View source for GlueX Offline Software

{| border
|-
|
'''News:'''
* July 19, 2022: [[GlueX_Software_Meeting,_July_18,_2022#Minutes|Minutes of the July 18th Software Meeting]] are available
* July 12, 2022: [https://halldweb.jlab.org/halld_versions/version_5.8.0.xml New version set: 5.8.0].
* June 7, 2022:  [[GlueX_Software_Meeting,_June_6,_2022#Minutes|Minutes of the June 6th Software Meeting]] are available
* May 23, 2022" [https://halldweb.jlab.org/wiki/index.php/GlueX_Tutorial_2022 GlueX Software and Analysis Tutorial 2022]
* 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...]]
|
'''Quick Links:'''
* [https://scicomptest.jlab.org/scicomp/tapeFile Listing of files missing from the tape library]
* [[GlueX Offline FAQ|Frequently Asked Questions]]
* [[Offline HOWTO List|HOWTO List]]
* [[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]]
|}

The legacy version of this page is [[Offline Software|here]].

==General Information==

[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.

===Shell Environment Set-Up===

* [https://halldweb.jlab.org/docs/build_scripts_web/node6.html#SECTION00062400000000000000 Simple Environment Set Up]

===Building GlueX Software===

* [[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.
* [[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==

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 [[ 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====

* [https://github.com/mashephe/AmpTools AmpTools]: Amplitude analysis package (aka partial wave analysis)
* [[Calibration Database|CCDB]]: Calibration Database
** [[Policy on CCDB Variations for Reconstructing Simulated Data]]
* [https://github.com/sdobbs/HDEventStore EventStore]: a package for managing and deploying data files and event lists
* [https://coda.jlab.org/drupal/content/event-io-evio EVIO]: The [https://coda.jlab.org/drupal/ CODA] event format.
* [https://github.com/jeffersonlab/halld_recon halld_recon]
* [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
** [https://halldsvn.jlab.org/repos/trunk/hdds/HDDS-1_1.xsd HDDS Schema]: Includes description of the HDDS mark-up language.
** [https://halldweb.jlab.org/doc-public/DocDB/ShowDocument?docid=64 Geometry Specification for Hall D]: General Description and Philosophy, September 2003
** [https://halldweb.jlab.org/doc-public/DocDB/ShowDocument?docid=654 Detector Models for GlueX Monte Carlo Simulation: A Status Report], June 2006
** [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]]
* [[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====

* [[Offline HOWTO List]]: Guides to performing various specific tasks.
* [[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]]
* [[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 on additional software packages used by GlueX. Development and maintenance of these are not directly related to GlueX.

{|
|-
|
* [http://cernlib.web.cern.ch/cernlib/ CERNLIB]
* [http://proj-clhep.web.cern.ch/proj-clhep/ CLHEP]
* [https://en.wikipedia.org/wiki/C%2B%2B C++]
|
* [http://www.stack.nl/~dimitri/doxygen/ Doxygen]
* [https://halldweb.jlab.org/manuals/geant.pdf GEANT 3 (manual)]
* [http://geant4.cern.ch/ GEANT4]
* [https://git-scm.com/ Git]
|
* [http://www.gnu.org/software/make/ GNU Make]
* [http://www.mysql.com/ MySQL]
* [https://www.python.org/ Python]
|
* [http://root.cern.ch/ ROOT]
* [http://www.scons.org/ SCons]
* [http://www.sqlite.org/ SQLite]
|
* [https://subversion.apache.org/ Subversion]
* [http://xerces.apache.org/ Xerces]
* [http://www.w3.org/TR/xmlschema11-1/ XSD]
|}

==Data Sets==

* [[Simulations]]: a guide to simulated data sets.

