Difference between revisions of "GlueX Offline Software"

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'''News:'''
 
'''News:'''
−
* July 26, 2017: [[GlueX_Offline_Meeting,_July_26,_2017#Minutes|Minutes of the July 26 Offline Software Meeting]] are available.
+
* July 19, 2022: [[GlueX_Software_Meeting,_July_18,_2022#Minutes|Minutes of the July 18th Software Meeting]] are available
−
* July 18, 2017: [https://mailman.jlab.org/pipermail/halld-offline/2017-July/002877.html hdpm 0.7.2]
+
* July 12, 2022: [https://halldweb.jlab.org/halld_versions/version_5.8.0.xml New version set: 5.8.0].
−
* July 18, 2017: [https://mailman.jlab.org/pipermail/halld-offline/2017-July/002876.html New sim-recon release: version 2.16.0 and version_2.13.2.xml]  
+
* June 7, 2022: [[GlueX_Software_Meeting,_June_6,_2022#Minutes|Minutes of the June 6th Software Meeting]] are available
−
* July 14, 2017: [https://mailman.jlab.org/pipermail/halld-offline/2017-July/002869.html Added capabilities in osg run scripts]
+
* May 23, 2022" [https://halldweb.jlab.org/wiki/index.php/GlueX_Tutorial_2022 GlueX Software and Analysis Tutorial 2022]
−
* July 13, 2017: [[GlueX_Offline_Meeting,_July_12,_2017#Minutes|Minutes of the July 12 Offline Software Meeting]] are available.
+
* May 19, 2022: [https://mailman.jlab.org/pipermail/halld-offline/2022-May/008816.html New version set: 5.7.1].
 
* [[Offline Software News Archive|Previous news items...]]
 
* [[Offline Software News Archive|Previous news items...]]
 
|
 
|
 
'''Quick Links:'''
 
'''Quick Links:'''
−
* [https://github.com/orgs/JeffersonLab/teams/gluex/repositories Repositories on GitHub]
+
* [https://scicomptest.jlab.org/scicomp/tapeFile Listing of files missing from the tape library]
 
* [[GlueX Offline FAQ|Frequently Asked Questions]]
 
* [[GlueX Offline FAQ|Frequently Asked Questions]]
−
* [https://mailman.jlab.org/pipermail/halld-offline/ halld-offline@jlab.org Email List Archive]
+
* [[Offline HOWTO List|HOWTO List]]
−
* [https://groups.google.com/forum/#!forum/gluex-software GlueX Software Help Google Group]
+
* [[GlueX_Offline_FAQ#Where_do_I_find_version_set_files.3F|Version Set Files]]
 +
* [https://github.com/orgs/JeffersonLab/teams/gluex/repositories Repositories on GitHub]
 
* [[GlueX Offline Software Meetings]]
 
* [[GlueX Offline Software Meetings]]
 
|}
 
|}
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==General Information==
 
==General Information==
  
−
[https://halldweb.jlab.org/docs/gluex_build_web/ A Version Management System for GlueX] describes a standard directory structure for GlueX software, how to create complete or partial builds, and how to specify versions of individual packages, both for building and for use. It is also available as [https://halldweb.jlab.org/doc-public/DocDB/ShowDocument?docid=2793 GlueX Note 2793].
+
[https://halldweb.jlab.org/docs/build_scripts_web/ Build Scripts: A Version Management System for GlueX] describes a standard directory structure for GlueX software, how to create complete or partial builds, and how to specify versions of individual packages, both for building and for use. It is also available as [https://halldweb.jlab.org/doc-public/DocDB/ShowDocument?docid=2793 GlueX Note 2793].
  
 
See below for other helpful links.
 
See below for other helpful links.
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===Shell Environment Set-Up===
 
===Shell Environment Set-Up===
  
−
* [[Setting Up the GlueX Environment]]
+
* [https://halldweb.jlab.org/docs/build_scripts_web/node6.html#SECTION00062400000000000000 Simple Environment Set Up]
  
 
===Building GlueX Software===
 
===Building GlueX Software===
  
−
* [https://halldweb.jlab.org/docs/gluex_build_web/node34.html Scripts for Installing GlueX Software]: Do a complete build of all standard components of GlueX software or add new versions to an existing build tree.
+
* [[Building_Private_Versions_of_GlueX_Software:_my_sim-recon.sh|Building private versions of GlueX software at JLab]]
 +
* [https://halldweb.jlab.org/docs/build_scripts_web/node10.html Scripts for Installing GlueX Software]: Do a complete build of all standard components of GlueX software or add new versions to an existing build tree.
 
