person you want to add.<br /> <br /> === DUNE Slack ===<br /> To get added to the DUNE workspace, write to ''dune-slack@fnal.gov'' to request access.<br /> <br /> = FNAL =<br /> <br /> == FNAL Account =<br /> A Fermilab account is needed to get access to some DUNE ressources and to the Fermilab site. To request the account please follow these [https://get-connected.fnal.gov/users-affiliates-access/ instructions]. To get the on-site access visit the [[Access to Fermilab]] page<br /> <br /> == FNAL Mailing list ==<br /> A lot of information are transmitted through the Fermilab mailing list. Here are the instcruction to suscribe<br /> <br /> <br /> = NERSC =<br /> The ''National Energy Research Scientific Computing Center'' (NERSC) is a US computing facility with dedicated DUNE resources. Most of the data are accessible from there and the infrastructure allows to run demanding jobs. The [https://docs.nersc.gov/getting-started/ get started] page will give you addidtional information (including how ot create an account). The associated Jupyter hub can be accessed under [https://jupyter.nersc.gov/hub/login?next=%2Fhub%2Fhome Jupyter@NERSC]<br /> <br /> = DUNE Github =<br /> Most to the code scripts are stored on the DUNE Github under the ''ndlar-flow'' project. Information to join it can be found one the [[Ndlar-flow]] page.<br /> <br /> = LHEP =<br /> Some ressources are also available directly from LHEP.<br /> <br /> === Mailing list ===<br /> There are also several lhep mailing lists, you can see more information [https://listserv.unibe.ch/mailman/listinfo | here]. The general lhep mailing list is *lhep* and the neutrino group one is *lhep.neutrino* (Note that for shady reasons we are currently using *lhep-newprojects* as our group one)<br /> <br /> === Servers ===<br /> 2 Servers are available, neutrino01 and neutrino02 under the address &lt;code&gt;neutrino0X.lhep.unibe.ch&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === Google Drive ===<br /> A lot of documents are available on our common google drive under the username &lt;code&gt;argoncube@gmail.com&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === ELOG ===<br /> The LHEP [https://elog.lhep.unibe.ch ELOG] is used to store diverse information. Ask somebody from the LHEP IT to be added.<br /> <br /> === Github ===<br /> An LHEP neutrino Github is also available [https://github.com/LHEP-neutrino here]. Ask one of the owner to be added.<br /> <br /> = CERN account =<br /> The CERN account allows you to access computing ressources and on-site access. To request it, ask Michele to fill the relevant form and follow the procedure detailed in the email resulting from the access request.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Get_Started&diff=945 2026-02-16T15:06:03Z

<p>Nsallin: </p> <hr /> <div>Welcome in the neutrino group, on this page you will find information about how to get access to the resources necessary to work and some useful tips to get started. The first requirement is to get a ''UNIBE email account'', please ask the LHEP secretary if you don't have one yet.<br /> <br /> = Slack =<br /> Slack is a very practical tool to exchange with other collaborators. We have a dedicated workspace for LHEP people and there is a DUNE collaboration one.<br /> <br /> === LHEP Slack ===<br /> To obtain an access to the LHEP Slack workspace, simply ask someone already in the workplace to add you. How to add a person: Under ''home'' you can click on the title of the workspace, which open a scroll-down menu. Then click on ''invite people to join...'' and provide the email address of the person you want to add.<br /> <br /> === DUNE Slack ===<br /> To get added to the DUNE workspace, write to ''dune-slack@fnal.gov'' to request access.<br /> <br /> = FNAL =<br /> <br /> == FNAL Account =<br /> A Fermilab account is needed to get access to some DUNE ressources and to the Fermilab site. To request the account please follow these [https://get-connected.fnal.gov/users-affiliates-access/ instructions]. To get the on-site access visit the [[Access to Fermilab]] page<br /> <br /> == FNAL Mailing list ==<br /> A lot of information are transmitted through the Fermilab mailing list. Here are the instcruction to suscribe<br /> <br /> <br /> = NERSC =<br /> The ''National Energy Research Scientific Computing Center'' (NERSC) is a US computing facility with dedicated DUNE resources. Most of the data are accessible from there and the infrastructure allows to run demanding jobs. The [https://docs.nersc.gov/getting-started/ get started] page will give you addidtional information (including how ot create an account). The associated Jupyter hub can be accessed under [https://jupyter.nersc.gov/hub/login?next=%2Fhub%2Fhome Jupyter@NERSC]<br /> <br /> = DUNE Github =<br /> Most to the code scripts are stored on the DUNE Github under the ''ndlar-flow'' project. Information to join it can be found one the [[Ndlar-flow]] page.<br /> <br /> = LHEP =<br /> Some ressources are also available directly from LHEP.<br /> <br /> === Servers ===<br /> 2 Servers are available, neutrino01 and neutrino02 under the address &lt;code&gt;neutrino0X.lhep.unibe.ch&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === Google Drive ===<br /> A lot of documents are available on our common google drive under the username &lt;code&gt;argoncube@gmail.com&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === ELOG ===<br /> The LHEP [https://elog.lhep.unibe.ch ELOG] is used to store diverse information. Ask somebody from the LHEP IT to be added.<br /> <br /> === Github ===<br /> An LHEP neutrino Github is also available [https://github.com/LHEP-neutrino here]. Ask one of the owner to be added.<br /> <br /> = CERN account =<br /> The CERN account allows you to access computing ressources and on-site access. To request it, ask Michele to fill the relevant form and follow the procedure detailed in the email resulting from the access request.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=944 2025-12-10T16:40:48Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> Recall, to connect to neutrino01:<br /> &lt;pre&gt;<br /> [user@computer ~]$ ssh user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the ''README'' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed).<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is too old to install the latest Jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> The default python version on ''neutrino01''is <br /> &lt;!-- <br /> &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; <br /> --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is unfortunately too old support the latest Jupyter version. A lot of programmes depend on python which make it quite an hassle to upgrade it and additionally the admin right are needed to do it. A solution is to install a new python via the package ''pyenv'' and to do it in the virtual environment previously created.<br /> First clone the ''pyenv'' repository<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.11.9<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> , the star indicating the currently used one. Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> === ''h5flow'' framework ===<br /> Now we can install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd h5flow<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ pip install -e .<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ cd ..<br /> (ndlar_flow.venv) [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> === ''ndlar_flow'' ===<br /> And finally we can install ''ndlar_flow''<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone git@github.com:DUNE/ndlar_flow.git<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd ndlar_flow<br /> (ndlar_flow.venv) [user@neutrino01 ndlar_flow]$ pip install -e .<br /> &lt;/pre&gt;<br /> Note that the &lt;code&gt;-e&lt;/code&gt; option installs the packages in &quot;editable&quot; mode, meaning any changes you make will take effect without the need to re-run &lt;code&gt;pip install&lt;/code&gt;.<br /> <br /> == How to use == <br /> A good starting point is the [https://github.com/DUNE/ndlar_flow# ''README''] of the git repo, it describes how to run simple workflow such as light event building and also propose some tutorials. If you want to develop new script or update current one, a good practice is to create a new branch in the git project and work there. To edit the scripts, traditional editors like ''vim'' are available on the server, but there are also possibilities to open the repository on your local machine. An interactive solution is to start a Jupyter server on the remote neutrino01 server and then open a Jupyter Notebook from your local machine through a ssh tunnel. A second possibility is to ssh to the server through Visual Studio Code (VS Code), which provides a nice coding environment. In both case you also have access to the remote terminal inside the programme. In my opinion the two options are very complementary, VS Code to write code easily and jupyter notebook to use it and play around with it.<br /> <br /> === Visual Studio Code ===<br /> To use this program you will simply have to download VS Code and the ssh extension. Detailed information can be found [https://code.visualstudio.com/docs/remote/ssh here].<br /> <br /> === Jupyter Notebook ===<br /> First you will have to install Jupyter in your virtual environment on the server<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pip install jupyter<br /> &lt;/pre&gt;<br /> Then, once the installed successfully, you can start a jupyter server without opening a browser by running<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ jupyter notebook --no-browser --port=8080<br /> &lt;/pre&gt;<br /> ,the no-browser open is necessary but you can choose the desired port number. When the server is running, from a new terminal on your local machine you can open an ssh tunnel to the previously chosen port on the remote server<br /> &lt;pre&gt;<br /> user_local ~/$ ssh -L 8080:localhost:8080 user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> When the connexion is established, you can go back to the first terminal where the jupyter server is running and look for the following line<br /> &lt;pre&gt;<br /> [C 2025-06-18 14:27:48.107 ServerApp] <br /> <br /> To access the server, open this file in a browser:<br /> file:///terabig/user/.local/share/jupyter/runtime/jpserver-664549-open.html<br /> Or copy and paste one of these URLs:<br /> http://localhost:8080/tree?token=&lt;some number and letter&gt;<br /> http://127.0.0.1:8080/tree?token=&lt;some number and letter&gt;<br /> &lt;/pre&gt;<br /> . Copy the address of the server, e.g. here &lt;code&gt;http://localhost:8080/tree?token=&lt;some number and letter&gt;&lt;/code&gt; in your favourite browser on your local machine, it will allow you to access the Jupyter server. Note that some browser have difficulties with Jupyter notebooks, download an other one if yours is not compatible. Now you can select a file and start to work on it, good luck :).<br /> <br /> <br /> = AFI viewer =<br /> On neutrino01:<br /> &lt;pre&gt;<br /> cd ~/../jkunzmann/afi-viewer/adc64-tlv/AFIViewer/build2/<br /> ./ADC64Viewer<br /> &lt;/pre&gt;<br /> Ask Jan for more details.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=943 2025-12-10T16:39:29Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> Recall, to connect to neutrino01:<br /> &lt;pre&gt;<br /> [user@computer ~]$ ssh user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the ''README'' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed).<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is too old to install the latest Jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> The default python version on ''neutrino01''is <br /> &lt;!-- <br /> &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; <br /> --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is unfortunately too old support the latest Jupyter version. A lot of programmes depend on python which make it quite an hassle to upgrade it and additionally the admin right are needed to do it. A solution is to install a new python via the package ''pyenv'' and to do it in the virtual environment previously created.<br /> First clone the ''pyenv'' repository<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.11.9<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> , the star indicating the currently used one. Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> === ''h5flow'' framework ===<br /> Now we can install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd h5flow<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ pip install -e .<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ cd ..<br /> (ndlar_flow.venv) [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> === ''ndlar_flow'' ===<br /> And finally we can install ''ndlar_flow''<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone git@github.com:DUNE/ndlar_flow.git<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd ndlar_flow<br /> (ndlar_flow.venv) [user@neutrino01 ndlar_flow]$ pip install -e .<br /> &lt;/pre&gt;<br /> Note that the &lt;code&gt;-e&lt;/code&gt; option installs the packages in &quot;editable&quot; mode, meaning any changes you make will take effect without the need to re-run &lt;code&gt;pip install&lt;/code&gt;.<br /> <br /> == How to use == <br /> A good starting point is the [https://github.com/DUNE/ndlar_flow# ''README''] of the git repo, it describes how to run simple workflow such as light event building and also propose some tutorials. If you want to develop new script or update current one, a good practice is to create a new branch in the git project and work there. To edit the scripts, traditional editors like ''vim'' are available on the server, but there are also possibilities to open the repository on your local machine. An interactive solution is to start a Jupyter server on the remote neutrino01 server and then open a Jupyter Notebook from your local machine through a ssh tunnel. A second possibility is to ssh to the server through Visual Studio Code (VS Code), which provides a nice coding environment. In both case you also have access to the remote terminal inside the programme. In my opinion the two options are very complementary, VS Code to write code easily and jupyter notebook to use it and play around with it.<br /> <br /> === Visual Studio Code ===<br /> To use this program you will simply have to download VS Code and the ssh extension. Detailed information can be found [https://code.visualstudio.com/docs/remote/ssh here].<br /> <br /> === Jupyter Notebook ===<br /> First you will have to install Jupyter in your virtual environment on the server<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pip install jupyter<br /> &lt;/pre&gt;<br /> Then, once the installed successfully, you can start a jupyter server without opening a browser by running<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ jupyter notebook --no-browser --port=8080<br /> &lt;/pre&gt;<br /> ,the no-browser open is necessary but you can choose the desired port number. When the server is running, from a new terminal on your local machine you can open an ssh tunnel to the previously chosen port on the remote server<br /> &lt;pre&gt;<br /> user_local ~/$ ssh -L 8080:localhost:8080 user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> When the connexion is established, you can go back to the first terminal where the jupyter server is running and look for the following line<br /> &lt;pre&gt;<br /> [C 2025-06-18 14:27:48.107 ServerApp] <br /> <br /> To access the server, open this file in a browser:<br /> file:///terabig/user/.local/share/jupyter/runtime/jpserver-664549-open.html<br /> Or copy and paste one of these URLs:<br /> http://localhost:8080/tree?token=&lt;some number and letter&gt;<br /> http://127.0.0.1:8080/tree?token=&lt;some number and letter&gt;<br /> &lt;/pre&gt;<br /> . Copy the address of the server, e.g. here &lt;code&gt;http://localhost:8080/tree?token=&lt;some number and letter&gt;&lt;/code&gt; in your favourite browser on your local machine, it will allow you to access the Jupyter server. Note that some browser have difficulties with Jupyter notebooks, download an other one if yours is not compatible. Now you can select a file and start to work on it, good luck :).<br /> <br /> <br /> = AFI viewer =<br /> On neutrino01:<br /> &lt;pre&gt;<br /> cd afi-viewer/adc64-tlv/AFIViewer/build2/<br /> ./ADC64Viewer<br /> &lt;/pre&gt;<br /> Ask Jan for more details.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=942 2025-11-27T10:17:33Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> Recall, to connect to neutrino01:<br /> &lt;pre&gt;<br /> [user@computer ~]$ ssh user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the ''README'' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed).<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is too old to install the latest Jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> The default python version on ''neutrino01''is <br /> &lt;!-- <br /> &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; <br /> --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is unfortunately too old support the latest Jupyter version. A lot of programmes depend on python which make it quite an hassle to upgrade it and additionally the admin right are needed to do it. A solution is to install a new python via the package ''pyenv'' and to do it in the virtual environment previously created.<br /> First clone the ''pyenv'' repository<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.11.9<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> , the star indicating the currently used one. Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> === ''h5flow'' framework ===<br /> Now we can install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd h5flow<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ pip install -e .<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ cd ..<br /> (ndlar_flow.venv) [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> === ''ndlar_flow'' ===<br /> And finally we can install ''ndlar_flow''<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone git@github.com:DUNE/ndlar_flow.git<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd ndlar_flow<br /> (ndlar_flow.venv) [user@neutrino01 ndlar_flow]$ pip install -e .<br /> &lt;/pre&gt;<br /> Note that the &lt;code&gt;-e&lt;/code&gt; option installs the packages in &quot;editable&quot; mode, meaning any changes you make will take effect without the need to re-run &lt;code&gt;pip install&lt;/code&gt;.<br /> <br /> == How to use == <br /> A good starting point is the [https://github.com/DUNE/ndlar_flow# ''README''] of the git repo, it describes how to run simple workflow such as light event building and also propose some tutorials. If you want to develop new script or update current one, a good practice is to create a new branch in the git project and work there. To edit the scripts, traditional editors like ''vim'' are available on the server, but there are also possibilities to open the repository on your local machine. An interactive solution is to start a Jupyter server on the remote neutrino01 server and then open a Jupyter Notebook from your local machine through a ssh tunnel. A second possibility is to ssh to the server through Visual Studio Code (VS Code), which provides a nice coding environment. In both case you also have access to the remote terminal inside the programme. In my opinion the two options are very complementary, VS Code to write code easily and jupyter notebook to use it and play around with it.<br /> <br /> === Visual Studio Code ===<br /> To use this program you will simply have to download VS Code and the ssh extension. Detailed information can be found [https://code.visualstudio.com/docs/remote/ssh here].<br /> <br /> === Jupyter Notebook ===<br /> First you will have to install Jupyter in your virtual environment on the server<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pip install jupyter<br /> &lt;/pre&gt;<br /> Then, once the installed successfully, you can start a jupyter server without opening a browser by running<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ jupyter notebook --no-browser --port=8080<br /> &lt;/pre&gt;<br /> ,the no-browser open is necessary but you can choose the desired port number. When the server is running, from a new terminal on your local machine you can open an ssh tunnel to the previously chosen port on the remote server<br /> &lt;pre&gt;<br /> user_local ~/$ ssh -L 8080:localhost:8080 user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> When the connexion is established, you can go back to the first terminal where the jupyter server is running and look for the following line<br /> &lt;pre&gt;<br /> [C 2025-06-18 14:27:48.107 ServerApp] <br /> <br /> To access the server, open this file in a browser:<br /> file:///terabig/user/.local/share/jupyter/runtime/jpserver-664549-open.html<br /> Or copy and paste one of these URLs:<br /> http://localhost:8080/tree?token=&lt;some number and letter&gt;<br /> http://127.0.0.1:8080/tree?token=&lt;some number and letter&gt;<br /> &lt;/pre&gt;<br /> . Copy the address of the server, e.g. here &lt;code&gt;http://localhost:8080/tree?token=&lt;some number and letter&gt;&lt;/code&gt; in your favourite browser on your local machine, it will allow you to access the Jupyter server. Note that some browser have difficulties with Jupyter notebooks, download an other one if yours is not compatible. Now you can select a file and start to work on it, good luck :).<br /> <br /> <br /> = AFI viewer =<br /> Ask Jan.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=941 2025-11-27T10:17:20Z

