Page Comparison

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1. Request an interactive session on the login node: ie scu-login01/scu-login02

   1. If you need to run with X-forwarding & relion - make sure to add the --x11 in the srun command

srun -n1 -N1 --cpus-per-task=1 --partition=scucryo-cpu --mem=4G --pty bash -l

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If you have any questions or problems, please feel free to reach out to Derek Shore or the SCU.

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This software is limited to those who have purchase the license only. SBGRID membership is centered around a PI and their lab with an annual membership fee.

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Troubleshooting

• Are you added to the sbgrid group on the cluster?

  • Check using the command id → 1081(sbgrid) should appear in the results

  • If you the group doesn’t appear, please email SCU - scu@med.cornell.edu

    Code Block
    [cwid@scu-login02 ~ ]$ id uid=12345(cwid) gid=538(wmcstaff) groups=538(wmcstaff),1081(sbgrid)

• Using Remote Desktop Protocol(RDP)

  • On the login node insert command: type -a srun

  • Code Block
    srun () { if id -nG | grep --color=auto -qw 'sbgrid'; then sg sbgrid "/usr/bin/srun $*"; else sg $default_group_per_slurm "/usr/bin/srun $*"; fi } srun is /usr/bin/srun

  • If you do not have the results above, then copy the code below and add into your ~./bashrc and then save and source ~./bashrc

    Code Block

    #change the users group if [[ $(id -un) != "root" ]] ; then default_group_per_slurm=`sacctmgr -p -n show user $USER | awk -F '|' '{print $2}'` if [[ $default_group_per_slurm == "rhauptlab" ]]; then default_group_per_slurm="riegelhauptlab" fi srun() { if id -nG | grep -qw 'sbgrid'; then sg sbgrid "/usr/bin/srun $*" else sg $default_group_per_slurm "/usr/bin/srun $*" fi } sbatch() { if id -nG | grep -qw 'sbgrid'; then sg sbgrid "/usr/bin/sbatch $*" else sg $default_group_per_slurm "/usr/bin/sbatch $*" fi } fi