* [[Hall D Package Manager|hdpm - Hall D Package Manager]]: A package manager for Hall-D software, which provides an alternative method for installing GlueX software.
 
* [[Hall D Package Manager|hdpm - Hall D Package Manager]]: A package manager for Hall-D software, which provides an alternative method for installing GlueX software.
 
* [[Legacy Build Instructions]]: Guides to various aspects of the build process. Up-to-date-ness may vary.
 
* [[Legacy Build Instructions]]: Guides to various aspects of the build process. Up-to-date-ness may vary.
 +
* [[GlueX_Offline_FAQ#Where_do_I_find_version_set_files.3F|Version Sets Files]]
 +
 +
=== GlueX and Containers ===
 +
 +
* [[GlueX Software on Oasis]]
 +
* [https://github.com/JeffersonLab/hd_singularity Package for Building Singularity Containers]
 +
* [[GlueX Containers Meetings]]
 +
* [[HOWTO use the GlueX Singularity Container]]
  
 
==Software Documentation==
 
==Software Documentation==
 +
 +
Packages used in the GlueX software stack with links to package-specific documentation.
  
 
===GlueX Software===
 
===GlueX Software===
−
Documentation for software systems closely related to GlueX.
+
 
 +
Documentation for software packages specific to GlueX or to JLab.
 +
* A brief overview of the GlueX-specific software can be found [[ Software | here ]]
 +
* Best practices in writing code for the HallD/GlueX software environment check out this link of [[Coding Conventions| '''''HallD/GlueX Coding Conventions''''']]
 +
* A convenient way to enhance the impact of comments inside the code is to use [https://halldweb.jlab.org/talks/2021/usedoxy.pdf '''''Doxygen''''']. The hooks and infrastructures are already implemented for the packages ''halld_recon'' and ''halld_sim''.
 +
* [[Documentation Initiative]]
  
 
====Software Packages====
 
====Software Packages====
  
−
* sim-recon
+
* [https://github.com/mashephe/AmpTools AmpTools]: Amplitude analysis package (aka partial wave analysis)
−
** [http://www.jlab.org/Hall-D/software/HDSoftware_Documentation/ Doxygen Documentation]: Descriptions of sim-recon C++ classes and their relationships.
+
* [[Calibration Database|CCDB]]: Calibration Database
−
** [[Sim-Recon Tagged Releases]]
+
** [[Policy on CCDB Variations for Reconstructing Simulated Data]]
−
** [[GlueX_Analysis_Software | Analysis Software in sim-recon]]
+
* [https://github.com/sdobbs/HDEventStore EventStore]: a package for managing and deploying data files and event lists
−
** [[SCons Build System]] (SBMS)
+
* [https://coda.jlab.org/drupal/content/event-io-evio EVIO]: The [https://coda.jlab.org/drupal/ CODA] event format.
−
** [[How HDGeant defines time-zero for physics events]]
+
* [https://github.com/jeffersonlab/halld_recon halld_recon]
−
* [https://www.jlab.org/JANA/ JANA]
+
* [https://github.com/jeffersonlab/halld_sim halld_sim]
 +
* [[HDDM Programmer's Interface|HDDM]]: The Hall D Data Model, a compact xml-based format for event-based data.
 
* HDDS: Detector geometry specification
 
* HDDS: Detector geometry specification
 
** [https://halldsvn.jlab.org/repos/trunk/hdds/HDDS-1_1.xsd HDDS Schema]: Includes description of the HDDS mark-up language.
 
** [https://halldsvn.jlab.org/repos/trunk/hdds/HDDS-1_1.xsd HDDS Schema]: Includes description of the HDDS mark-up language.
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** [https://halldweb.jlab.org/doc-public/DocDB/ShowDocument?docid=732 Detector Models for GlueX Monte Carlo Simulation: the CD2 Baseline], January 2007
 
** [https://halldweb.jlab.org/doc-public/DocDB/ShowDocument?docid=732 Detector Models for GlueX Monte Carlo Simulation: the CD2 Baseline], January 2007
 
** [[HDDS Tagged Releases]]
 
** [[HDDS Tagged Releases]]
−
* [[HDDM Programmer's Interface|HDDM]]: The Hall D Data Model, a compact xml-based format for event-based data.
 
