Difference between revisions of "GlueX Offline Software"

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'''News:'''
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* 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]]
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* [[GlueX_Offline_FAQ#Where_do_I_find_version_set_files.3F|Version Set Files]]
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* [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]].
 
The legacy version of this page is [[Offline Software|here]].
  
−
=GlueX Software Documentation=
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==General Information==
−
Documentation on software developed by GlueX collaborators.
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−
=Other Software Documentation=
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−
Documentation on software used by GlueX, but developed outside of the collaboration.
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=Software Management=
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−
Topics on governance, conventions, standard practices, etc.
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−
=Meetings and Reviews=
+
  
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# [[Quick Start Guide to building GlueX Software| Using a tagged release to quickly start with Hall-D Software]]
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[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].
−
# [[Getting started with GlueX Software|Detailed information to get started with all the Hall-D Software]]
+
 
−
# [[Building and Using the GlueX Software|Build and use all Software used in GlueX]]
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See below for other helpful links.
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## [[Quick Start Guide to building GlueX Software]]
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−
## [[Build Scripts and Makefiles]]
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===Shell Environment Set-Up===
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## [[HOWTO set up the GlueX environment]]
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−
## [[HOWTO use a pre-built release]]
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* [https://halldweb.jlab.org/docs/build_scripts_web/node6.html#SECTION00062400000000000000 Simple Environment Set Up]
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## [[Scripts for Installing GlueX Software]] (new, beta)
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−
# [[Getting started with Hall-D Software on the JLab CUE|If you are at JLAB get started with Hall-D Software on the CUE cluster]]
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===Building GlueX Software===
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# [[GlueX Offline FAQ]]
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−
# [http://halldweb1.jlab.org/websvn/prod/ Browse the subversion code repository]
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* [[Building_Private_Versions_of_GlueX_Software:_my_sim-recon.sh|Building private versions of GlueX software at JLab]]
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# [http://clasweb.jlab.org/websvn/prod/ legacy version]
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* [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.
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# [[Using the Grid]]
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* [[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.
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# [https://halldweb1.jlab.org/talks/2011-2Q/gridmake-6-2011.ppt Gridmake]
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* [[Legacy Build Instructions]]: Guides to various aspects of the build process. Up-to-date-ness may vary.
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# [[Weekly Tests of GlueX Software]]
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* [[GlueX_Offline_FAQ#Where_do_I_find_version_set_files.3F|Version Sets Files]]
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# [https://halldweb1.jlab.org/b1pi/ b1π results]
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−
# [https://halldweb1.jlab.org/single_track/ Single track results]
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=== GlueX and Containers ===
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# [[Data Challenges]]
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## [[Data Challenge 2: Ideas]]
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* [[GlueX Software on Oasis]]
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## [[Online Data Challenge 2013]]
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* [https://github.com/JeffersonLab/hd_singularity Package for Building Singularity Containers]
−
## [[GlueX Data Challenge Meetings]]
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* [[GlueX Containers Meetings]]
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# [[Offline HOWTO List| Offline HOWTO List]]
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* [[HOWTO use the GlueX Singularity Container]]
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# [[Trigger/DAQ/Monitoring/Controls#Software_HOWTO.27s|This is a link to the ONLINE HOWTO's]]
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−
# [http://www.jlab.org/Hall-D/software/GlueXCodingStandard.html GlueX Coding Conventions]
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==Software Documentation==
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# [[Data_Monitoring_Procedures]]
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−
# [[Media:Data Management Plan Hall D v2.pdf|Data Management Plan]]
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Packages used in the GlueX software stack with links to package-specific documentation.
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# [[Beam Simulations]]
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−
# [[Offline Software Topics]]
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===GlueX Software===
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## [[Hall-D Software Meetings]]
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−
## [http://www.jlab.org/Hall-D/software/wiki/index.php/GlueX_Communications Communication Instructions]
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Documentation for software packages specific to GlueX or to JLab.
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## [[EVO]]
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* A brief overview of the GlueX-specific software can be found [[ Software | here ]]
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## [[Role of the Software Coordinator]]  
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* Best practices in writing code for the HallD/GlueX software environment check out this link of [[Coding Conventions| '''''HallD/GlueX Coding Conventions''''']]
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## [[Offline Computing Project Management]]  
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* 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''.
−
## [[Versioning of Calibration Constants]]
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* [[Documentation Initiative]]
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## [[Releases of GlueX Software]]
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## [https://data.jlab.org/drupal/?q=system/files/Offline%20Plan%20FY10.pdf JLab Offline Computing Plan, FY2010]
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====Software Packages====
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## [[Reconstruction Tasks and Topics for Further Development]]
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−
## [http://www.jlab.org/Hall-D/software/HDSoftware_Documentation Doxygen generated documentation]
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* [https://github.com/mashephe/AmpTools AmpTools]: Amplitude analysis package (aka partial wave analysis)
−
## [http://clasweb.jlab.org/websvn/prod/ Browse the subversion code repository]
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* [[Calibration Database|CCDB]]: Calibration Database
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## [[Needed Studies]]
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** [[Policy on CCDB Variations for Reconstructing Simulated Data]]
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## [[How HDGeant defines time-zero for physics events]]
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* [https://github.com/sdobbs/HDEventStore EventStore]: a package for managing and deploying data files and event lists
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## [[Calibration Constants, Tagged Versions]]
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* [https://coda.jlab.org/drupal/content/event-io-evio EVIO]: The [https://coda.jlab.org/drupal/ CODA] event format.
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## [[Experimental_Sensitivity_to_Solenoidal_Field|Sensitivity to Magnetic Field Strength]]
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* [https://github.com/jeffersonlab/halld_recon halld_recon]
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## [[Sim-Recon Tagged Releases]]
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* [https://github.com/jeffersonlab/halld_sim halld_sim]
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## [[HDDS Tagged Releases]]
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* [[HDDM Programmer's Interface|HDDM]]: The Hall D Data Model, a compact xml-based format for event-based data.
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## [[Nightly Builds of GlueX Software]]
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* HDDS: Detector geometry specification
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## [[Weekly Tests of GlueX Software]]
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** [https://halldsvn.jlab.org/repos/trunk/hdds/HDDS-1_1.xsd HDDS Schema]: Includes description of the HDDS mark-up language.
−
## [[GlueX shared account on the JLab CUE]]
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** [https://halldweb.jlab.org/doc-public/DocDB/ShowDocument?docid=64 Geometry Specification for Hall D]: General Description and Philosophy, September 2003
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## [[GlueX Offline FAQ]]
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** [https://halldweb.jlab.org/doc-public/DocDB/ShowDocument?docid=654 Detector Models for GlueX Monte Carlo Simulation: A Status Report], June 2006
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## [[Running jobs on the grid]]
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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
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## [[Diagnosing segmentation faults in reconstruction software]]
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** [[HDDS Tagged Releases]]
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## [https://halldweb1.jlab.org/manuals/geant.pdf GEANT 3 manual]
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* [[HOWTO install and run HDGeant4|HDGeant4]]: Geant4-based simulation of the GlueX Detector and Hall D beamline
−
## [[osrelease.pl script]]
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* [https://www.jlab.org/JANA/ JANA]
−
## [https://halldweb1.jlab.org/mantisbt Offline Issue Tracking]
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* MCwrapper
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##* Legacy page: [[Action Items From Hall-D Software Meetings]]
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**[https://halldweb.jlab.org/gluex_sim/Dashboard.html '''Active Sample Dashboard''']
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## [http://www.jlab.org/Hall-D/offline/Software_tasks.php Software Task List]
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**[https://halldweb.jlab.org/gluex_sim/SubmitSim.html '''MC Submission Form''']
−
## [[Coding Conventions]]
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* [https://pypwa.jlab.org/index.html PyPWA:] [https://pypwa.readthedocs.io/ Python-based Partial Wave Analysis Toolkit]
−
## [[JANA/DANA]]
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* [https://github.com/JeffersonLab/rcdb/wiki RCDB]: Run Conditions Database
−
## [[Simulation Software]]
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** [https://halldweb.jlab.org/rcdb/ Web Interface]
−
## [[Geometry]]
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** [[GlueX Implementation of the RCDB]]
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## [[Magnetic Field Maps for Solenoid]]
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* sim-recon (deprecated, July 2018)
−
## [http://argus.phys.uregina.ca/cgi-bin/public/DocDB/ShowDocument?docid=473 The Build Management System (BMS)]
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** [http://www.jlab.org/Hall-D/software/HDSoftware_Documentation/ Doxygen Documentation]: Descriptions of sim-recon C++ classes and their relationships.
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## [[Reconstruction Software]]
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** [[Sim-Recon Tagged Releases]]
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## [[GlueX_Analysis_Software | Analysis Software]]
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** [[GlueX_Analysis_Software | Analysis Software in sim-recon]]
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## [[Deprecated Software Links]]
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** [[SCons Build System]] (SBMS)
−
# [http://halldweb1.jlab.org/mantisbt/my_view_page.php Mantis Bug Tracker] <--
+
 