<p>Nsallin: add neutrino01 address</p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> Recall, to connect to neutrino01:<br /> &lt;pre&gt;<br /> [user@computer ~]$ssh user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the ''README'' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed).<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is too old to install the latest Jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> The default python version on ''neutrino01''is <br /> &lt;!-- <br /> &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; <br /> --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is unfortunately too old support the latest Jupyter version. A lot of programmes depend on python which make it quite an hassle to upgrade it and additionally the admin right are needed to do it. A solution is to install a new python via the package ''pyenv'' and to do it in the virtual environment previously created.<br /> First clone the ''pyenv'' repository<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.11.9<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> , the star indicating the currently used one. Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> === ''h5flow'' framework ===<br /> Now we can install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd h5flow<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ pip install -e .<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ cd ..<br /> (ndlar_flow.venv) [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> === ''ndlar_flow'' ===<br /> And finally we can install ''ndlar_flow''<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone git@github.com:DUNE/ndlar_flow.git<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd ndlar_flow<br /> (ndlar_flow.venv) [user@neutrino01 ndlar_flow]$ pip install -e .<br /> &lt;/pre&gt;<br /> Note that the &lt;code&gt;-e&lt;/code&gt; option installs the packages in &quot;editable&quot; mode, meaning any changes you make will take effect without the need to re-run &lt;code&gt;pip install&lt;/code&gt;.<br /> <br /> == How to use == <br /> A good starting point is the [https://github.com/DUNE/ndlar_flow# ''README''] of the git repo, it describes how to run simple workflow such as light event building and also propose some tutorials. If you want to develop new script or update current one, a good practice is to create a new branch in the git project and work there. To edit the scripts, traditional editors like ''vim'' are available on the server, but there are also possibilities to open the repository on your local machine. An interactive solution is to start a Jupyter server on the remote neutrino01 server and then open a Jupyter Notebook from your local machine through a ssh tunnel. A second possibility is to ssh to the server through Visual Studio Code (VS Code), which provides a nice coding environment. In both case you also have access to the remote terminal inside the programme. In my opinion the two options are very complementary, VS Code to write code easily and jupyter notebook to use it and play around with it.<br /> <br /> === Visual Studio Code ===<br /> To use this program you will simply have to download VS Code and the ssh extension. Detailed information can be found [https://code.visualstudio.com/docs/remote/ssh here].<br /> <br /> === Jupyter Notebook ===<br /> First you will have to install Jupyter in your virtual environment on the server<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pip install jupyter<br /> &lt;/pre&gt;<br /> Then, once the installed successfully, you can start a jupyter server without opening a browser by running<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ jupyter notebook --no-browser --port=8080<br /> &lt;/pre&gt;<br /> ,the no-browser open is necessary but you can choose the desired port number. When the server is running, from a new terminal on your local machine you can open an ssh tunnel to the previously chosen port on the remote server<br /> &lt;pre&gt;<br /> user_local ~/$ ssh -L 8080:localhost:8080 user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> When the connexion is established, you can go back to the first terminal where the jupyter server is running and look for the following line<br /> &lt;pre&gt;<br /> [C 2025-06-18 14:27:48.107 ServerApp] <br /> <br /> To access the server, open this file in a browser:<br /> file:///terabig/user/.local/share/jupyter/runtime/jpserver-664549-open.html<br /> Or copy and paste one of these URLs:<br /> http://localhost:8080/tree?token=&lt;some number and letter&gt;<br /> http://127.0.0.1:8080/tree?token=&lt;some number and letter&gt;<br /> &lt;/pre&gt;<br /> . Copy the address of the server, e.g. here &lt;code&gt;http://localhost:8080/tree?token=&lt;some number and letter&gt;&lt;/code&gt; in your favourite browser on your local machine, it will allow you to access the Jupyter server. Note that some browser have difficulties with Jupyter notebooks, download an other one if yours is not compatible. Now you can select a file and start to work on it, good luck :).<br /> <br /> <br /> = AFI viewer =<br /> Ask Jan.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=932 2025-11-05T07:50:11Z

<p>Nsallin: /* ArClight */</p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == ND-LAr ==<br /> [[https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]] &lt;br&gt;<br /> [[https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]] &lt;br&gt;<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository. See the FSD data chapter for a short introduction.<br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> A short introduction to 2x2 and FSD data can be found on the [[Setup to process FSD data on neutrino01]] page.<br /> <br /> == 2x2 ==<br /> nothing yet<br /> <br /> == ArCLight ==<br /> <br /> === Production ===<br /> Documentation of the production can be found [[Production of ArCLights|here]].<br /> <br /> === QC/QA ===<br /> Documentation for the quality control can be found [[ACL Quality Control|here]]<br /> <br /> == Tutorials ==<br /> Here are regrouped a few, hopefully soon many, tutorials.<br /> <br /> === Git repo ===<br /> How to set up a (or many) [[Git repository]].<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://www.reiseplattform.unibe.ch/before_you_start/index_eng.html UNIBE travel platform]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=931 2025-11-05T07:49:52Z

<p>Nsallin: /* Production = */</p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == ND-LAr ==<br /> [[https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]] &lt;br&gt;<br /> [[https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]] &lt;br&gt;<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository. See the FSD data chapter for a short introduction.<br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> A short introduction to 2x2 and FSD data can be found on the [[Setup to process FSD data on neutrino01]] page.<br /> <br /> == 2x2 ==<br /> nothing yet<br /> <br /> == ArClight ==<br /> <br /> === Production ===<br /> Documentation of the production can be found [[Production of ArCLights|here]].<br /> <br /> === QC/QA ===<br /> Documentation for the quality control can be found [[ACL Quality Control|here]]<br /> <br /> == Tutorials ==<br /> Here are regrouped a few, hopefully soon many, tutorials.<br /> <br /> === Git repo ===<br /> How to set up a (or many) [[Git repository]].<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://www.reiseplattform.unibe.ch/before_you_start/index_eng.html UNIBE travel platform]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=930 2025-11-05T07:49:36Z

<p>Nsallin: </p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == ND-LAr ==<br /> [[https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]] &lt;br&gt;<br /> [[https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]] &lt;br&gt;<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository. See the FSD data chapter for a short introduction.<br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> A short introduction to 2x2 and FSD data can be found on the [[Setup to process FSD data on neutrino01]] page.<br /> <br /> == 2x2 ==<br /> nothing yet<br /> <br /> == ArClight ==<br /> <br /> === Production ====<br /> Documentation of the production can be found [[Production of ArCLights|here]].<br /> <br /> === QC/QA ===<br /> Documentation for the quality control can be found [[ACL Quality Control|here]]<br /> <br /> == Tutorials ==<br /> Here are regrouped a few, hopefully soon many, tutorials.<br /> <br /> === Git repo ===<br /> How to set up a (or many) [[Git repository]].<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://www.reiseplattform.unibe.ch/before_you_start/index_eng.html UNIBE travel platform]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Git_repository&diff=917 2025-08-08T21:02:29Z

<p>Nsallin: </p> <hr /> <div>From the [[https://docs.github.com/en/get-started/start-your-journey/about-github-and-git official Github website]]: <br /> &lt;blockquote&gt;<br /> GitHub is a cloud-based platform where you can store, share, and work together with others to write code.<br /> <br /> Storing your code in a &quot;repository&quot; on GitHub allows you to:<br /> <br /> * Showcase or share your work.<br /> * Track and manage changes to your code over time.<br /> * Let others review your code, and make suggestions to improve it.<br /> * Collaborate on a shared project, without worrying that your changes will impact the work of your collaborators before you're ready to integrate them.<br /> * Collaborative working, one of GitHub’s fundamental features, is made possible by the open-source software, Git, upon which GitHub is built.<br /> &lt;/blockquote&gt;<br /> The [https://github.com/LHEP-neutrino LHEP Github] is the place where the repos should be stored in order to be accessible throughout LHEP members. It is a very good practice to work from repos, as cited, this helps keeping track of your work and allow others to easily use it.<br /> <br /> == Getting access to LHEP Github ==<br /> If you aren't a member yet, (once you have an [https://github.com/signup account]) contact an owner (e.g. [[mailto:serhan.tufanli@unibe.ch Serhan]] or [[mailto:nicolas.sallin@unibe.ch Nicolas]]) to get added. Then you will be able to create your repository or use an already existing one. <br /> <br /> == Cloning the repo on a local machine ==<br /> The '''remote''' github acts as the main repository. You can '''clone''' this repository on '''local''' machine which allows you to work on it. Once your work done, you can '''push''' your work from your local to the remote repo, such that it is saved in the cloud and other people can access it. On the other way around, if somebody else pushed something from their local repo to the remote one, then you can '''pull''' the changes from the remote repo to your local one such that you can use the work from others.<br /> <br /> To clone a repo, first you will have to 'link' your machine to the remote repo. An easy way to do this is to set up an ssh key pair on your local machine and register it on github, follow [https://docs.github.com/en/authentication/connecting-to-github-with-ssh this tutorial], under generate a new ssh key. Note that if you want to clone many repo on the same machine, you will have to generate one key per repo. If you do not want to add your ssh key to your agent everytime you connect to your machine, you can add the following commands in the ''.bashrc'' or ''.bash_profile'':<br /> &lt;div class=&quot;toccolours mw-collapsible mw-collapsed&quot; style=&quot;width=100%; overflow:auto;&quot;&gt;<br /> &lt;div style=&quot;font-weight:bold;line-height:1.6;&quot;&gt;Automatically add your ssh key(s) to the ssh-agent &lt;/div&gt;<br /> &lt;div class=&quot;mw-collapsible-content&quot;&gt;<br /> &lt;pre&gt;<br /> # Run the ssh-agent if not running yet<br /> <br /> # Function to start a new agent and save its info<br /> # from https://docs.vscentrum.be/accounts/ssh_agent.html<br /> start-ssh-agent() {<br /> #<br /> # Start an ssh agent if none is running already.<br /> # * First we try to connect to one via SSH_AUTH_SOCK<br /> # * If that doesn't work out, we try via the file ssh-agent-environment<br /> # * And if that doesn't work out either, we just start a fresh one and write<br /> # the information about it to ssh-agent-environment for future use.<br /> #<br /> # We don't really test for a correct value of SSH_AGENT_PID as the only<br /> # consequence of not having it set seems to be that one cannot kill<br /> # the ssh-agent with ssh-agent -k. But starting another one wouldn't<br /> # help to clean up the old one anyway.<br /> #<br /> # Note: ssh-add return codes:<br /> # 0 = success,<br /> # 1 = specified command fails (e.g., no keys with ssh-add -l)<br /> # 2 = unable to contact the authentication agent<br /> #<br /> sshfile=~/.ssh/ssh-agent-env<br /> #<br /> # First effort: Via SSH_AUTH_SOCK/SSH_AGENT_PID<br /> #<br /> if [ -n &quot;$SSH_AUTH_SOCK&quot; ]; then<br /> # SSH_AUTH_SOCK is defined, so try to connect to the authentication agent<br /> # it should point to. If it succeeds, reset newsshagent.<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by SSH_AUTH_SOCK, trying more...&quot;<br /> fi<br /> fi<br /> #<br /> # Second effort: If we're still looking for an ssh-agent, try via $sshfile<br /> #<br /> if [ -e &quot;$sshfile&quot; ]; then<br /> # Load the environment given in $sshfile<br /> . $sshfile &amp;&gt;/dev/null<br /> # Try to contact the ssh-agent<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running; reconfigured the environment.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by $sshfile.&quot;<br /> fi<br /> fi<br /> #<br /> # And if we haven't found a working one, start a new one...<br /> #<br /> #Create a new ssh-agent<br /> echo &quot;Creating new SSH agent.&quot;<br /> ssh-agent -s &gt; $sshfile &amp;&amp; . $sshfile<br /> unset sshfile<br /> }<br /> <br /> # Start the ssh-agent<br /> start-ssh-agent <br /> #&amp;&gt;/dev/null<br /> <br /> # Add the key<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key0 &amp;&gt;/dev/null<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key1 &amp;&gt;/dev/null<br /> &lt;/pre&gt;<br /> &lt;/div&gt;&lt;/div&gt;<br /> <br /> Once your key is set up, you are ready to clone the repo on your local machine. See the following screenshot for the number references<br /> <br /> [[File:Git_HowToClone_LHEP.png|thumb|upright=2.3|Where to find the ssh address of the git repo]]<br /> # Click on the expandable green clone button<br /> # Select ssh<br /> # Copy the repo link<br /> <br /> Note that if you have many repos on the same machine you will have to use an alias host instead of ''github.com'' and register it in a config file as described [https://docs.github.com/en/authentication/connecting-to-github-with-ssh/managing-deploy-keys#using-multiple-repositories-on-one-server here].<br /> <br /> Finally go on your local machine and use the ''git clone'' command:<br /> &lt;pre&gt;<br /> git clone git@github.com:LHEP-neutrino/&lt;your_repo&gt;.git<br /> &lt;/pre&gt;<br /> You are ready to go and do your super important work that now can be easily saved! Don't forget to pick the good manners like working on a branch, pulling the remote regularly to get the latest changes and pushing your work regularly to save it on the remote repo, and so on. You can find plenty of tutorials on basic uses or advances uses (like issue report, version release, CI/CO pipeline integration, ...), don't hesitate to ameliorate the LHEP github :).</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Git_repository&diff=916 2025-08-08T21:02:13Z