−
* [https://coda.jlab.org/drupal/content/event-io-evio EVIO]: The [https://coda.jlab.org/drupal/ CODA] event format.
 
−
* [[Calibration Database|CCDB]]: Calibration Database
 
−
** [[Policy on CCDB Variations for Reconstructing Simulated Data]]
 
−
* [https://github.com/JeffersonLab/rcdb/wiki RCDB]: Run Conditions Database
 
−
* [http://amptools.sourceforge.net/index.php/Main_Page AmpTools]: Amplitude analysis package (aka partial wave analysis)
 
−
* [https://github.com/sdobbs/HDEventStore EventStore]: a package for managing and deploying data files and event lists
 
 
* [[HOWTO install and run HDGeant4|HDGeant4]]: Geant4-based simulation of the GlueX Detector and Hall D beamline
 
* [[HOWTO install and run HDGeant4|HDGeant4]]: Geant4-based simulation of the GlueX Detector and Hall D beamline
 +
* [https://www.jlab.org/JANA/ JANA]
 +
* [https://jeffersonlab.github.io/JANA2 JANA2]
 +
** [[Transition to JANA2]]
 +
* MCwrapper
 +
**[https://halldweb.jlab.org/gluex_sim/Dashboard.html '''Active Sample Dashboard''']
 +
**[https://halldweb.jlab.org/gluex_sim/SubmitSim.html '''MC Submission Form''']
 +
* [https://pypwa.jlab.org/index.html PyPWA:] [https://pypwa.readthedocs.io/ Python-based Partial Wave Analysis Toolkit]
 +
* [https://github.com/JeffersonLab/rcdb/wiki RCDB]: Run Conditions Database
 +
** [https://halldweb.jlab.org/rcdb/ Web Interface]
 +
** [[GlueX Implementation of the RCDB]]
 +
* sim-recon (deprecated, July 2018)
 +
** [http://www.jlab.org/Hall-D/software/HDSoftware_Documentation/ Doxygen Documentation]: Descriptions of sim-recon C++ classes and their relationships.
 +
** [[Sim-Recon Tagged Releases]]
 +
** [[GlueX_Analysis_Software | Analysis Software in sim-recon]]
 +
** [[SCons Build System]] (SBMS)
  
 
====Special Topics====
 
====Special Topics====
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* [[Offline HOWTO List]]: Guides to performing various specific tasks.
 
* [[Offline HOWTO List]]: Guides to performing various specific tasks.
 
* [[Beam Simulations]]: Geant simulations of the Hall D Tagger Hall
 
* [[Beam Simulations]]: Geant simulations of the Hall D Tagger Hall
 +
* [[Magnetic Field Maps for Solenoid]]
 
* [[Experimental_Sensitivity_to_Solenoidal_Field|Sensitivity to Magnetic Field Strength]]
 
* [[Experimental_Sensitivity_to_Solenoidal_Field|Sensitivity to Magnetic Field Strength]]
 +
* [[How HDGeant defines time-zero for physics events]]
 +
* [[Guide to Monte Carlo event timing and detached vertices in HDGeant/4]]
 +
* [[Guide to roll-your-own python hddm transforms]]
 +
* [[Geometry]]
 +
* [[Reconstruction Software]]
 +
* [[Kinematic Fitting]]
 +
# [[Splitoff_Information | Material on Splitoffs]]
  
 
===Documentation for External Software Packages===
 
===Documentation for External Software Packages===
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|
 
|
 
* [http://www.stack.nl/~dimitri/doxygen/ Doxygen]
 
* [http://www.stack.nl/~dimitri/doxygen/ Doxygen]
 +
* [https://halldweb.jlab.org/manuals/geant.pdf GEANT 3 (manual)]
 
* [http://geant4.cern.ch/ GEANT4]
 
* [http://geant4.cern.ch/ GEANT4]
 
* [https://git-scm.com/ Git]
 
* [https://git-scm.com/ Git]
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===JLab===
 
===JLab===
 +
* [https://halldweb.jlab.org/disk_management/halld_status.html Hall D Offline System Status Plots] [[File:User jobs 0 thumb.png|link=https://halldweb.jlab.org/disk_management/halld_status.html]]
 +
* [[Computing Services and Servers|Hall D and JLab Servers]]: Web servers, database servers, etc.
 
