Notes on using Alma 9 nodes at STAR

Ref: @[July 14, 2025] > STAR Software Mattermost chat with link to tutorial page

Ref: @[July 14, 2025] > Jerome Tutorial on running Alma 9

Ref: @[July 14, 2025] > STAR Software Mattermost chat link to issue with STAR_ROOT not found

Ref: @[July 14, 2025] > STAR Software Mattermost chat link to fix issue with STAR_ROOT not found

The information contained herein is valid as of the time of writing January 30, 2026 and may change as the STAR software develops

Summary

• Use Alma 9 nodes to have access to a larger pool of condor nodes
  • Alma 9 nodes are starsub0X where “X” is a number between 1 and 7 (1 and 2 having older versions of condor)
  • For example to login to the gateway and Alma 9 node in one go do ssh -t username@ssh.sdcc.bnl.gov ssh starsub04
    • This assumes you have your ssh private key loaded into the agent see.
• Alma 9 can only use NFS formatted disks
  • To setup NFS disks do the following (note that the first three of these thing have to actually be done in your .login or .cshrc scripts. you cannot do this later. You can set up root later, I believe):
    1. In your .cshrc login script replace setenv GROUP_DIR /afs/rhic.bnl.gov/star/group to setenv GROUP_DIR /star/nfs4/AFS/star/group
    2. One line above where you just did the replacement in the .cshrc file add setenv USE_NFS4 1
    3. If you have a .login script replace setenv GROUP_DIR /afs/rhic.bnl.gov/star/group to setenv GROUP_DIR /star/nfs4/AFS/star/group - NB: If you want to use ROOT6 you must then add the following lines to your login script setup 64b followed by setup ROOT 6.20.08. I believe this number may change as the versions of root6 change.
• STAR software doesn’t run or compile on Alma 9 and must use the container singularity
  • To use singularity first setup NFS environment following instructions above
  • To run or compile STAR code interactively on an Alma 9 node do singularity exec -e -B /direct -B /star -B /afs -B /gpfs -B /sdcc/lustre02 /cvmfs/star.sdcc.bnl.gov/containers/rhic_sl7.sif csh
    • This will start the singularity environment for STAR
      • You can now compile STAR software with cons
      • You can now run your STAR scripts normally
• Condor jobs must also be handled differently to use the container
  • NB: If you want to run jobs using condor in the singularity container, compile all code in the singularity container. This will use all the libraries available in the container. It also uses ROOT5.
  • For STAR scheduler
    1. add to your xml <shell>singularity exec -e -B /direct -B /star -B /afs -B /gpfs -B /sdcc/lustre02 /cvmfs/star.sdcc.bnl.gov/containers/rhic_sl7.sif</shell>
    2. Submit using star-submit-beta or star-submit-template-beta
  • For condor jobs
    1. The executable should be /bin/env
    2. The arguments should be singularity exec -e -B /direct -B /star -B /afs -B /gpfs -B /sdcc/lustre02 /cvmfs/star.sdcc.bnl.gov/containers/rhic_sl7.sif /path/to/script.csh rest of arguments to csh script
       • Note that if your script was copied to the condor node the path need only be “./”, i.e. the current directory

Background

The end of life for Scientific Linux 7 (SL7) has made it necessary and prudent for SDCC to switch to a different operating system (OS). This is the Alma 9 OS. However, The STAR software does not work out of the box on the Alma 9 OS. This could be due to the switch to a 64 bit OS. Also, on Alma 9, the AFS formatted disks are not accessible and only NFS formatted disks are. To run STAR software on Alma 9 one must use a “virtual box” to run code that uses the STAR libraries. This “virtual box” is called singularity. singularity is a container that will allow you to use the STAR software on STAR nodes running Alma 9.

The Alma 9 nodes cannot be reached with the usual rterm -i command. You need to ssh to them directly from the gateway. The nodes are starsub0X where “X” is a number from 1 to 7, e.g. ssh starsub04. The nodes numbered 3 and above have the latest version of condor and are thus recommended.

Q&A

• Fatal in <TVirtualStreamerInfo::Factory>: Cannot find the plugin handler for TVirtualStreamerInfo! However $ROOTSYS/etc/plugins/TVirtualStreamerInfo is accessible, Check the content of this directory!
  • This happens for older version of star libraries, use newer version (>= SL22c) to avoid this error.

To check if in a singularity container check if environment variable $SINGULARITY_ENVIRONMENT exists To exit container use command exit