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Benjamin Hokanson-Fasig edited this page Jan 14, 2020 · 5 revisions

Finding CVMFS

If using the Wisconsin computing cluster, or another computing cluster which mounts CVMFS, then the ARA software should be located at /cvmfs/ara.opensciencegrid.org. Note that if you are the first to access this directory it may not appear in an ls /cvmfs until the directory is auto-mounted. Trying cd /cvmfs/ara.opensciencegrid.org should force the directory to appear.

Directory Structure

Inside /cvmfs/ara.opensciencegrid.org/ you will find a directory structure similar to the following:

/cvmfs/ara.opensciencegrid.org/
  trunk/
    centos7/
      build/
      root_build/
      source/
      setup.sh
  v1.0/
    centos7/
      build/
      root_build/
      source/
      setup.sh
  ...

The first level of directories act as version control. The trunk directory contains the latest, if slightly unstable, builds of the software. Other versions are frozen upon request of the collaboration and provide stable environments for working or repeating previous analyses. Here you should choose which version of the software you want to use based on your needs.

The second level of directories are the operating systems under which the software is compiled. Here just match the operating system of your cluster. If your operating system is not represented, let us know and we can look into adding it to the build process.

Finally then the third level contains the build directories which contain the software, plus source directories and a setup script.

Setup

In order to use the ARA software you will need to set environment variables to point to the software. This is where the setup scripts come in. To set all the necessary variables, run source /cvmfs/ara.opensciencegrid.org/VERSION/OPERATING_SYSTEM/setup.sh (replacing VERSION and OPERATING_SYSTEM with the appropriate directories). After running the setup script your PATH should point to the proper executables and library paths should be set to find the appropriate ARA software libraries and the libraries of any dependencies.

Testing

While the cvmfs repository is in its current beta-testing phase, we need help determining whether this software installation satisfies the needs of the collaboration. Try doing anything you would have done with software in /net/ara using the software in this repository instead and report back on anything that goes wrong. The preferred method of communication for now is a simple message to the #software-migration Slack channel.

Known Differences

We are already aware of some differences between the /net/ara space and the new cvmfs space which you may want to keep in mind while testing:

  • Write Protection: It is not possible for users to write files in the cvmfs space. As a result any code compiled against e.g. AraRoot will have to exist in a separate user directory and treat AraRoot as a library.

  • GCC Compatibility: The software is currently being compiled with gcc version 4.8.5. If your system uses a gcc version more recent than this, it is possible you will need to add the -D_GLIBCXX_USE_CXX11_ABI=0 flag to any gcc calls in the compilation process to avoid compilation errors.

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