* [https://cc.jlab.org/ Computer Center]
 
* [https://cc.jlab.org/ Computer Center]
−
* [https://scicomp.jlab.org/scicomp/ Scientific Computing]
+
* [https://scicomptest.jlab.org/scicomp/ Scientific Computing]
 
** [https://scicomp.jlab.org/scicomp/#/auger/jobs Farm Job Status] Auger job status from SciComp
 
** [https://scicomp.jlab.org/scicomp/#/auger/jobs Farm Job Status] Auger job status from SciComp
 
*** [https://halldweb.jlab.org/cgi-bin/jproj_status.pl jproj Job Status] Status of jobs using the jproj system
 
*** [https://halldweb.jlab.org/cgi-bin/jproj_status.pl jproj Job Status] Status of jobs using the jproj system
Line 119: Line 156:
 
*** [https://halldweb.jlab.org/disk_management/group_report.html /group/halld leader board]
 
*** [https://halldweb.jlab.org/disk_management/group_report.html /group/halld leader board]
 
** [https://scicomp.jlab.org/scicomp/#/disk/cache-family Cache]
 
** [https://scicomp.jlab.org/scicomp/#/disk/cache-family Cache]
−
*** [https://halldweb.jlab.org/disk_management/cache_report.html /cache/halld leader board]
+
*** [https://halldweb.jlab.org/disk_management/cache_oldest.html oldest files under /cache/halld]
 
** [https://scicomp.jlab.org/scicomp/#/disk/volatile Volatile]
 
** [https://scicomp.jlab.org/scicomp/#/disk/volatile Volatile]
−
*** [https://halldweb.jlab.org/disk_management/volatile_report.html /volatile/halld leader board]
+
*** [https://halldweb.jlab.org/disk_management/volatile_oldest.html oldest files under /volatile/halld]
 
** [https://scicomp.jlab.org/scicomp/#/disk/work Work]
 
** [https://scicomp.jlab.org/scicomp/#/disk/work Work]
 
*** [https://halldweb.jlab.org/disk_management/work_report.html /work/halld leader board]
 
*** [https://halldweb.jlab.org/disk_management/work_report.html /work/halld leader board]
−
*** [https://halldweb.jlab.org/disk_management/work2_report.html /work/halld2 leader board]
 
 
* [[GlueX-related shared accounts on the JLab CUE]]
 
* [[GlueX-related shared accounts on the JLab CUE]]
 
* [[Hall D MySQL/MariaDB Servers and Replication Relationship]]: a list of database servers
 
* [[Hall D MySQL/MariaDB Servers and Replication Relationship]]: a list of database servers
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* [http://www.opensciencegrid.org/ Open Science Grid]
 
* [http://www.opensciencegrid.org/ Open Science Grid]
 +
** [https://mailman.jlab.org/pipermail/halld-offline/2017-June/002827.html Using the Grid with Containers]
 
** [[Using the Grid]]
 
** [[Using the Grid]]
 +
** [[Updating Oasis for the GlueX VO]]
 
** [https://halldweb.jlab.org/talks/2011-2Q/gridmake-6-2011.ppt Gridmake]
 
** [https://halldweb.jlab.org/talks/2011-2Q/gridmake-6-2011.ppt Gridmake]
  
−
===Other Computing Resources===
+
===Off-Site Computing Resources===
  
−
* [[Computer Farms]]: Clusters at GlueX-collaborating institutions.
+
* [[Off-site Computing Resources]]: Status of applications, current and past allocations
  
 
==Software Management==
 
==Software Management==
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===Source Code Management===
 
===Source Code Management===
  
 +
* [https://git-scm.com/ Git]
 +
** [https://github.com/orgs/JeffersonLab/teams/gluex/repositories GlueX Git Repositories]
 +
** [[Instructions for Working with GlueX Git Repositories]]. Workflow description.
 +
** [https://mailman.jlab.org/pipermail/halld-offline/2015-July/002086.html Instructions for joining the GlueX team on GitHub]
 +
** [[Git Help Resources]], July 14
 +
** [[Guide to Using Git]]. General usage tips.
 +
** [[GlueX_Offline_FAQ#Git|Git questions and answers in the Offline FAQ]]
 +
** [[Splitting sim-recon]]
 +
** [[Conversion from Subversion to Git]] (Summer 2015)
 