<p>Nsallin: </p> <hr /> <div>From the [[https://docs.github.com/en/get-started/start-your-journey/about-github-and-git official Github website]]: <br /> &lt;blockquote&gt;<br /> GitHub is a cloud-based platform where you can store, share, and work together with others to write code.<br /> <br /> Storing your code in a &quot;repository&quot; on GitHub allows you to:<br /> <br /> * Showcase or share your work.<br /> * Track and manage changes to your code over time.<br /> * Let others review your code, and make suggestions to improve it.<br /> * Collaborate on a shared project, without worrying that your changes will impact the work of your collaborators before you're ready to integrate them.<br /> * Collaborative working, one of GitHub’s fundamental features, is made possible by the open-source software, Git, upon which GitHub is built.<br /> &lt;/blockquote&gt;<br /> The [https://github.com/LHEP-neutrino LHEP Github] is the place where the repos should be stored in order to be accessible throughout LHEP members. It is a very good practice to work from repos, as cited, this helps keeping track of your work and allow others to easily use it.<br /> <br /> == Getting access to LHEP Github ==<br /> If you aren't a member yet, (once you have an [https://github.com/signup account]) contact an owner (e.g. [[mailto:serhan.tufanli@unibe.ch Serhan]] or [[mailto:nicolas.sallin@unibe.ch Nicolas]]) to get added. Then you will be able to create your repository or use an already existing one. <br /> <br /> == Cloning the repo on a local machine ==<br /> The '''remote''' github acts as the main repository. You can '''clone''' this repository on '''local''' machine which allows you to work on it. Once your work done, you can '''push''' your work from your local to the remote repo, such that it is saved in the cloud and other people can access it. On the other way around, if somebody else pushed something from their local repo to the remote one, then you can '''pull''' the changes from the remote repo to your local one such that you can use the work from others.<br /> <br /> To clone a repo, first you will have to 'link' your machine to the remote repo. An easy way to do this is to set up an ssh key pair on your local machine and register it on github, follow [https://docs.github.com/en/authentication/connecting-to-github-with-ssh this tutorial], under generate a new ssh key. Note that if you want to clone many repo on the same machine, you will have to generate one key per repo. If you do not want to add your ssh key to your agent everytime you connect to your machine, you can add the following commands in the ''.bashrc'' or ''.bash_profile'':<br /> &lt;div class=&quot;toccolours mw-collapsible mw-collapsed&quot; style=&quot;width=100%; overflow:auto;&quot;&gt;<br /> &lt;div style=&quot;font-weight:bold;line-height:1.6;&quot;&gt;Automatically add your ssh key(s) to the ssh-agent &lt;/div&gt;<br /> &lt;div class=&quot;mw-collapsible-content&quot;&gt;<br /> &lt;pre&gt;<br /> # Run the ssh-agent if not running yet<br /> <br /> # Function to start a new agent and save its info<br /> # from https://docs.vscentrum.be/accounts/ssh_agent.html<br /> start-ssh-agent() {<br /> #<br /> # Start an ssh agent if none is running already.<br /> # * First we try to connect to one via SSH_AUTH_SOCK<br /> # * If that doesn't work out, we try via the file ssh-agent-environment<br /> # * And if that doesn't work out either, we just start a fresh one and write<br /> # the information about it to ssh-agent-environment for future use.<br /> #<br /> # We don't really test for a correct value of SSH_AGENT_PID as the only<br /> # consequence of not having it set seems to be that one cannot kill<br /> # the ssh-agent with ssh-agent -k. But starting another one wouldn't<br /> # help to clean up the old one anyway.<br /> #<br /> # Note: ssh-add return codes:<br /> # 0 = success,<br /> # 1 = specified command fails (e.g., no keys with ssh-add -l)<br /> # 2 = unable to contact the authentication agent<br /> #<br /> sshfile=~/.ssh/ssh-agent-env<br /> #<br /> # First effort: Via SSH_AUTH_SOCK/SSH_AGENT_PID<br /> #<br /> if [ -n &quot;$SSH_AUTH_SOCK&quot; ]; then<br /> # SSH_AUTH_SOCK is defined, so try to connect to the authentication agent<br /> # it should point to. If it succeeds, reset newsshagent.<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by SSH_AUTH_SOCK, trying more...&quot;<br /> fi<br /> fi<br /> #<br /> # Second effort: If we're still looking for an ssh-agent, try via $sshfile<br /> #<br /> if [ -e &quot;$sshfile&quot; ]; then<br /> # Load the environment given in $sshfile<br /> . $sshfile &amp;&gt;/dev/null<br /> # Try to contact the ssh-agent<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running; reconfigured the environment.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by $sshfile.&quot;<br /> fi<br /> fi<br /> #<br /> # And if we haven't found a working one, start a new one...<br /> #<br /> #Create a new ssh-agent<br /> echo &quot;Creating new SSH agent.&quot;<br /> ssh-agent -s &gt; $sshfile &amp;&amp; . $sshfile<br /> unset sshfile<br /> }<br /> <br /> # Start the ssh-agent<br /> start-ssh-agent <br /> #&amp;&gt;/dev/null<br /> <br /> # Add the key<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key0 &amp;&gt;/dev/null<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key1 &amp;&gt;/dev/null<br /> &lt;/pre&gt;<br /> &lt;/div&gt;&lt;/div&gt;<br /> <br /> Once your key is set up, you are ready to clone the repo on your local machine. See the following screenshot for the number references<br /> <br /> [[File:Git_HowToClone_LHEP.png|thumb|upright=2.3|Where to find the ssh address of the git repo]]<br /> # Click on the expandable green clone button<br /> # Select ssh<br /> # Copy the repo link<br /> <br /> Note that if you have many repos on the same machine you will have to use an alias host instead of ''github.com'' and register it in a config file as described [https://docs.github.com/en/authentication/connecting-to-github-with-ssh/managing-deploy-keys#using-multiple-repositories-on-one-server here].<br /> <br /> Finally go on your local machine and use the ''git clone'' command:<br /> &lt;pre&gt;&lt;code&gt;<br /> git clone git@github.com:LHEP-neutrino/&lt;your_repo&gt;.git<br /> &lt;/code&gt;&lt;/pre&gt;<br /> You are ready to go and do your super important work that now can be easily saved! Don't forget to pick the good manners like working on a branch, pulling the remote regularly to get the latest changes and pushing your work regularly to save it on the remote repo, and so on. You can find plenty of tutorials on basic uses or advances uses (like issue report, version release, CI/CO pipeline integration, ...), don't hesitate to ameliorate the LHEP github :).</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Git_repository&diff=915 2025-08-08T21:01:18Z

<p>Nsallin: </p> <hr /> <div>From the [[https://docs.github.com/en/get-started/start-your-journey/about-github-and-git official Github website]]: <br /> &lt;blockquote&gt;<br /> GitHub is a cloud-based platform where you can store, share, and work together with others to write code.<br /> <br /> Storing your code in a &quot;repository&quot; on GitHub allows you to:<br /> <br /> * Showcase or share your work.<br /> * Track and manage changes to your code over time.<br /> * Let others review your code, and make suggestions to improve it.<br /> * Collaborate on a shared project, without worrying that your changes will impact the work of your collaborators before you're ready to integrate them.<br /> * Collaborative working, one of GitHub’s fundamental features, is made possible by the open-source software, Git, upon which GitHub is built.<br /> &lt;/blockquote&gt;<br /> The [https://github.com/LHEP-neutrino LHEP Github] is the place where the repos should be stored in order to be accessible throughout LHEP members. It is a very good practice to work from repos, as cited, this helps keeping track of your work and allow others to easily use it.<br /> <br /> == Getting access to LHEP Github ==<br /> If you aren't a member yet, (once you have an [https://github.com/signup account]) contact an owner (e.g. [[mailto:serhan.tufanli@unibe.ch Serhan]] or [[mailto:nicolas.sallin@unibe.ch Nicolas]]) to get added. Then you will be able to create your repository or use an already existing one. <br /> <br /> == Cloning the repo on a local machine ==<br /> The '''remote''' github acts as the main repository. You can '''clone''' this repository on '''local''' machine which allows you to work on it. Once your work done, you can '''push''' your work from your local to the remote repo, such that it is saved in the cloud and other people can access it. On the other way around, if somebody else pushed something from their local repo to the remote one, then you can '''pull''' the changes from the remote repo to your local one such that you can use the work from others.<br /> <br /> To clone a repo, first you will have to 'link' your machine to the remote repo. An easy way to do this is to set up an ssh key pair on your local machine and register it on github, follow [https://docs.github.com/en/authentication/connecting-to-github-with-ssh this tutorial], under generate a new ssh key. Note that if you want to clone many repo on the same machine, you will have to generate one key per repo. If you do not want to add your ssh key to your agent everytime you connect to your machine, you can add the following commands in the ''.bashrc'' or ''.bash_profile'':<br /> &lt;div class=&quot;toccolours mw-collapsible mw-collapsed&quot; style=&quot;width=100%; overflow:auto;&quot;&gt;<br /> &lt;div style=&quot;font-weight:bold;line-height:1.6;&quot;&gt;Automatically add your ssh key(s) to the ssh-agent &lt;/div&gt;<br /> &lt;div class=&quot;mw-collapsible-content&quot;&gt;<br /> &lt;pre&gt;<br /> # Run the ssh-agent if not running yet<br /> <br /> # Function to start a new agent and save its info<br /> # from https://docs.vscentrum.be/accounts/ssh_agent.html<br /> start-ssh-agent() {<br /> #<br /> # Start an ssh agent if none is running already.<br /> # * First we try to connect to one via SSH_AUTH_SOCK<br /> # * If that doesn't work out, we try via the file ssh-agent-environment<br /> # * And if that doesn't work out either, we just start a fresh one and write<br /> # the information about it to ssh-agent-environment for future use.<br /> #<br /> # We don't really test for a correct value of SSH_AGENT_PID as the only<br /> # consequence of not having it set seems to be that one cannot kill<br /> # the ssh-agent with ssh-agent -k. But starting another one wouldn't<br /> # help to clean up the old one anyway.<br /> #<br /> # Note: ssh-add return codes:<br /> # 0 = success,<br /> # 1 = specified command fails (e.g., no keys with ssh-add -l)<br /> # 2 = unable to contact the authentication agent<br /> #<br /> sshfile=~/.ssh/ssh-agent-env<br /> #<br /> # First effort: Via SSH_AUTH_SOCK/SSH_AGENT_PID<br /> #<br /> if [ -n &quot;$SSH_AUTH_SOCK&quot; ]; then<br /> # SSH_AUTH_SOCK is defined, so try to connect to the authentication agent<br /> # it should point to. If it succeeds, reset newsshagent.<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by SSH_AUTH_SOCK, trying more...&quot;<br /> fi<br /> fi<br /> #<br /> # Second effort: If we're still looking for an ssh-agent, try via $sshfile<br /> #<br /> if [ -e &quot;$sshfile&quot; ]; then<br /> # Load the environment given in $sshfile<br /> . $sshfile &amp;&gt;/dev/null<br /> # Try to contact the ssh-agent<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running; reconfigured the environment.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by $sshfile.&quot;<br /> fi<br /> fi<br /> #<br /> # And if we haven't found a working one, start a new one...<br /> #<br /> #Create a new ssh-agent<br /> echo &quot;Creating new SSH agent.&quot;<br /> ssh-agent -s &gt; $sshfile &amp;&amp; . $sshfile<br /> unset sshfile<br /> }<br /> <br /> # Start the ssh-agent<br /> start-ssh-agent <br /> #&amp;&gt;/dev/null<br /> <br /> # Add the key<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key0 &amp;&gt;/dev/null<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key1 &amp;&gt;/dev/null<br /> &lt;/pre&gt;<br /> &lt;/div&gt;&lt;/div&gt;<br /> <br /> Once your key is set up, you are ready to clone the repo on your local machine. See the following screenshot for the number references<br /> <br /> [[File:Git_HowToClone_LHEP.png|thumb|upright=2.3|Where to find the ssh address of the git repo]]<br /> # Click on the expandable green clone button<br /> # Select ssh<br /> # Copy the repo link<br /> <br /> Note that if you have many repos on the same machine you will have to use an alias host instead of ''github.com'' and register it in a config file as described [https://docs.github.com/en/authentication/connecting-to-github-with-ssh/managing-deploy-keys#using-multiple-repositories-on-one-server here].<br /> <br /> Finally go on your local machine and use the ''git clone'' command:<br /> &lt;code&gt;<br /> git clone git@github.com:LHEP-neutrino/&lt;your_repo&gt;.git<br /> &lt;/code&gt;<br /> You are ready to go and do your super important work that now can be easily saved! Don't forget to pick the good manners like working on a branch, pulling the remote regularly to get the latest changes and pushing your work regularly to save it on the remote repo, and so on. You can find plenty of tutorials on basic uses or advances uses (like issue report, version release, CI/CO pipeline integration, ...), don't hesitate to ameliorate the LHEP github :).</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Git_repository&diff=914 2025-08-08T20:35:38Z