−
# [[Calibration Database]] (CCDB)
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====Special Topics====
−
# [[SCons Build System]] (SBMS)
+
 
−
# [[Offline Projects]]
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* [[Offline HOWTO List]]: Guides to performing various specific tasks.
−
# [[Version Management]]
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* [[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]]
 
# [[Splitoff_Information | Material on Splitoffs]]
−
# [[EVO]]
+
 
−
# [[GlueX Communications]] More on ESNET,EVO ...
+
===Documentation for External Software Packages===
−
# [[Simple Email Lists]]: get notifications from automated tests
+
 
−
# [[Computer Farms]]
+
Documentation on additional software packages used by GlueX. Development and maintenance of these are not directly related to GlueX.
−
# [[Computing Services and Servers]]
+
 
−
# [[Private:Using VNC]]
+
{|
−
# [[2013 Software Review]]
+
|-
−
# [[2012 Software Review]]
+
|
−
# [http://argus.phys.uregina.ca/cgi-bin/private/DocDB/ShowDocument?docid=1782 IT in the 12-GeV Era: close-out slides]
+
* [http://cernlib.web.cern.ch/cernlib/ CERNLIB]
−
# [[Geometries for 2008 DC Review]]
+
* [http://proj-clhep.web.cern.ch/proj-clhep/ CLHEP]
−
# [[Tracking resolution estimator (REZEST)]]
+
* [https://en.wikipedia.org/wiki/C%2B%2B C++]
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# [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]
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* [http://www.stack.nl/~dimitri/doxygen/ Doxygen]
−
# [[ded]]
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* [https://halldweb.jlab.org/manuals/geant.pdf GEANT 3 (manual)]
−
# [[Private:Members of the halld group at JLab]]
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* [http://geant4.cern.ch/ GEANT4]
−
# [[GlueX Cron Jobs]]
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* [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]
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* [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]]
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** [[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]]

Latest revision as of 18:52, 31 January 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://halldweb1.jlab.org/wiki/index.php?title=GlueX_Offline_Software&oldid=124508"