* [https://subversion.apache.org/ Subversion]
 
* [https://subversion.apache.org/ Subversion]
 
** [http://halldweb.jlab.org/websvn/prod/ Browse the Hall D Subversion Repository]
 
** [http://halldweb.jlab.org/websvn/prod/ Browse the Hall D Subversion Repository]
 
*** [http://clasweb.jlab.org/websvn/prod/ Legacy version]
 
*** [http://clasweb.jlab.org/websvn/prod/ Legacy version]
−
* [https://git-scm.com/ Git]
 
−
** [[Git Repositories|GlueX Git Repositories]]
 
−
** [[Guide to Using Git]]
 
−
** [[Conversion from Subversion to Git]] (Summer 2015)
 
  
 
===Testing and Debugging===
 
===Testing and Debugging===
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* [https://data.jlab.org/drupal/?q=system/files/Offline%20Plan%20FY10.pdf JLab Offline Computing Plan, FY2010]
 
* [https://data.jlab.org/drupal/?q=system/files/Offline%20Plan%20FY10.pdf JLab Offline Computing Plan, FY2010]
 
* [[Role of the Software Coordinator]]
 
* [[Role of the Software Coordinator]]
 +
 +
=== Containers ===
 +
 +
* [[GlueX and Containers]]: an overview of the use of containers in GlueX
  
 
==Meetings and Reviews==
 
==Meetings and Reviews==
  
 
* [[GlueX Offline Software Meetings]]: Agendas and minutes
 
* [[GlueX Offline Software Meetings]]: Agendas and minutes
−
* [[Software Review 3]] JLab, February 10-11, 2015
+
* [[HDGeant4 Meetings]]
−
* [[2013 Software Review|Software Review]] (JLab November 25-26, 2013)
+
* [[GlueX Containers Meetings]]
−
* [[2012 Software Review Follow-up| Follow-up to the Software Review]]
+
* [[Software and Computing Reviews]]
−
* [[2012 Software Review|Software Review]] (JLab June 2012)
+
* [[Geometries for 2008 DC Review]]
  
 
==Communication and Help==
 
==Communication and Help==
  
−
* [https://groups.google.com/forum/#!forum/gluex-software Google Group for GlueX Software]
 
−
**[[GlueX-Related Google Groups|Help on GlueX-related Google Groups]]
 
−
* [https://mailman.jlab.org/pipermail/halld-offline/2016-April/002297.html GlueX Software Help Email List]: Ask a question!
 
 
* Offline Software Email List: announcements and discussion
 
* Offline Software Email List: announcements and discussion
 
** [mailto:halld-offline@jlab.org Send email to the list]
 
** [mailto:halld-offline@jlab.org Send email to the list]
Line 186: Line 230:
 
** [https://www.google.com/cse/publicurl?cx=001547825138043056762:dydinmymrvu Google search of archive]
 
** [https://www.google.com/cse/publicurl?cx=001547825138043056762:dydinmymrvu Google search of archive]
 
** [https://mailman.jlab.org/mailman/listinfo/halld-offline Information page] (subscribe, unsubscribe, list members, etc.)
 
** [https://mailman.jlab.org/mailman/listinfo/halld-offline Information page] (subscribe, unsubscribe, list members, etc.)
 +
* [https://groups.google.com/forum/#!forum/gluex-software Google Group for GlueX Software]
 +
**[[GlueX-Related Google Groups|Help on GlueX-related Google Groups]]
 +
** [https://mailman.jlab.org/pipermail/halld-offline/2016-April/002297.html Original announcement]
 +
* [https://slack.com/ Slack]
 +
** Chat application using the workspace '''jlab12gev'''
 +
** Click [https://jlab12gev.slack.com/signup here] to join. You must use your JLab email address.
 