<p>Nsallin: </p> <hr /> <div>From the [[https://docs.github.com/en/get-started/start-your-journey/about-github-and-git official Github website]]: <br /> &lt;blockquote&gt;<br /> GitHub is a cloud-based platform where you can store, share, and work together with others to write code.<br /> <br /> Storing your code in a &quot;repository&quot; on GitHub allows you to:<br /> <br /> * Showcase or share your work.<br /> * Track and manage changes to your code over time.<br /> * Let others review your code, and make suggestions to improve it.<br /> * Collaborate on a shared project, without worrying that your changes will impact the work of your collaborators before you're ready to integrate them.<br /> * Collaborative working, one of GitHub’s fundamental features, is made possible by the open-source software, Git, upon which GitHub is built.<br /> &lt;/blockquote&gt;<br /> The [https://github.com/LHEP-neutrino LHEP Github] is the place where the repos should be stored in order to be accessible throughout LHEP members. It is a very good practice to work from repos, as cited, this helps keeping track of your work and allow others to easily use it.<br /> <br /> == Getting access to LHEP Github ==<br /> If you aren't a member yet, (once you have an [https://github.com/signup account]) contact an owner (e.g. [[mailto:serhan.tufanli@unibe.ch Serhan]] or [[mailto:nicolas.sallin@unibe.ch Nicolas]]) to get added. Then you will be able to create your repository or use an already existing one. <br /> <br /> == Cloning the repo on a local machine ==<br /> The '''remote''' github acts as the main repository. You can '''clone''' this repository on '''local''' machine which allows you to work on it. Once your work done, you can '''push''' your work from your local to the remote repo, such that it is saved in the cloud and other people can access it. On the other way around, if somebody else pushed something from their local repo to the remote one, then you can '''pull''' the changes from the remote repo to your local one such that you can use the work from others.<br /> <br /> To clone a repo, first you will have to 'link' your machine to the remote repo. An easy way to do this is to set up an ssh key, follow [https://docs.github.com/en/authentication/connecting-to-github-with-ssh this tutorial], under generate a new ssh key. Note that if you want to clone many repo on the same machine, you will have to generate one key per repo. If you do not want to add your ssh key to your agent everytime you connect to your machine, you can add the following commands in the ''.bashrc'' or ''.bash_profile'':<br /> &lt;div class=&quot;toccolours mw-collapsible mw-collapsed&quot; style=&quot;width=100%; overflow:auto;&quot;&gt;<br /> &lt;div style=&quot;font-weight:bold;line-height:1.6;&quot;&gt;Automatically add your ssh key(s) to the ssh-agent &lt;/div&gt;<br /> &lt;div class=&quot;mw-collapsible-content&quot;&gt;<br /> &lt;pre&gt;<br /> # Run the ssh-agent if not running yet<br /> <br /> # Function to start a new agent and save its info<br /> # from https://docs.vscentrum.be/accounts/ssh_agent.html<br /> start-ssh-agent() {<br /> #<br /> # Start an ssh agent if none is running already.<br /> # * First we try to connect to one via SSH_AUTH_SOCK<br /> # * If that doesn't work out, we try via the file ssh-agent-environment<br /> # * And if that doesn't work out either, we just start a fresh one and write<br /> # the information about it to ssh-agent-environment for future use.<br /> #<br /> # We don't really test for a correct value of SSH_AGENT_PID as the only<br /> # consequence of not having it set seems to be that one cannot kill<br /> # the ssh-agent with ssh-agent -k. But starting another one wouldn't<br /> # help to clean up the old one anyway.<br /> #<br /> # Note: ssh-add return codes:<br /> # 0 = success,<br /> # 1 = specified command fails (e.g., no keys with ssh-add -l)<br /> # 2 = unable to contact the authentication agent<br /> #<br /> sshfile=~/.ssh/ssh-agent-env<br /> #<br /> # First effort: Via SSH_AUTH_SOCK/SSH_AGENT_PID<br /> #<br /> if [ -n &quot;$SSH_AUTH_SOCK&quot; ]; then<br /> # SSH_AUTH_SOCK is defined, so try to connect to the authentication agent<br /> # it should point to. If it succeeds, reset newsshagent.<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by SSH_AUTH_SOCK, trying more...&quot;<br /> fi<br /> fi<br /> #<br /> # Second effort: If we're still looking for an ssh-agent, try via $sshfile<br /> #<br /> if [ -e &quot;$sshfile&quot; ]; then<br /> # Load the environment given in $sshfile<br /> . $sshfile &amp;&gt;/dev/null<br /> # Try to contact the ssh-agent<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running; reconfigured the environment.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by $sshfile.&quot;<br /> fi<br /> fi<br /> #<br /> # And if we haven't found a working one, start a new one...<br /> #<br /> #Create a new ssh-agent<br /> echo &quot;Creating new SSH agent.&quot;<br /> ssh-agent -s &gt; $sshfile &amp;&amp; . $sshfile<br /> unset sshfile<br /> }<br /> <br /> # Start the ssh-agent<br /> start-ssh-agent <br /> #&amp;&gt;/dev/null<br /> <br /> # Add the key<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key0 &amp;&gt;/dev/null<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key1 &amp;&gt;/dev/null<br /> &lt;/pre&gt;<br /> &lt;/div&gt;&lt;/div&gt;<br /> <br /> Once your key is set up, you are ready to clone the repo on your local machine.<br /> <br /> [[File:Git_HowToClone_LHEP.png|thumb|upright=2.3|Where to find the ssh address of the git repo]]<br /> # Click on the expandable green clone button<br /> # Select ssh<br /> # Copy the repo link</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Git_repository&diff=913 2025-08-08T20:34:54Z

<p>Nsallin: </p> <hr /> <div>From the [[https://docs.github.com/en/get-started/start-your-journey/about-github-and-git official Github website]]: <br /> &lt;blockquote&gt;<br /> GitHub is a cloud-based platform where you can store, share, and work together with others to write code.<br /> <br /> Storing your code in a &quot;repository&quot; on GitHub allows you to:<br /> <br /> * Showcase or share your work.<br /> * Track and manage changes to your code over time.<br /> * Let others review your code, and make suggestions to improve it.<br /> * Collaborate on a shared project, without worrying that your changes will impact the work of your collaborators before you're ready to integrate them.<br /> * Collaborative working, one of GitHub’s fundamental features, is made possible by the open-source software, Git, upon which GitHub is built.<br /> &lt;/blockquote&gt;<br /> The [https://github.com/LHEP-neutrino LHEP Github] is the place where the repos should be stored in order to be accessible throughout LHEP members. It is a very good practice to work from repos, as cited, this helps keeping track of your work and allow others to easily use it.<br /> <br /> == Getting access to LHEP Github ==<br /> If you aren't a member yet, (once you have an [https://github.com/signup account]) contact an owner (e.g. [[mailto:serhan.tufanli@unibe.ch Serhan]] or [[mailto:nicolas.sallin@unibe.ch Nicolas]]) to get added. Then you will be able to create your repository or use an already existing one. <br /> <br /> == Cloning the repo on a local machine ==<br /> The '''remote''' github acts as the main repository. You can '''clone''' this repository on '''local''' machine which allows you to work on it. Once your work done, you can '''push''' your work from your local to the remote repo, such that it is saved in the cloud and other people can access it. On the other way around, if somebody else pushed something from their local repo to the remote one, then you can '''pull''' the changes from the remote repo to your local one such that you can use the work from others.<br /> <br /> To clone a repo, first you will have to 'link' your machine to the remote repo. An easy way to do this is to set up an ssh key, follow [https://docs.github.com/en/authentication/connecting-to-github-with-ssh this tutorial], under generate a new ssh key. Note that if you want to clone many repo on the same machine, you will have to generate one key per repo. If you do not want to add your ssh key to your agent everytime you connect to your machine, you can add the following commands in the ''.bashrc'' or ''.bash_profile'':<br /> &lt;div class=&quot;toccolours mw-collapsible mw-collapsed&quot; style=&quot;width=100%; overflow:auto;&quot;&gt;<br /> &lt;div style=&quot;font-weight:bold;line-height:1.6;&quot;&gt;Automatically add your ssh key(s) to the ssh-agent &lt;/div&gt;<br /> &lt;div class=&quot;mw-collapsible-content&quot;&gt;<br /> &lt;pre&gt;<br /> # Run the ssh-agent if not running yet<br /> <br /> # Function to start a new agent and save its info<br /> # from https://docs.vscentrum.be/accounts/ssh_agent.html<br /> start-ssh-agent() {<br /> #<br /> # Start an ssh agent if none is running already.<br /> # * First we try to connect to one via SSH_AUTH_SOCK<br /> # * If that doesn't work out, we try via the file ssh-agent-environment<br /> # * And if that doesn't work out either, we just start a fresh one and write<br /> # the information about it to ssh-agent-environment for future use.<br /> #<br /> # We don't really test for a correct value of SSH_AGENT_PID as the only<br /> # consequence of not having it set seems to be that one cannot kill<br /> # the ssh-agent with ssh-agent -k. But starting another one wouldn't<br /> # help to clean up the old one anyway.<br /> #<br /> # Note: ssh-add return codes:<br /> # 0 = success,<br /> # 1 = specified command fails (e.g., no keys with ssh-add -l)<br /> # 2 = unable to contact the authentication agent<br /> #<br /> sshfile=~/.ssh/ssh-agent-env<br /> #<br /> # First effort: Via SSH_AUTH_SOCK/SSH_AGENT_PID<br /> #<br /> if [ -n &quot;$SSH_AUTH_SOCK&quot; ]; then<br /> # SSH_AUTH_SOCK is defined, so try to connect to the authentication agent<br /> # it should point to. If it succeeds, reset newsshagent.<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by SSH_AUTH_SOCK, trying more...&quot;<br /> fi<br /> fi<br /> #<br /> # Second effort: If we're still looking for an ssh-agent, try via $sshfile<br /> #<br /> if [ -e &quot;$sshfile&quot; ]; then<br /> # Load the environment given in $sshfile<br /> . $sshfile &amp;&gt;/dev/null<br /> # Try to contact the ssh-agent<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running; reconfigured the environment.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by $sshfile.&quot;<br /> fi<br /> fi<br /> #<br /> # And if we haven't found a working one, start a new one...<br /> #<br /> #Create a new ssh-agent<br /> echo &quot;Creating new SSH agent.&quot;<br /> ssh-agent -s &gt; $sshfile &amp;&amp; . $sshfile<br /> unset sshfile<br /> }<br /> <br /> # Start the ssh-agent<br /> start-ssh-agent <br /> #&amp;&gt;/dev/null<br /> <br /> # Add the key<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key0 &amp;&gt;/dev/null<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key1 &amp;&gt;/dev/null<br /> &lt;/pre&gt;<br /> &lt;/div&gt;&lt;/div&gt;<br /> <br /> Once your key is set up, you are ready to clone the repo on your local machine.<br /> <br /> [[File:Git_HowToClone_LHEP.png|thumb|upright=2.3|How to clone a git repo.]]<br /> # Click on the expandable green clone button<br /> # Select ssh<br /> # Copy the repo link</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Git_repository&diff=912 2025-08-08T20:32:51Z

<p>Nsallin: </p> <hr /> <div>From the [[https://docs.github.com/en/get-started/start-your-journey/about-github-and-git official Github website]]: <br /> &lt;blockquote&gt;<br /> GitHub is a cloud-based platform where you can store, share, and work together with others to write code.<br /> <br /> Storing your code in a &quot;repository&quot; on GitHub allows you to:<br /> <br /> * Showcase or share your work.<br /> * Track and manage changes to your code over time.<br /> * Let others review your code, and make suggestions to improve it.<br /> * Collaborate on a shared project, without worrying that your changes will impact the work of your collaborators before you're ready to integrate them.<br /> * Collaborative working, one of GitHub’s fundamental features, is made possible by the open-source software, Git, upon which GitHub is built.<br /> &lt;/blockquote&gt;<br /> The [https://github.com/LHEP-neutrino LHEP Github] is the place where the repos should be stored in order to be accessible throughout LHEP members. It is a very good practice to work from repos, as cited, this helps keeping track of your work and allow others to easily use it.<br /> <br /> == Getting access to LHEP Github ==<br /> If you aren't a member yet, (once you have an [https://github.com/signup account]) contact an owner (e.g. [[mailto:serhan.tufanli@unibe.ch Serhan]] or [[mailto:nicolas.sallin@unibe.ch Nicolas]]) to get added. Then you will be able to create your repository or use an already existing one. <br /> <br /> == Cloning the repo on a local machine ==<br /> The '''remote''' github acts as the main repository. You can '''clone''' this repository on '''local''' machine which allows you to work on it. Once your work done, you can '''push''' your work from your local to the remote repo, such that it is saved in the cloud and other people can access it. On the other way around, if somebody else pushed something from their local repo to the remote one, then you can '''pull''' the changes from the remote repo to your local one such that you can use the work from others.<br /> <br /> To clone a repo, first you will have to 'link' your machine to the remote repo. An easy way to do this is to set up an ssh key, follow [https://docs.github.com/en/authentication/connecting-to-github-with-ssh this tutorial], under generate a new ssh key. Note that if you want to clone many repo on the same machine, you will have to generate one key per repo. If you do not want to add your ssh key to your agent everytime you connect to your machine, you can add the following commands in the ''.bashrc'' or ''.bash_profile'':<br /> &lt;div class=&quot;toccolours mw-collapsible mw-collapsed&quot; style=&quot;width=100%; overflow:auto;&quot;&gt;<br /> &lt;div style=&quot;font-weight:bold;line-height:1.6;&quot;&gt;Automatically add your ssh key(s) to the ssh-agent &lt;/div&gt;<br /> &lt;div class=&quot;mw-collapsible-content&quot;&gt;<br /> &lt;pre&gt;<br /> # Run the ssh-agent if not running yet<br /> <br /> # Function to start a new agent and save its info<br /> # from https://docs.vscentrum.be/accounts/ssh_agent.html<br /> start-ssh-agent() {<br /> #<br /> # Start an ssh agent if none is running already.<br /> # * First we try to connect to one via SSH_AUTH_SOCK<br /> # * If that doesn't work out, we try via the file ssh-agent-environment<br /> # * And if that doesn't work out either, we just start a fresh one and write<br /> # the information about it to ssh-agent-environment for future use.<br /> #<br /> # We don't really test for a correct value of SSH_AGENT_PID as the only<br /> # consequence of not having it set seems to be that one cannot kill<br /> # the ssh-agent with ssh-agent -k. But starting another one wouldn't<br /> # help to clean up the old one anyway.<br /> #<br /> # Note: ssh-add return codes:<br /> # 0 = success,<br /> # 1 = specified command fails (e.g., no keys with ssh-add -l)<br /> # 2 = unable to contact the authentication agent<br /> #<br /> sshfile=~/.ssh/ssh-agent-env<br /> #<br /> # First effort: Via SSH_AUTH_SOCK/SSH_AGENT_PID<br /> #<br /> if [ -n &quot;$SSH_AUTH_SOCK&quot; ]; then<br /> # SSH_AUTH_SOCK is defined, so try to connect to the authentication agent<br /> # it should point to. If it succeeds, reset newsshagent.<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by SSH_AUTH_SOCK, trying more...&quot;<br /> fi<br /> fi<br /> #<br /> # Second effort: If we're still looking for an ssh-agent, try via $sshfile<br /> #<br /> if [ -e &quot;$sshfile&quot; ]; then<br /> # Load the environment given in $sshfile<br /> . $sshfile &amp;&gt;/dev/null<br /> # Try to contact the ssh-agent<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running; reconfigured the environment.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by $sshfile.&quot;<br /> fi<br /> fi<br /> #<br /> # And if we haven't found a working one, start a new one...<br /> #<br /> #Create a new ssh-agent<br /> echo &quot;Creating new SSH agent.&quot;<br /> ssh-agent -s &gt; $sshfile &amp;&amp; . $sshfile<br /> unset sshfile<br /> }<br /> <br /> # Start the ssh-agent<br /> start-ssh-agent <br /> #&amp;&gt;/dev/null<br /> <br /> # Add the key<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key0 &amp;&gt;/dev/null<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key1 &amp;&gt;/dev/null<br /> &lt;/pre&gt;<br /> &lt;/div&gt;&lt;/div&gt;<br /> <br /> Once your key is set up, you are ready to clone the repo on your local machine<br /> <br /> [[File:Git_HowToClone_LHEP.png|thumb|upright=1.5|center|How to clone a git repo.]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=File:Git_HowToClone_LHEP.png&diff=911 2025-08-08T20:29:41Z