==Offline Data Monitoring==

* [[Data_Monitoring_Procedures]]: Information on offline monitoring of recently-taken data

==Computing Facilities==

===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://scicomptest.jlab.org/scicomp/ Scientific Computing]
** [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://scicomp.jlab.org/scicomp/#/jasmine/jobs Tape Request Status]
* Disk space usage
** Group
*** [https://halldweb.jlab.org/disk_management/group_report.html /group/halld leader board]
** [https://scicomp.jlab.org/scicomp/#/disk/cache-family Cache]
*** [https://halldweb.jlab.org/disk_management/cache_oldest.html oldest files under /cache/halld]
** [https://scicomp.jlab.org/scicomp/#/disk/volatile Volatile]
*** [https://halldweb.jlab.org/disk_management/volatile_oldest.html oldest files under /volatile/halld]
** [https://scicomp.jlab.org/scicomp/#/disk/work Work]
*** [https://halldweb.jlab.org/disk_management/work_report.html /work/halld leader board]
* [[GlueX-related shared accounts on the JLab CUE]]
* [[Hall D MySQL/MariaDB Servers and Replication Relationship]]: a list of database servers

===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]]
** [[Updating Oasis for the GlueX VO]]
** [https://halldweb.jlab.org/talks/2011-2Q/gridmake-6-2011.ppt Gridmake]

===Off-Site Computing Resources===

* [[Off-site Computing Resources]]: Status of applications, current and past allocations

==Software 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]
** [http://halldweb.jlab.org/websvn/prod/ Browse the Hall D Subversion Repository]
*** [http://clasweb.jlab.org/websvn/prod/ Legacy version]

===Testing and Debugging===

* [[Automatic Builds of GlueX Software]]: nightly build, pull-request-initiated test build, scan-build
* [[Automatic Tests of GlueX Software]]
* [[Diagnosing segmentation faults in reconstruction software]]

===Governance, Conventions, Standard Practices===

* [https://github.com/JeffersonLab/sim-recon/issues Offline Issue Tracking] using GitHub Issue Tracking
* [https://halldweb.jlab.org/mantisbt Offline Issue Tracking] using the Mantis Bug Tracker
* [[Coding Conventions|GlueX Coding Standards]]
* [[Version Management]]
* [[GlueX Cron Jobs]]
* [[Data Challenges]]: Large-scale tests of computing infrastructure
* [https://halldweb.jlab.org/doc-public/DocDB/ShowDocument?docid=2808 Data Management Plan for Hall D]: Long-term preservation of data and data-analysis tools
* [https://data.jlab.org/drupal/?q=system/files/Offline%20Plan%20FY10.pdf JLab Offline Computing Plan, FY2010]
* [[Role of the Software Coordinator]]

=== Containers ===

* [[GlueX and Containers]]: an overview of the use of containers in GlueX

==Meetings and Reviews==

* [[GlueX Offline Software Meetings]]: Agendas and minutes
* [[HDGeant4 Meetings]]
* [[GlueX Containers Meetings]]
* [[Software and Computing Reviews]]
* [[Geometries for 2008 DC Review]]

==Communication and Help==

* Offline Software Email List: announcements and discussion
** [mailto:halld-offline@jlab.org Send email to the list]
** [https://mailman.jlab.org/pipermail/halld-offline/ Message 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://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
* [[GlueX_Communications|Communication Instructions]]: Guides to communication systems used by GlueX

===FAQ===

* [[GlueX Offline FAQ|The GlueX Offline Frequently Asked Questions List]]

==Legacy Links==

* [[Offline Computing Project Management]]
* [[Versioning of Calibration Constants]]
* [[Releases of GlueX Software]]
* [[Reconstruction Tasks and Topics for Further Development]]
* [[Running jobs on the grid]]
* [[Calibration Constants, Tagged Versions]]
* [[Action Items Archive (May 4, 2010 and before)]]
* [http://www.jlab.org/Hall-D/offline/Software_tasks.php Software Task List]
* [[Tracking resolution estimator (REZEST)]]
* [[ded]]