* [[Email Lists#Simple Email Lists|Simple Email Lists]]: get notifications from automated tests
 
* [[Email Lists#Simple Email Lists|Simple Email Lists]]: get notifications from automated tests
 
* [[GlueX_Communications|Communication Instructions]]: Guides to communication systems used by GlueX
 
* [[GlueX_Communications|Communication Instructions]]: Guides to communication systems used by GlueX
Line 201: Line 251:
 
* [[Running jobs on the grid]]
 
* [[Running jobs on the grid]]
 
* [[Calibration Constants, Tagged Versions]]
 
* [[Calibration Constants, Tagged Versions]]
−
 
+
* [[Action Items Archive (May 4, 2010 and before)]]
−
=Uncategorized Links=
+
* [http://www.jlab.org/Hall-D/offline/Software_tasks.php Software Task List]
−
 
+
* [[Tracking resolution estimator (REZEST)]]
−
# [[Offline Software Topics]]
+
* [[ded]]
−
## [https://halldweb.jlab.org/manuals/geant.pdf GEANT 3 manual]
+
−
## [[osrelease.pl script]]
+
−
##* Legacy page: [[Action Items From Hall-D Software Meetings]]
+
−
## [http://www.jlab.org/Hall-D/offline/Software_tasks.php Software Task List]
+
−
## [[JANA/DANA]]
+
−
## [[Simulation Software]]
+
−
## [[Geometry]]
+
−
## [[Magnetic Field Maps for Solenoid]]
+
−
## [https://halldweb.jlab.org/doc-public/DocDB/ShowDocument?docid=473 The Build Management System (BMS)]
+
−
## [[Reconstruction Software]]
+
−
## [[Deprecated Software Links]]
+
−
# [[Offline Projects]]
+
−
# [[Splitoff_Information | Material on Splitoffs]]
+
−
# [[EVO]]
+
−
# [[GlueX Communications]] More on ESNET,EVO ...
+
−
# [[Private:Using VNC]]
+
−
# [[2013 Software Review]]
+
−
# [[2012 Software Review]]
+
−
# [https://halldweb.jlab.org/doc-private/DocDB/ShowDocument?docid=1782 IT in the 12-GeV Era: close-out slides]
+
−
# [[Geometries for 2008 DC Review]]
+
−
# [[Tracking resolution estimator (REZEST)]]
+
−
# [http://clasweb.jlab.org/wiki/index.php/HDDS2GEANT4_Installation_Notes Installing HDDS-to-GEANT4 converter]
+
−
# [http://dustbunny.physics.indiana.edu/mailman/private/gluex/2009-April/002627.html Duties of the GlueX Software Coordinator]
+
−
# [[ded]]
+
−
# [[Action Items From Hall-D Software Meetings|Action Items]]
+
−
# [[Action Items Archive]]
+
−
# [[Computing Services and Servers|Hall D and JLab Servers]]: Web servers, database servers, etc.
+

Latest revision as of 15:11, 18 September 2024

News:

Quick Links:

The legacy version of this page is here.

General Information

Build Scripts: A Version Management System for GlueX describes a standard directory structure for GlueX software, how to create complete or partial builds, and how to specify versions of individual packages, both for building and for use. It is also available as GlueX Note 2793.

See below for other helpful links.

Shell Environment Set-Up

Building GlueX Software

GlueX and Containers

Software Documentation

Packages used in the GlueX software stack with links to package-specific documentation.

GlueX Software

Documentation for software packages specific to GlueX or to JLab.

  • A brief overview of the GlueX-specific software can be found here
  • Best practices in writing code for the HallD/GlueX software environment check out this link of HallD/GlueX Coding Conventions
  • A convenient way to enhance the impact of comments inside the code is to use Doxygen. The hooks and infrastructures are already implemented for the packages halld_recon and halld_sim.
  • Documentation Initiative

Software Packages

Special Topics

  1. Material on Splitoffs

Documentation for External Software Packages

Documentation on additional software packages used by GlueX. Development and maintenance of these are not directly related to GlueX.

Data Sets

Offline Data Monitoring

Computing Facilities

JLab

Grid

Off-Site Computing Resources

Software Management

Source Code Management

Testing and Debugging

Governance, Conventions, Standard Practices

Containers

Meetings and Reviews

Communication and Help

FAQ

Legacy Links

Retrieved from "https://halldweb.jlab.org/wiki/index.php?title=GlueX_Offline_Software&oldid=126910"