<p>Nsallin: Screen shot showing the steps to find the ssh link to clone a git repo</p> <hr /> <div>== Summary ==<br /> Screen shot showing the steps to find the ssh link to clone a git repo</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Git_repository&diff=910 2025-08-08T20:25:47Z

<p>Nsallin: </p> <hr /> <div>From the [[https://docs.github.com/en/get-started/start-your-journey/about-github-and-git official Github website]]: <br /> &lt;blockquote&gt;<br /> GitHub is a cloud-based platform where you can store, share, and work together with others to write code.<br /> <br /> Storing your code in a &quot;repository&quot; on GitHub allows you to:<br /> <br /> * Showcase or share your work.<br /> * Track and manage changes to your code over time.<br /> * Let others review your code, and make suggestions to improve it.<br /> * Collaborate on a shared project, without worrying that your changes will impact the work of your collaborators before you're ready to integrate them.<br /> * Collaborative working, one of GitHub’s fundamental features, is made possible by the open-source software, Git, upon which GitHub is built.<br /> &lt;/blockquote&gt;<br /> The [https://github.com/LHEP-neutrino LHEP Github] is the place where the repos should be stored in order to be accessible throughout LHEP members. It is a very good practice to work from repos, as cited, this helps keeping track of your work and allow others to easily use it.<br /> <br /> == Getting access to LHEP Github ==<br /> If you aren't a member yet, (once you have an [https://github.com/signup account]) contact an owner (e.g. [[mailto:serhan.tufanli@unibe.ch Serhan]] or [[mailto:nicolas.sallin@unibe.ch Nicolas]]) to get added. Then you will be able to create your repository or use an already existing one. <br /> <br /> == Cloning the repo on a local machine ==<br /> The '''remote''' github acts as the main repository. You can '''clone''' this repository on '''local''' machine which allows you to work on it. Once your work done, you can '''push''' your work from your local to the remote repo, such that it is saved in the cloud and other people can access it. On the other way around, if somebody else pushed something from their local repo to the remote one, then you can '''pull''' the changes from the remote repo to your local one such that you can use the work from others.<br /> <br /> To clone a repo, first you will have to 'link' your machine to the remote repo. An easy way to do this is to set up an ssh key, follow [https://docs.github.com/en/authentication/connecting-to-github-with-ssh this tutorial], under generate a new ssh key. Note that if you want to clone many repo on the same machine, you will have to generate one key per repo. If you do not want to add your ssh key to your agent everytime you connect to your machine, you can add the following commands in the ''.bashrc'' or ''.bash_profile'':<br /> &lt;div class=&quot;toccolours mw-collapsible mw-collapsed&quot; style=&quot;width=100%; overflow:auto;&quot;&gt;<br /> &lt;div style=&quot;font-weight:bold;line-height:1.6;&quot;&gt;Automatically add your ssh key(s) to the ssh-agent &lt;/div&gt;<br /> &lt;div class=&quot;mw-collapsible-content&quot;&gt;<br /> &lt;pre&gt;<br /> # Run the ssh-agent if not running yet<br /> <br /> # Function to start a new agent and save its info<br /> # from https://docs.vscentrum.be/accounts/ssh_agent.html<br /> start-ssh-agent() {<br /> #<br /> # Start an ssh agent if none is running already.<br /> # * First we try to connect to one via SSH_AUTH_SOCK<br /> # * If that doesn't work out, we try via the file ssh-agent-environment<br /> # * And if that doesn't work out either, we just start a fresh one and write<br /> # the information about it to ssh-agent-environment for future use.<br /> #<br /> # We don't really test for a correct value of SSH_AGENT_PID as the only<br /> # consequence of not having it set seems to be that one cannot kill<br /> # the ssh-agent with ssh-agent -k. But starting another one wouldn't<br /> # help to clean up the old one anyway.<br /> #<br /> # Note: ssh-add return codes:<br /> # 0 = success,<br /> # 1 = specified command fails (e.g., no keys with ssh-add -l)<br /> # 2 = unable to contact the authentication agent<br /> #<br /> sshfile=~/.ssh/ssh-agent-env<br /> #<br /> # First effort: Via SSH_AUTH_SOCK/SSH_AGENT_PID<br /> #<br /> if [ -n &quot;$SSH_AUTH_SOCK&quot; ]; then<br /> # SSH_AUTH_SOCK is defined, so try to connect to the authentication agent<br /> # it should point to. If it succeeds, reset newsshagent.<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by SSH_AUTH_SOCK, trying more...&quot;<br /> fi<br /> fi<br /> #<br /> # Second effort: If we're still looking for an ssh-agent, try via $sshfile<br /> #<br /> if [ -e &quot;$sshfile&quot; ]; then<br /> # Load the environment given in $sshfile<br /> . $sshfile &amp;&gt;/dev/null<br /> # Try to contact the ssh-agent<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running; reconfigured the environment.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by $sshfile.&quot;<br /> fi<br /> fi<br /> #<br /> # And if we haven't found a working one, start a new one...<br /> #<br /> #Create a new ssh-agent<br /> echo &quot;Creating new SSH agent.&quot;<br /> ssh-agent -s &gt; $sshfile &amp;&amp; . $sshfile<br /> unset sshfile<br /> }<br /> <br /> # Start the ssh-agent<br /> start-ssh-agent <br /> #&amp;&gt;/dev/null<br /> <br /> # Add the key<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key0 &amp;&gt;/dev/null<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key1 &amp;&gt;/dev/null<br /> &lt;/pre&gt;<br /> &lt;/div&gt;&lt;/div&gt;<br /> <br /> Once your key is set up, you are ready to clone the repo on your local machine<br /> <br /> [[File:Git_HowToClone_LHEP.png|thumb|center|How to clone a git repo.]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Git_repository&diff=909 2025-08-08T20:11:52Z

<p>Nsallin: </p> <hr /> <div>From the [[https://docs.github.com/en/get-started/start-your-journey/about-github-and-git official Github website]]: <br /> &lt;blockquote&gt;<br /> GitHub is a cloud-based platform where you can store, share, and work together with others to write code.<br /> <br /> Storing your code in a &quot;repository&quot; on GitHub allows you to:<br /> <br /> * Showcase or share your work.<br /> * Track and manage changes to your code over time.<br /> * Let others review your code, and make suggestions to improve it.<br /> * Collaborate on a shared project, without worrying that your changes will impact the work of your collaborators before you're ready to integrate them.<br /> * Collaborative working, one of GitHub’s fundamental features, is made possible by the open-source software, Git, upon which GitHub is built.<br /> &lt;/blockquote&gt;<br /> The [https://github.com/LHEP-neutrino LHEP Github] is the place where the repos should be stored in order to be accessible throughout LHEP members. It is a very good practice to work from repos, as cited, this helps keeping track of your work and allow others to easily use it.<br /> <br /> == Getting access to LHEP Github ==<br /> If you aren't a member yet, (once you have an [https://github.com/signup account]) contact an owner (e.g. [[mailto:serhan.tufanli@unibe.ch Serhan]] or [[mailto:nicolas.sallin@unibe.ch Nicolas]]) to get added. Then you will be able to create your repository or use an already existing one. <br /> <br /> == Cloning the repo on a local machine ==<br /> The '''remote''' github acts as the main repository. You can '''clone''' this repository on '''local''' machine which allows you to work on it. Once your work done, you can '''push''' your work from your local to the remote repo, such that it is saved in the cloud and other people can access it. On the other way around, if somebody else pushed something from their local repo to the remote one, then you can '''pull''' the changes from the remote repo to your local one such that you can use the work from others.<br /> <br /> To clone a repo, first you will have to 'link' your machine to the remote repo. An easy way to do this is to set up an ssh key, follow [https://docs.github.com/en/authentication/connecting-to-github-with-ssh this tutorial], under generate a new ssh key. Note that if you want to clone many repo on the same machine, you will have to generate one key per repo. If you do not want to add your ssh key to your agent everytime you connect to your machine, you can add the following commands in the ''.bashrc'' or ''.bash_profile'':<br /> &lt;div class=&quot;toccolours mw-collapsible mw-collapsed&quot; style=&quot;width=100%; overflow:auto;&quot;&gt;<br /> &lt;div style=&quot;font-weight:bold;line-height:1.6;&quot;&gt;Automatically add your ssh key(s) to the ssh-agent &lt;/div&gt;<br /> &lt;div class=&quot;mw-collapsible-content&quot;&gt;<br /> &lt;pre&gt;<br /> # Run the ssh-agent if not running yet<br /> <br /> # Function to start a new agent and save its info<br /> # from https://docs.vscentrum.be/accounts/ssh_agent.html<br /> start-ssh-agent() {<br /> #<br /> # Start an ssh agent if none is running already.<br /> # * First we try to connect to one via SSH_AUTH_SOCK<br /> # * If that doesn't work out, we try via the file ssh-agent-environment<br /> # * And if that doesn't work out either, we just start a fresh one and write<br /> # the information about it to ssh-agent-environment for future use.<br /> #<br /> # We don't really test for a correct value of SSH_AGENT_PID as the only<br /> # consequence of not having it set seems to be that one cannot kill<br /> # the ssh-agent with ssh-agent -k. But starting another one wouldn't<br /> # help to clean up the old one anyway.<br /> #<br /> # Note: ssh-add return codes:<br /> # 0 = success,<br /> # 1 = specified command fails (e.g., no keys with ssh-add -l)<br /> # 2 = unable to contact the authentication agent<br /> #<br /> sshfile=~/.ssh/ssh-agent-env<br /> #<br /> # First effort: Via SSH_AUTH_SOCK/SSH_AGENT_PID<br /> #<br /> if [ -n &quot;$SSH_AUTH_SOCK&quot; ]; then<br /> # SSH_AUTH_SOCK is defined, so try to connect to the authentication agent<br /> # it should point to. If it succeeds, reset newsshagent.<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by SSH_AUTH_SOCK, trying more...&quot;<br /> fi<br /> fi<br /> #<br /> # Second effort: If we're still looking for an ssh-agent, try via $sshfile<br /> #<br /> if [ -e &quot;$sshfile&quot; ]; then<br /> # Load the environment given in $sshfile<br /> . $sshfile &amp;&gt;/dev/null<br /> # Try to contact the ssh-agent<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running; reconfigured the environment.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by $sshfile.&quot;<br /> fi<br /> fi<br /> #<br /> # And if we haven't found a working one, start a new one...<br /> #<br /> #Create a new ssh-agent<br /> echo &quot;Creating new SSH agent.&quot;<br /> ssh-agent -s &gt; $sshfile &amp;&amp; . $sshfile<br /> unset sshfile<br /> }<br /> <br /> # Start the ssh-agent<br /> start-ssh-agent <br /> #&amp;&gt;/dev/null<br /> <br /> # Add the key<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key0 &amp;&gt;/dev/null<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key1 &amp;&gt;/dev/null<br /> &lt;/pre&gt;<br /> &lt;/div&gt;&lt;/div&gt;</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Git_repository&diff=908 2025-08-08T20:10:39Z

