GlueX Offline Software

News: July 19, 2022: Minutes of the July 18th Software Meeting are available July 12, 2022: New version set: 5.8.0. June 7, 2022: Minutes of the June 6th Software Meeting are available May 23, 2022" GlueX Software and Analysis Tutorial 2022 May 19, 2022: New version set: 5.7.1. Previous news items...

Quick Links: Listing of files missing from the tape library Frequently Asked Questions HOWTO List Version Set Files Repositories on GitHub GlueX Offline Software Meetings

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

• Simple Environment Set Up

Building GlueX Software

• Building private versions of GlueX software at JLab
• 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.
• 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.
• Version Sets Files

GlueX and Containers

• GlueX Software on Oasis
• 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 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

• AmpTools: Amplitude analysis package (aka partial wave analysis)
• CCDB: Calibration Database
  • Policy on CCDB Variations for Reconstructing Simulated Data
• EventStore: a package for managing and deploying data files and event lists
• EVIO: The CODA event format.
• halld_recon
• halld_sim
• HDDM: The Hall D Data Model, a compact xml-based format for event-based data.
• HDDS: Detector geometry specification
  • HDDS Schema: Includes description of the HDDS mark-up language.
  • Geometry Specification for Hall D: General Description and Philosophy, September 2003
  • Detector Models for GlueX Monte Carlo Simulation: A Status Report, June 2006
  • Detector Models for GlueX Monte Carlo Simulation: the CD2 Baseline, January 2007
  • HDDS Tagged Releases
• HDGeant4: Geant4-based simulation of the GlueX Detector and Hall D beamline
• JANA
• JANA2
  • Transition to JANA2
• MCwrapper
  • Active Sample Dashboard
  • MC Submission Form
• PyPWA: Python-based Partial Wave Analysis Toolkit
• RCDB: Run Conditions Database
  • Web Interface
  • GlueX Implementation of the RCDB
• sim-recon (deprecated, July 2018)
  • Doxygen Documentation: Descriptions of sim-recon C++ classes and their relationships.
  • Sim-Recon Tagged Releases
  • 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
• 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

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.

CERNLIB CLHEP C++

Doxygen GEANT 3 (manual) GEANT4 Git

GNU Make MySQL Python

ROOT SCons SQLite

Subversion Xerces 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

• Hall D Offline System Status Plots
• Hall D and JLab Servers: Web servers, database servers, etc.
• Computer Center
• Scientific Computing
  • Farm Job Status Auger job status from SciComp
    • jproj Job Status Status of jobs using the jproj system
  • Tape Request Status
• Disk space usage
  • Group
    • /group/halld leader board
  • Cache
    • oldest files under /cache/halld
  • Volatile
    • oldest files under /volatile/halld
  • Work
    • /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

• Open Science Grid
  • Using the Grid with Containers
  • Using the Grid
  • Updating Oasis for the GlueX VO
  • Gridmake

Off-Site Computing Resources

• Off-site Computing Resources: Status of applications, current and past allocations

Software Management

Source Code Management

• Git
  • GlueX Git Repositories
  • Instructions for Working with GlueX Git Repositories. Workflow description.
  • Instructions for joining the GlueX team on GitHub
  • Git Help Resources, July 14
  • Guide to Using Git. General usage tips.
  • Git questions and answers in the Offline FAQ
  • Splitting sim-recon
  • Conversion from Subversion to Git (Summer 2015)
• Subversion
  • Browse the Hall D Subversion Repository
    • 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

• Offline Issue Tracking using GitHub Issue Tracking
• Offline Issue Tracking using the Mantis Bug Tracker
• GlueX Coding Standards
• Version Management
• GlueX Cron Jobs
• Data Challenges: Large-scale tests of computing infrastructure
• Data Management Plan for Hall D: Long-term preservation of data and data-analysis tools
• 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
  • Send email to the list
  • Message archive
  • Google search of archive
  • Information page (subscribe, unsubscribe, list members, etc.)
• Google Group for GlueX Software
  • Help on GlueX-related Google Groups
  • Original announcement
• Slack
  • Chat application using the workspace jlab12gev
  • Click here to join. You must use your JLab email address.
• Simple Email Lists: get notifications from automated tests
• Communication Instructions: Guides to communication systems used by GlueX

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)
• Software Task List
• Tracking resolution estimator (REZEST)
• ded