<p>Nsallin: Created page with &quot;From the https://docs.github.com/en/get-started/start-your-journey/about-github-and-git official Github website: &lt;blockquote&gt; GitHub is a cloud-based platform where you can store, share, and work together with others to write code. Storing your code in a &quot;repository&quot; on GitHub allows you to: * Showcase or share your work. * Track and manage changes to your code over time. * Let others review your code, and make suggestions to improve it. * Collaborate on a shared...&quot;</p> <hr /> <div>From the [[https://docs.github.com/en/get-started/start-your-journey/about-github-and-git official Github website]]: <br /> &lt;blockquote&gt;<br /> GitHub is a cloud-based platform where you can store, share, and work together with others to write code.<br /> <br /> Storing your code in a &quot;repository&quot; on GitHub allows you to:<br /> <br /> * Showcase or share your work.<br /> * Track and manage changes to your code over time.<br /> * Let others review your code, and make suggestions to improve it.<br /> * Collaborate on a shared project, without worrying that your changes will impact the work of your collaborators before you're ready to integrate them.<br /> * Collaborative working, one of GitHub’s fundamental features, is made possible by the open-source software, Git, upon which GitHub is built.<br /> &lt;/blockquote&gt;<br /> The [https://github.com/LHEP-neutrino LHEP Github] is the place where the repos should be stored in order to be accessible throughout LHEP members. It is a very good practice to work from repos, as cited, this helps keeping track of your work and allow others to easily use it.<br /> <br /> == Getting access to LHEP Github ==<br /> If you aren't a member yet, (once you have an [https://github.com/signup account]) contact an owner (e.g. [[mailto:serhan.tufanli@unibe.ch Serhan]] or [[mailto:nicolas.sallin@unibe.ch Nicolas]]) to get added. Then you will be able to create your repository or use an already existing one. <br /> <br /> == Cloning the repo on a local machine ==<br /> The '''remote''' github acts as the main repository. You can '''clone''' this repository on '''local''' machine which allows you to work on it. Once your work done, you can '''push''' your work from your local to the remote repo, such that it is saved in the cloud and other people can access it. On the other way around, if somebody else pushed something from their local repo to the remote one, then you can '''pull''' the changes from the remote repo to your local one such that you can use the work from others.<br /> <br /> To clone a repo, first you will have to 'link' your machine to the remote repo. An easy way to do this is to set up an ssh key, follow [https://docs.github.com/en/authentication/connecting-to-github-with-ssh this tutorial], under generate a new ssh key. Note that if you want to clone many repo on the same machine, you will have to generate one key per repo. If you do not want to add your ssh key to your agent everytime you connect to your machine, you can add the following commands in the ''.bashrc'' or ''.bash_profile'':<br /> &lt;div class=&quot;toccolours mw-collapsible mw-collapsed&quot; style=&quot;width=100%; overflow:auto;&quot;&gt;<br /> &lt;div style=&quot;font-weight:bold;line-height:1.6;&quot;&gt;Automatically add your ssh key(s) to the ssh-agent &lt;/div&gt;<br /> &lt;div class=&quot;mw-collapsible-content&quot;&gt;<br /> &lt;syntaxhighlight lang=&quot;bash&quot;&gt;<br /> # Run the ssh-agent if not running yet<br /> <br /> # Function to start a new agent and save its info<br /> # from https://docs.vscentrum.be/accounts/ssh_agent.html<br /> start-ssh-agent() {<br /> #<br /> # Start an ssh agent if none is running already.<br /> # * First we try to connect to one via SSH_AUTH_SOCK<br /> # * If that doesn't work out, we try via the file ssh-agent-environment<br /> # * And if that doesn't work out either, we just start a fresh one and write<br /> # the information about it to ssh-agent-environment for future use.<br /> #<br /> # We don't really test for a correct value of SSH_AGENT_PID as the only<br /> # consequence of not having it set seems to be that one cannot kill<br /> # the ssh-agent with ssh-agent -k. But starting another one wouldn't<br /> # help to clean up the old one anyway.<br /> #<br /> # Note: ssh-add return codes:<br /> # 0 = success,<br /> # 1 = specified command fails (e.g., no keys with ssh-add -l)<br /> # 2 = unable to contact the authentication agent<br /> #<br /> sshfile=~/.ssh/ssh-agent-env<br /> #<br /> # First effort: Via SSH_AUTH_SOCK/SSH_AGENT_PID<br /> #<br /> if [ -n &quot;$SSH_AUTH_SOCK&quot; ]; then<br /> # SSH_AUTH_SOCK is defined, so try to connect to the authentication agent<br /> # it should point to. If it succeeds, reset newsshagent.<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by SSH_AUTH_SOCK, trying more...&quot;<br /> fi<br /> fi<br /> #<br /> # Second effort: If we're still looking for an ssh-agent, try via $sshfile<br /> #<br /> if [ -e &quot;$sshfile&quot; ]; then<br /> # Load the environment given in $sshfile<br /> . $sshfile &amp;&gt;/dev/null<br /> # Try to contact the ssh-agent<br /> ssh-add -l &amp;&gt;/dev/null<br /> if [[ $? != 2 ]]; then<br /> echo &quot;SSH agent already running; reconfigured the environment.&quot;<br /> unset sshfile<br /> return 0<br /> else<br /> echo &quot;Could not contact the ssh-agent pointed at by $sshfile.&quot;<br /> fi<br /> fi<br /> #<br /> # And if we haven't found a working one, start a new one...<br /> #<br /> #Create a new ssh-agent<br /> echo &quot;Creating new SSH agent.&quot;<br /> ssh-agent -s &gt; $sshfile &amp;&amp; . $sshfile<br /> unset sshfile<br /> }<br /> <br /> # Start the ssh-agent<br /> start-ssh-agent <br /> #&amp;&gt;/dev/null<br /> <br /> # Add the key<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key0 &amp;&gt;/dev/null<br /> ssh-add ~/.ssh/id_ed25519_your_ssh_key1 &amp;&gt;/dev/null<br /> &lt;/syntaxhighlight&gt;<br /> &lt;/div&gt;&lt;/div&gt;</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=907 2025-08-08T19:31:45Z

<p>Nsallin: add tuto section</p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == ND-LAr ==<br /> [[https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]] &lt;br&gt;<br /> [[https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]] &lt;br&gt;<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository. See the FSD data chapter for a short introduction.<br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> A short introduction to 2x2 and FSD data can be found on the [[Setup to process FSD data on neutrino01]] page.<br /> <br /> == 2x2 ==<br /> nothing yet<br /> <br /> == Tutorials ==<br /> Here are regrouped a few, hopefully soon many, tutorials.<br /> === Git repo ===<br /> How to set up a (or many) [[Git repository]].<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://www.reiseplattform.unibe.ch/before_you_start/index_eng.html UNIBE travel platform]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=906 2025-08-06T14:15:06Z

<p>Nsallin: </p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == ND-LAr ==<br /> [[https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]] &lt;br&gt;<br /> [[https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]] &lt;br&gt;<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository. See the FSD data chapter for a short introduction.<br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> A short introduction to 2x2 and FSD data can be found on the [[Setup to process FSD data on neutrino01]] page.<br /> <br /> == 2x2 ==<br /> nothing yet<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://www.reiseplattform.unibe.ch/before_you_start/index_eng.html UNIBE travel platform]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=905 2025-08-06T14:14:25Z

<p>Nsallin: </p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == ND-LAr ==<br /> [[https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]] &lt;br&gt;<br /> [[https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]] &lt;br&gt;<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository. See <br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> A short introduction to 2x2 and FSD data can be found on the [[Setup to process FSD data on neutrino01]] page.<br /> <br /> == 2x2 ==<br /> nothing yet<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://www.reiseplattform.unibe.ch/before_you_start/index_eng.html UNIBE travel platform]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=903 2025-06-23T11:49:41Z

<p>Nsallin: </p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == ND-LAr ==<br /> [[https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]] &lt;br&gt;<br /> [[https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]] &lt;br&gt;<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository. A short introduction to 2x2 and FSD data can be found on the [[Setup to process FSD data on neutrino01]] page.<br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> <br /> <br /> == 2x2 ==<br /> nothing yet<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://www.reiseplattform.unibe.ch/before_you_start/index_eng.html UNIBE travel platform]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=902 2025-06-19T09:32:33Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the ''README'' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed).<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is too old to install the latest Jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> The default python version on ''neutrino01''is <br /> &lt;!-- <br /> &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; <br /> --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is unfortunately too old support the latest Jupyter version. A lot of programmes depend on python which make it quite an hassle to upgrade it and additionally the admin right are needed to do it. A solution is to install a new python via the package ''pyenv'' and to do it in the virtual environment previously created.<br /> First clone the ''pyenv'' repository<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.11.9<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> , the star indicating the currently used one. Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> === ''h5flow'' framework ===<br /> Now we can install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd h5flow<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ pip install -e .<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ cd ..<br /> (ndlar_flow.venv) [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> === ''ndlar_flow'' ===<br /> And finally we can install ''ndlar_flow''<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone git@github.com:DUNE/ndlar_flow.git<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd ndlar_flow<br /> (ndlar_flow.venv) [user@neutrino01 ndlar_flow]$ pip install -e .<br /> &lt;/pre&gt;<br /> Note that the &lt;code&gt;-e&lt;/code&gt; option installs the packages in &quot;editable&quot; mode, meaning any changes you make will take effect without the need to re-run &lt;code&gt;pip install&lt;/code&gt;.<br /> <br /> == How to use == <br /> A good starting point is the [https://github.com/DUNE/ndlar_flow# ''README''] of the git repo, it describes how to run simple workflow such as light event building and also propose some tutorials. If you want to develop new script or update current one, a good practice is to create a new branch in the git project and work there. To edit the scripts, traditional editors like ''vim'' are available on the server, but there are also possibilities to open the repository on your local machine. An interactive solution is to start a Jupyter server on the remote neutrino01 server and then open a Jupyter Notebook from your local machine through a ssh tunnel. A second possibility is to ssh to the server through Visual Studio Code (VS Code), which provides a nice coding environment. In both case you also have access to the remote terminal inside the programme. In my opinion the two options are very complementary, VS Code to write code easily and jupyter notebook to use it and play around with it.<br /> <br /> === Visual Studio Code ===<br /> To use this program you will simply have to download VS Code and the ssh extension. Detailed information can be found [https://code.visualstudio.com/docs/remote/ssh here].<br /> <br /> === Jupyter Notebook ===<br /> First you will have to install Jupyter in your virtual environment on the server<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pip install jupyter<br /> &lt;/pre&gt;<br /> Then, once the installed successfully, you can start a jupyter server without opening a browser by running<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ jupyter notebook --no-browser --port=8080<br /> &lt;/pre&gt;<br /> ,the no-browser open is necessary but you can choose the desired port number. When the server is running, from a new terminal on your local machine you can open an ssh tunnel to the previously chosen port on the remote server<br /> &lt;pre&gt;<br /> user_local ~/$ ssh -L 8080:localhost:8080 user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> When the connexion is established, you can go back to the first terminal where the jupyter server is running and look for the following line<br /> &lt;pre&gt;<br /> [C 2025-06-18 14:27:48.107 ServerApp] <br /> <br /> To access the server, open this file in a browser:<br /> file:///terabig/user/.local/share/jupyter/runtime/jpserver-664549-open.html<br /> Or copy and paste one of these URLs:<br /> http://localhost:8080/tree?token=&lt;some number and letter&gt;<br /> http://127.0.0.1:8080/tree?token=&lt;some number and letter&gt;<br /> &lt;/pre&gt;<br /> . Copy the address of the server, e.g. here &lt;code&gt;http://localhost:8080/tree?token=&lt;some number and letter&gt;&lt;/code&gt; in your favourite browser on your local machine, it will allow you to access the Jupyter server. Note that some browser have difficulties with Jupyter notebooks, download an other one if yours is not compatible. Now you can select a file and start to work on it, good luck :).<br /> <br /> <br /> = AFI viewer =<br /> Ask Jan.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=901 2025-06-18T12:42:50Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the ''README'' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed).<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is too old to install the latest Jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> The default python version on ''neutrino01''is <br /> &lt;!-- <br /> &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; <br /> --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is unfortunately too old support the latest Jupyter version. A lot of programmes depend on python which make it quite an hassle to upgrade it and additionally the admin right are needed to do it. A solution is to install a new python via the package ''pyenv'' and to do it in the virtual environment previously created.<br /> First clone the ''pyenv'' repository<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.11.9<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> , the star indicating the currently used one. Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> === ''h5flow'' framework ===<br /> Now we can install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd h5flow<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ pip install -e .<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ cd ..<br /> (ndlar_flow.venv) [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> === ''ndlar_flow'' ===<br /> And finally we can install ''ndlar_flow''<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone git@github.com:DUNE/ndlar_flow.git<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd ndlar_flow<br /> (ndlar_flow.venv) [user@neutrino01 ndlar_flow]$ pip install -e .<br /> &lt;/pre&gt;<br /> Note that the &lt;code&gt;-e&lt;/code&gt; option installs the packages in &quot;editable&quot; mode, meaning any changes you make will take effect without the need to re-run &lt;code&gt;pip install&lt;/code&gt;.<br /> <br /> == How to use == <br /> A good starting point is the [https://github.com/DUNE/ndlar_flow# ''README''] of the git repo, it describes how to run simple workflow such as light event building and also propose some tutorials. If you want to develop new script or update current one, a good practice is to create a new branch in the git project and work there. To edit the scripts traditional editors like ''vim'' are available on the server, but there is also the possibility to open the repository on the local machine. A very interactive solution is to start a jupyter server on the remote neutrino01 server and then open a jupyter notebook from your local machine through an ssh tunnel. A second practical possibility is to ssh to the server through Visual Studio Code (VS Code), which provides a nice coding environment. In both case you also have access to the remote terminal inside the programme. In my opinion the two options are very complementary, VS Code to write code easily and jupyter notebook to use it and play around with it.<br /> <br /> === Visual Studio Code ===<br /> To use this program you will simply have to download VS Code and the ssh extension. Detailed information can be found [https://code.visualstudio.com/docs/remote/ssh here].<br /> <br /> === Jupyter Notebook ===<br /> The Jupyter Notebook option is slightly more demanding but also accessible. First you will have to download jupyter in your virtual environment on the server<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pip install jupyter<br /> &lt;/pre&gt;<br /> Then once the installation success full you can start a jupyter server without openning a browser by running<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ jupyter notebook --no-browser --port=8080<br /> &lt;/pre&gt;<br /> , you can choose the desired port number. Once the server is running you can open a new terminal on your local machine and open an ssh tunnel to the previously chosen port on the remote server<br /> &lt;pre&gt;<br /> user_local ~/$ ssh -L 8080:localhost:8080 user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> Once this is done, you can go back to the first terminal where the jupyter server is running and look for the following line<br /> &lt;pre&gt;<br /> [C 2025-06-18 14:27:48.107 ServerApp] <br /> <br /> To access the server, open this file in a browser:<br /> file:///terabig/user/.local/share/jupyter/runtime/jpserver-664549-open.html<br /> Or copy and paste one of these URLs:<br /> http://localhost:8080/tree?token=&lt;some number and letter&gt;<br /> http://127.0.0.1:8080/tree?token=&lt;some number and letter&gt;<br /> &lt;/pre&gt;<br /> and copy the address of the server, e.g. here &lt;code&gt;http://localhost:8080/tree?token=&lt;some number and letter&gt;&lt;/code&gt; in your favorite browser on your local machine. Note that some browser have difficulties with jupyter notebook, download an other one if your is not compatible. Now you can select a file and start work on it, good luck :).<br /> <br /> <br /> = AFI viewer =<br /> Ask Jan.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=900 2025-06-18T12:41:55Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the ''README'' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed).<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is too old to install the latest Jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> The default python version on ''neutrino01''is <br /> &lt;!-- <br /> &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; <br /> --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is unfortunately too old support the latest Jupyter version. A lot of programmes depend on python which make it quite an hassle to upgrade it and additionally the admin right are needed to do it. A solution is to install a new python via the package ''pyenv'' and to do it in the virtual environment previously created.<br /> First clone the ''pyenv'' repository<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.10.4<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> , the star indicating the currently used one. Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> === ''h5flow'' framework ===<br /> Now we can install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd h5flow<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ pip install -e .<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ cd ..<br /> (ndlar_flow.venv) [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> === ''ndlar_flow'' ===<br /> And finally we can install ''ndlar_flow''<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone git@github.com:DUNE/ndlar_flow.git<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd ndlar_flow<br /> (ndlar_flow.venv) [user@neutrino01 ndlar_flow]$ pip install -e .<br /> &lt;/pre&gt;<br /> Note that the &lt;code&gt;-e&lt;/code&gt; option installs the packages in &quot;editable&quot; mode, meaning any changes you make will take effect without the need to re-run &lt;code&gt;pip install&lt;/code&gt;.<br /> <br /> == How to use == <br /> A good starting point is the [https://github.com/DUNE/ndlar_flow# ''README''] of the git repo, it describes how to run simple workflow such as light event building and also propose some tutorials. If you want to develop new script or update current one, a good practice is to create a new branch in the git project and work there. To edit the scripts traditional editors like ''vim'' are available on the server, but there is also the possibility to open the repository on the local machine. A very interactive solution is to start a jupyter server on the remote neutrino01 server and then open a jupyter notebook from your local machine through an ssh tunnel. A second practical possibility is to ssh to the server through Visual Studio Code (VS Code), which provides a nice coding environment. In both case you also have access to the remote terminal inside the programme. In my opinion the two options are very complementary, VS Code to write code easily and jupyter notebook to use it and play around with it.<br /> <br /> === Visual Studio Code ===<br /> To use this program you will simply have to download VS Code and the ssh extension. Detailed information can be found [https://code.visualstudio.com/docs/remote/ssh here].<br /> <br /> === Jupyter Notebook ===<br /> The Jupyter Notebook option is slightly more demanding but also accessible. First you will have to download jupyter in your virtual environment on the server<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pip install jupyter<br /> &lt;/pre&gt;<br /> Then once the installation success full you can start a jupyter server without openning a browser by running<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ jupyter notebook --no-browser --port=8080<br /> &lt;/pre&gt;<br /> , you can choose the desired port number. Once the server is running you can open a new terminal on your local machine and open an ssh tunnel to the previously chosen port on the remote server<br /> &lt;pre&gt;<br /> user_local ~/$ ssh -L 8080:localhost:8080 user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> Once this is done, you can go back to the first terminal where the jupyter server is running and look for the following line<br /> &lt;pre&gt;<br /> [C 2025-06-18 14:27:48.107 ServerApp] <br /> <br /> To access the server, open this file in a browser:<br /> file:///terabig/user/.local/share/jupyter/runtime/jpserver-664549-open.html<br /> Or copy and paste one of these URLs:<br /> http://localhost:8080/tree?token=&lt;some number and letter&gt;<br /> http://127.0.0.1:8080/tree?token=&lt;some number and letter&gt;<br /> &lt;/pre&gt;<br /> and copy the address of the server, e.g. here &lt;code&gt;http://localhost:8080/tree?token=&lt;some number and letter&gt;&lt;/code&gt; in your favorite browser on your local machine. Note that some browser have difficulties with jupyter notebook, download an other one if your is not compatible. Now you can select a file and start work on it, good luck :).<br /> <br /> <br /> = AFI viewer =<br /> Ask Jan.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=899 2025-06-18T12:41:18Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the ''README'' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed).<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is too old to install the latest Jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> The default python version on ''neutrino01'' is <br /> is &lt;!-- &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is unfortunately too old support the latest Jupyter version. A lot of programmes depend on python which make it quite an hassle to upgrade it and additionally the admin right are needed to do it. A solution is to install a new python via the package ''pyenv'' and to do it in the virtual environment previously created.<br /> First clone the ''pyenv'' repository<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.10.4<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> , the star indicating the currently used one. Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> === ''h5flow'' framework ===<br /> Now we can install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd h5flow<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ pip install -e .<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ cd ..<br /> (ndlar_flow.venv) [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> === ''ndlar_flow'' ===<br /> And finally we can install ''ndlar_flow''<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone git@github.com:DUNE/ndlar_flow.git<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd ndlar_flow<br /> (ndlar_flow.venv) [user@neutrino01 ndlar_flow]$ pip install -e .<br /> &lt;/pre&gt;<br /> Note that the &lt;code&gt;-e&lt;/code&gt; option installs the packages in &quot;editable&quot; mode, meaning any changes you make will take effect without the need to re-run &lt;code&gt;pip install&lt;/code&gt;.<br /> <br /> == How to use == <br /> A good starting point is the [https://github.com/DUNE/ndlar_flow# ''README''] of the git repo, it describes how to run simple workflow such as light event building and also propose some tutorials. If you want to develop new script or update current one, a good practice is to create a new branch in the git project and work there. To edit the scripts traditional editors like ''vim'' are available on the server, but there is also the possibility to open the repository on the local machine. A very interactive solution is to start a jupyter server on the remote neutrino01 server and then open a jupyter notebook from your local machine through an ssh tunnel. A second practical possibility is to ssh to the server through Visual Studio Code (VS Code), which provides a nice coding environment. In both case you also have access to the remote terminal inside the programme. In my opinion the two options are very complementary, VS Code to write code easily and jupyter notebook to use it and play around with it.<br /> <br /> === Visual Studio Code ===<br /> To use this program you will simply have to download VS Code and the ssh extension. Detailed information can be found [https://code.visualstudio.com/docs/remote/ssh here].<br /> <br /> === Jupyter Notebook ===<br /> The Jupyter Notebook option is slightly more demanding but also accessible. First you will have to download jupyter in your virtual environment on the server<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pip install jupyter<br /> &lt;/pre&gt;<br /> Then once the installation success full you can start a jupyter server without openning a browser by running<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ jupyter notebook --no-browser --port=8080<br /> &lt;/pre&gt;<br /> , you can choose the desired port number. Once the server is running you can open a new terminal on your local machine and open an ssh tunnel to the previously chosen port on the remote server<br /> &lt;pre&gt;<br /> user_local ~/$ ssh -L 8080:localhost:8080 user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> Once this is done, you can go back to the first terminal where the jupyter server is running and look for the following line<br /> &lt;pre&gt;<br /> [C 2025-06-18 14:27:48.107 ServerApp] <br /> <br /> To access the server, open this file in a browser:<br /> file:///terabig/user/.local/share/jupyter/runtime/jpserver-664549-open.html<br /> Or copy and paste one of these URLs:<br /> http://localhost:8080/tree?token=&lt;some number and letter&gt;<br /> http://127.0.0.1:8080/tree?token=&lt;some number and letter&gt;<br /> &lt;/pre&gt;<br /> and copy the address of the server, e.g. here &lt;code&gt;http://localhost:8080/tree?token=&lt;some number and letter&gt;&lt;/code&gt; in your favorite browser on your local machine. Note that some browser have difficulties with jupyter notebook, download an other one if your is not compatible. Now you can select a file and start work on it, good luck :).<br /> <br /> <br /> = AFI viewer =<br /> Ask Jan.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=898 2025-06-18T12:40:59Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the ''README'' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed)<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is too old to install the latest Jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> The default python version on ''neutrino01'' is <br /> is &lt;!-- &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is unfortunately too old support the latest Jupyter version. A lot of programmes depend on python which make it quite an hassle to upgrade it and additionally the admin right are needed to do it. A solution is to install a new python via the package ''pyenv'' and to do it in the virtual environment previously created.<br /> First clone the ''pyenv'' repository<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.10.4<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> , the star indicating the currently used one. Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> === ''h5flow'' framework ===<br /> Now we can install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd h5flow<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ pip install -e .<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ cd ..<br /> (ndlar_flow.venv) [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> === ''ndlar_flow'' ===<br /> And finally we can install ''ndlar_flow''<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone git@github.com:DUNE/ndlar_flow.git<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd ndlar_flow<br /> (ndlar_flow.venv) [user@neutrino01 ndlar_flow]$ pip install -e .<br /> &lt;/pre&gt;<br /> Note that the &lt;code&gt;-e&lt;/code&gt; option installs the packages in &quot;editable&quot; mode, meaning any changes you make will take effect without the need to re-run &lt;code&gt;pip install&lt;/code&gt;.<br /> <br /> == How to use == <br /> A good starting point is the [https://github.com/DUNE/ndlar_flow# ''README''] of the git repo, it describes how to run simple workflow such as light event building and also propose some tutorials. If you want to develop new script or update current one, a good practice is to create a new branch in the git project and work there. To edit the scripts traditional editors like ''vim'' are available on the server, but there is also the possibility to open the repository on the local machine. A very interactive solution is to start a jupyter server on the remote neutrino01 server and then open a jupyter notebook from your local machine through an ssh tunnel. A second practical possibility is to ssh to the server through Visual Studio Code (VS Code), which provides a nice coding environment. In both case you also have access to the remote terminal inside the programme. In my opinion the two options are very complementary, VS Code to write code easily and jupyter notebook to use it and play around with it.<br /> <br /> === Visual Studio Code ===<br /> To use this program you will simply have to download VS Code and the ssh extension. Detailed information can be found [https://code.visualstudio.com/docs/remote/ssh here].<br /> <br /> === Jupyter Notebook ===<br /> The Jupyter Notebook option is slightly more demanding but also accessible. First you will have to download jupyter in your virtual environment on the server<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pip install jupyter<br /> &lt;/pre&gt;<br /> Then once the installation success full you can start a jupyter server without openning a browser by running<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ jupyter notebook --no-browser --port=8080<br /> &lt;/pre&gt;<br /> , you can choose the desired port number. Once the server is running you can open a new terminal on your local machine and open an ssh tunnel to the previously chosen port on the remote server<br /> &lt;pre&gt;<br /> user_local ~/$ ssh -L 8080:localhost:8080 user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> Once this is done, you can go back to the first terminal where the jupyter server is running and look for the following line<br /> &lt;pre&gt;<br /> [C 2025-06-18 14:27:48.107 ServerApp] <br /> <br /> To access the server, open this file in a browser:<br /> file:///terabig/user/.local/share/jupyter/runtime/jpserver-664549-open.html<br /> Or copy and paste one of these URLs:<br /> http://localhost:8080/tree?token=&lt;some number and letter&gt;<br /> http://127.0.0.1:8080/tree?token=&lt;some number and letter&gt;<br /> &lt;/pre&gt;<br /> and copy the address of the server, e.g. here &lt;code&gt;http://localhost:8080/tree?token=&lt;some number and letter&gt;&lt;/code&gt; in your favorite browser on your local machine. Note that some browser have difficulties with jupyter notebook, download an other one if your is not compatible. Now you can select a file and start work on it, good luck :).<br /> <br /> <br /> = AFI viewer =<br /> Ask Jan.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=897 2025-06-18T12:35:12Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the ''README'' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed)<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is &lt;!-- &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is too old to install the latest jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> Clone the repository<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.10.4<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> , the star indicating the currently used one. Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> === ''h5flow'' framework ===<br /> Now we can install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd h5flow<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ pip install -e .<br /> (ndlar_flow.venv) [user@neutrino01 h5flow]$ cd ..<br /> (ndlar_flow.venv) [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> === ''ndlar_flow'' ===<br /> And finally we can install ''ndlar_flow''<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ git clone git@github.com:DUNE/ndlar_flow.git<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ cd ndlar_flow<br /> (ndlar_flow.venv) [user@neutrino01 ndlar_flow]$ pip install -e .<br /> &lt;/pre&gt;<br /> Note that the &lt;code&gt;-e&lt;/code&gt; option installs the packages in &quot;editable&quot; mode, meaning any changes you make will take effect without the need to re-run &lt;code&gt;pip install&lt;/code&gt;.<br /> <br /> == How to use == <br /> A good starting point is the [https://github.com/DUNE/ndlar_flow# ''README''] of the git repo, it describes how to run simple workflow such as light event building and also propose some tutorials. If you want to develop new script or update current one, a good practice is to create a new branch in the git project and work there. To edit the scripts traditional editors like ''vim'' are available on the server, but there is also the possibility to open the repository on the local machine. A very interactive solution is to start a jupyter server on the remote neutrino01 server and then open a jupyter notebook from your local machine through an ssh tunnel. A second practical possibility is to ssh to the server through Visual Studio Code (VS Code), which provides a nice coding environment. In both case you also have access to the remote terminal inside the programme. In my opinion the two options are very complementary, VS Code to write code easily and jupyter notebook to use it and play around with it.<br /> <br /> === Visual Studio Code ===<br /> To use this program you will simply have to download VS Code and the ssh extension. Detailed information can be found [https://code.visualstudio.com/docs/remote/ssh here].<br /> <br /> === Jupyter Notebook ===<br /> The Jupyter Notebook option is slightly more demanding but also accessible. First you will have to download jupyter in your virtual environment on the server<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pip install jupyter<br /> &lt;/pre&gt;<br /> Then once the installation success full you can start a jupyter server without openning a browser by running<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ jupyter notebook --no-browser --port=8080<br /> &lt;/pre&gt;<br /> , you can choose the desired port number. Once the server is running you can open a new terminal on your local machine and open an ssh tunnel to the previously chosen port on the remote server<br /> &lt;pre&gt;<br /> user_local ~/$ ssh -L 8080:localhost:8080 user@neutrino01.lhep.unibe.ch<br /> &lt;/pre&gt;<br /> Once this is done, you can go back to the first terminal where the jupyter server is running and look for the following line<br /> &lt;pre&gt;<br /> [C 2025-06-18 14:27:48.107 ServerApp] <br /> <br /> To access the server, open this file in a browser:<br /> file:///terabig/user/.local/share/jupyter/runtime/jpserver-664549-open.html<br /> Or copy and paste one of these URLs:<br /> http://localhost:8080/tree?token=&lt;some number and letter&gt;<br /> http://127.0.0.1:8080/tree?token=&lt;some number and letter&gt;<br /> &lt;/pre&gt;<br /> and copy the address of the server, e.g. here &lt;code&gt;http://localhost:8080/tree?token=&lt;some number and letter&gt;&lt;/code&gt; in your favorite browser on your local machine. Note that some browser have difficulties with jupyter notebook, download an other one if your is not compatible. Now you can select a file and start work on it, good luck :).<br /> <br /> <br /> = AFI viewer =<br /> Ask Jan.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=896 2025-06-18T10:04:41Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the ''README'' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed)<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is &lt;!-- &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is too old to install the latest jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> Clone the repository<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.10.4<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> === ''h5flow'' framework ===<br /> Now we can install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> [user@neutrino01 ~]$ cd h5flow<br /> [user@neutrino01 h5flow]$ pip install -e .<br /> [user@neutrino01 h5flow]$ cd ..<br /> [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> === ''ndlar_flow'' ===<br /> And finally we can install ''ndlar_flow''<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ git clone git@github.com:DUNE/ndlar_flow.git<br /> [user@neutrino01 ~]$ cd ndlar_flow<br /> [user@neutrino01 ndlar_flow]$ pip install -e .<br /> &lt;/pre&gt;<br /> Note that the &lt;code&gt;-e&lt;/code&gt; option installs the packages in &quot;editable&quot; mode, meaning any changes you make will take effect without the need to re-run &lt;code&gt;pip install&lt;/code&gt;.<br /> <br /> === jupyter notebook ===<br /> <br /> <br /> = AFI viewer =</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=895 2025-06-18T10:01:12Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the 'README' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed)<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is &lt;!-- &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is too old to install the latest jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> Clone the repository<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.10.4<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> (it is also possible to switch only the local version if you replace the global parameter). Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> There is also an automatic installer if preferred, instruction and further documentation can be found in the git repo [https://github.com/pyenv/pyenv?tab=readme-ov-file ''README''].<br /> ==== ''h5flow'' framework ====<br /> Install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> [user@neutrino01 ~]$ cd h5flow<br /> [user@neutrino01 h5flow]$ pip install -e .<br /> [user@neutrino01 h5flow]$ cd ..<br /> [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> <br /> <br /> === pyenv === <br /> <br /> === jupyter notebook ===<br /> <br /> <br /> = AFI viewer =</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=894 2025-06-18T09:57:56Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the 'README' on the [https://github.com/DUNE/ndlar_flow# git repo] contains probably the most up-to-date information. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> == Installation ==<br /> A good practice is to work in a virtual envirnment, ''venv'' will be used in this tutorial. The ''ndlar_flow'' repo is based on the ''h5flow'' framework, therefore it will be installed first and finally ''ndlar_flow'' could be installed. If one wants to work with a jupyter notebook, an additional step would be needed due to the version of python installed on the server.<br /> <br /> === virtual environment ===<br /> Create and activate a virtual environment:<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python -m venv ndlar_flow.venv<br /> [user@neutrino01 ~]$ source ndlar_flow.venv/bin/activate<br /> &lt;/pre&gt;<br /> (Note that the name of the environment can be changed)<br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is &lt;!-- &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [user@neutrino01 ~]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is too old to install the latest jupyter version. A solution is to install ''pyenv'' in your virtual environment.<br /> <br /> === ''pyenv'' [optional] ===<br /> Clone the repository<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ git clone https://github.com/pyenv/pyenv.git ~/.pyenv<br /> &lt;/pre&gt;<br /> Then you will need to set up the environment variables and evaluate the initialisation script<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [user@neutrino01 ~]$ [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> [user@neutrino01 ~]$ eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/pre&gt;<br /> <br /> To avoid to run the initialisation every time the virtual environment is started, you can add it to the ''activate'' script. I would propose to create a setup script, e.g. &lt;code&gt;~/setup_venv.sh&lt;/code&gt; and add<br /> &lt;pre&gt;<br /> #!/bin/bash<br /> echo &quot;Running setup script...&quot;<br /> <br /> # Setup pyenv<br /> export PYENV_ROOT=&quot;$HOME/.pyenv&quot;<br /> [[ -d $PYENV_ROOT/bin ]] &amp;&amp; export PATH=&quot;$PYENV_ROOT/bin:$PATH&quot;<br /> eval &quot;$(pyenv init - bash)&quot;<br /> &lt;/code&gt;<br /> Then you can add the following commands to the &lt;code&gt;ndlar_flow.venv/bin/activate&lt;/code&gt; script:<br /> &lt;pre&gt;<br /> # Run a setup script if it exist<br /> SETUP_SCRIPT=&quot;~/setup_venv.sh&quot;<br /> if [ -f &quot;$SETUP_SCRIPT&quot; ]; then<br /> source &quot;$SETUP_SCRIPT&quot;<br /> fi<br /> &lt;/pre&gt;<br /> Then every time you activate the virtual environment the setup script will be run and pyenv configured.<br /> <br /> Finally to install a new python version, e.g. 3.11.9, activate your environment and run the following command:<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv install 3.10.4<br /> &lt;/pre&gt;<br /> To list the installed version run<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv versions<br /> &lt;/pre&gt;<br /> Then you can switch to the desired version (e.g. 3.11.9) with<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ pyenv global 3.11.9<br /> &lt;/pre&gt;<br /> Now if we check again which python version is used we get<br /> &lt;pre&gt;<br /> (ndlar_flow.venv) [user@neutrino01 ~]$ python --version<br /> Python 3.11.9<br /> &lt;/pre&gt;<br /> ==== ''h5flow'' framework ====<br /> Install the ''h5flow'' framework<br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ git clone https://github.com/larpix/h5flow<br /> [user@neutrino01 ~]$ cd h5flow<br /> [user@neutrino01 h5flow]$ pip install -e .<br /> [user@neutrino01 h5flow]$ cd ..<br /> [user@neutrino01 ~]$<br /> &lt;/pre&gt;<br /> <br /> <br /> <br /> === pyenv === <br /> <br /> === jupyter notebook ===<br /> <br /> <br /> = AFI viewer =</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=893 2025-06-18T08:44:50Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' the 'README' on the [https://github.com/DUNE/ndlar_flow# git repo] contain probably the most up-to-date. This page is based on the following [https://github.com/DUNE/ndlar_flow/commit/d16b9a2ac81366fd841f053b6ba9275ad748a05a commit]. <br /> <br /> === Installation ===<br /> <br /> To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is &lt;!-- &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [nsallin@neutrino01 ndlar_flow]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; --&gt; <br /> &lt;pre&gt;<br /> [user@neutrino01 ~]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> which is too old to install the latest jupyter version<br /> <br /> === pyenv === <br /> <br /> === jupyter notebook ===<br /> <br /> <br /> = AFI viewer =</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=892 2025-06-18T08:38:52Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' you will be have to follow the 'README' of the [https://github.com/DUNE/ndlar_flow# |git repo]. To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is &lt;!-- &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [nsallin@neutrino01 ndlar_flow]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt; --&gt; <br /> &lt;pre&gt;<br /> [nsallin@neutrino01 ndlar_flow]$ python --version<br /> Python 3.9.21<br /> &lt;/pre&gt;<br /> <br /> === Installation ===<br /> <br /> === pyenv === <br /> <br /> === jupyter notebook ===<br /> <br /> <br /> = AFI viewer =</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=891 2025-06-18T08:32:57Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' you will be have to follow the 'README' of the [https://github.com/DUNE/ndlar_flow# |git repo]. To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is &lt;syntaxhighlight lang=&quot;cpp&quot;&gt; [nsallin@neutrino01 ndlar_flow]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt;<br /> === Installation ===<br /> <br /> === pyenv === <br /> <br /> === jupyter notebook ===<br /> <br /> <br /> = AFI viewer =</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=890 2025-06-18T08:32:40Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' you will be have to follow the 'README' of the [https://github.com/DUNE/ndlar_flow# |git repo]. To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is &lt;syntaxhighlight lang=&quot;bash&quot;&gt; [nsallin@neutrino01 ndlar_flow]$ python --version<br /> Python 3.9.21 &lt;/syntaxhighlight&gt;<br /> === Installation ===<br /> <br /> === pyenv === <br /> <br /> === jupyter notebook ===<br /> <br /> <br /> = AFI viewer =</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=889 2025-06-18T08:28:53Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> To install ''ndlar_flow'' you will be have to follow the 'README' of the [https://github.com/DUNE/ndlar_flow# |git repo]. To be able to start a jupyter notebook later, an additional step is needer: On ''neutrino01'' the default python version is &lt;code&gt; [nsallin@neutrino01 ndlar_flow]$ python --version<br /> Python 3.9.21 &lt;/code&gt;<br /> === Installation ===<br /> <br /> === pyenv === <br /> <br /> === jupyter notebook ===<br /> <br /> <br /> = AFI viewer =</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=887 2025-06-11T15:54:02Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [[Debug]] page.<br /> <br /> = ndlar_flow =<br /> <br /> === Installation ===<br /> <br /> === pyenv === <br /> <br /> === jupyter notebook ===<br /> <br /> <br /> = AFI viewer =</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=886 2025-06-11T15:53:44Z

<p>Nsallin: </p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server. Some information concerning errors can be found on the [Debug] page.<br /> <br /> = ndlar_flow =<br /> <br /> === Installation ===<br /> <br /> === pyenv === <br /> <br /> === jupyter notebook ===<br /> <br /> <br /> = AFI viewer =</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Setup_to_process_FSD_data_on_neutrino01&diff=885 2025-06-11T15:49:41Z

<p>Nsallin: Created page with &quot;After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the &#039;&#039;hdf5&#039;&#039; format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server = ndlar_flow = === Installation === === pyenv === === jupyter notebook === = AFI viewer =&quot;</p> <hr /> <div>After the collection of data a few steps are needed to easily use them. One can flow the data to convert them in the ''hdf5'' format, easy to handle. Otherwise one can also directly look at the raw data using the afi viewer. We will see how to set this up on the &lt;code&gt;neutrino01&lt;/code&gt; server<br /> <br /> = ndlar_flow =<br /> <br /> === Installation ===<br /> <br /> === pyenv === <br /> <br /> === jupyter notebook ===<br /> <br /> <br /> = AFI viewer =</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=884 2025-06-11T15:41:21Z

<p>Nsallin: </p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == ND-LAr ==<br /> [[https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]] &lt;br&gt;<br /> [[https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]] &lt;br&gt;<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository. A short introduction to 2x2 and FSD data can be found on the [[Setup to process FSD data on neutrino01]] page.<br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> <br /> <br /> == 2x2 ==<br /> nothing yet<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Get_Started&diff=883 2025-06-11T15:30:44Z

<p>Nsallin: add get started nersc</p> <hr /> <div>Welcome in the neutrino group, on this page you will find information about how to get access to the resources necessary to work and some useful tips to get started. The first requirement is to get a ''UNIBE email account'', please ask the LHEP secretary if you don't have one yet.<br /> <br /> = Slack =<br /> Slack is a very practical tool to exchange with other collaborators. We have a dedicated workspace for LHEP people and there is a DUNE collaboration one.<br /> <br /> === LHEP Slack ===<br /> To obtain an access to the LHEP Slack workspace, simply ask someone already in the workplace to add you. How to add a person: Under ''home'' you can click on the title of the workspace, which open a scroll-down menu. Then click on ''invite people to join...'' and provide the email address of the person you want to add.<br /> <br /> === DUNE Slack ===<br /> To get added to the DUNE workspace, write to ''dune-slack@fnal.gov'' to request access.<br /> <br /> = FNAL account =<br /> A Fermilab account is needed to get access to some DUNE ressources and to the Fermilab site. To request the account please follow these [https://get-connected.fnal.gov/users-affiliates-access/ instructions]. To get the on-site access visit the [[Access to Fermilab]] page<br /> <br /> = NERSC =<br /> The ''National Energy Research Scientific Computing Center'' (NERSC) is a US computing facility with dedicated DUNE resources. Most of the data are accessible from there and the infrastructure allows to run demanding jobs. The [https://docs.nersc.gov/getting-started/ get started] page will give you addidtional information (including how ot create an account). The associated Jupyter hub can be accessed under [https://jupyter.nersc.gov/hub/login?next=%2Fhub%2Fhome Jupyter@NERSC]<br /> <br /> = DUNE Github =<br /> Most to the code scripts are stored on the DUNE Github under the ''ndlar-flow'' project. Information to join it can be found one the [[Ndlar-flow]] page.<br /> <br /> = LHEP =<br /> Some ressources are also available directly from LHEP.<br /> <br /> === Servers ===<br /> 2 Servers are available, neutrino01 and neutrino02 under the address &lt;code&gt;neutrino0X.lhep.unibe.ch&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === Google Drive ===<br /> A lot of documents are available on our common google drive under the username &lt;code&gt;argoncube@gmail.com&lt;/code&gt;. Ask Saba to get access.<br /> <br /> === ELOG ===<br /> The LHEP [https://elog.lhep.unibe.ch ELOG] is used to store diverse information. Ask somebody from the LHEP IT to be added.<br /> <br /> === Github ===<br /> An LHEP neutrino Github is also available [https://github.com/LHEP-neutrino here]. Ask one of the owner to be added.<br /> <br /> = CERN account =<br /> The CERN account allows you to access computing ressources and on-site access. To request it, ask Michele to fill the relevant form and follow the procedure detailed in the email resulting from the access request.</div>

Nsallin https://wiki.lhep.unibe.ch/index.php?title=Neutrino_group&diff=882 2025-05-26T11:35:23Z

<p>Nsallin: typo</p> <hr /> <div><br /> Welcome to the wiki page of the neutrino group. Here you can hopefully found information about how to use different systems or any other information. To get started, please visit this [[Get Started]] page.<br /> <br /> If you don't find something here and you would judge it useful, please add it! The [https://en.wikipedia.org/wiki/Help:Wikitext Help:Wikitext] page is a good summary of the grammatical rules used to edit wiki pages<br /> <br /> == ND-LAr ==<br /> [[https://indico.fnal.gov/event/48671/attachments/142649/182073/DUNE_ND_PDR___Liquid_Argon_TPC.pdf Link to PDR document]] &lt;br&gt;<br /> [[https://www.overleaf.com/project/677d95a83a5ff854c98e3bff Link to TDR document overleaf]] &lt;br&gt;<br /> <br /> === ndlar_flow ===<br /> Most of the scripts and codes pieces related to the treatment of NDLAr data can be found in the [[Ndlar-flow|ndlar-flow]] GitHub repository<br /> <br /> == FSD ==<br /> === [[cryo-system |Cryo System]] ===<br /> LAr Tank&lt;br&gt;<br /> PLC and Cryo control&lt;br&gt;<br /> Filter regeneration stand&lt;br&gt;<br /> Vacuum system&lt;br&gt;<br /> <br /> <br /> === Servers and Local Network Management ===<br /> nothing yet<br /> <br /> === Database and Monitoring Service ===<br /> nothing yet<br /> <br /> === HV system ===<br /> nothing yet<br /> <br /> === Light Readout System ===<br /> LRS Cold &lt;br&gt;<br /> LRS Warm &lt;br&gt;<br /> Timing scheme and synchronization&lt;br&gt;<br /> DAQ scheme and controls&lt;br&gt;<br /> <br /> === DAQ and Run Control ===<br /> nothing yet<br /> <br /> === Shifter instructions ===<br /> <br /> === FSD Run1 Data and Analysis Guide ===<br /> <br /> <br /> == 2x2 ==<br /> nothing yet<br /> <br /> == Debug ==<br /> Some issues encountered during the procedures described on the page can be found on the [[Debug]] page. An other good source of information to resolve problems is the [https://elog.lhep.unibe.ch/ LHEP ELOG].<br /> <br /> == Useful links ==<br /> ==== UNIBE ====<br /> * [https://www.lhep.unibe.ch/index_eng.html LHEP]<br /> * [https://elog.lhep.unibe.ch/ LHEP ELOG]<br /> * [https://github.com/LHEP-neutrino LHEP Github]<br /> * [https://login.microsoftonline.com/ UNIBE email]<br /> * [https://www.ksl.unibe.ch/KSL/home?1 KSL]<br /> * [https://eforms.unibe.ch/?cmd=logout&amp;redirect=false Eforms]<br /> * [https://www.selfservice.studis.unibe.ch/login.html Selfservice UNIBE]<br /> * [https://www.unibe.ch/universitaet/campus__und__infrastruktur/hausdienst_und_hauskommissionen/hausdienstgruppen/hausdienstgruppe_exakte_wissenschaften/index_ger.html Hausdienst ExWi]<br /> <br /> ==== DUNE ====<br /> * [https://github.com/DUNE/ndlar_flow/ NDLAr flow GitHub]<br /> * [https://jupyter.nersc.gov/hub/login NERSC Jupyter]<br /> * [https://indico.fnal.gov/ Indico FNAL]<br /> * [https://atwork.dunescience.org/ DUNE website]<br /> * [https://atwork.dunescience.org/tools/ DUNE tools]<br /> * [[Access to Fermilab]]<br /> * [https://dune.github.io/computing-basics/setup.html Connect to DUNE FNAL machines]<br /> * [https://fermi.servicenowservices.com/kb_view.do?sysparm_article=KB0011388 Change your SERVICES domain account password]<br /> <br /> === File ===<br /> [[File:TRAVELING REIMBURSEMENT.pdf|Form to request a reimbursement]]</div>

Nsallin