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SBGrid site installation for BRB cluster

 

Regarding, personal computers/workstations:

You can install SBGrid on individual machines (and select only the software you want). A few small caveats:

  • You’ll need to create an account with SBGrid: https://sbgrid.org/registration/register/

  • Every member of a lab that wants to install SBGrid on a personal/work laptop should do this

  • Once they review the submitted form, they will send you the credentials you need to use the software on your machine.  

Note: using an individual installation of SBGrid is primarily handy for GUI-intensive applications (e.g., Schrödinger, PyMol, etc.); however, it could be difficult to run analysis on local machines, unless the data is on that machine. 

Once you have the needed credentials, you can install SBGrid using the instructions found here:

https://sbgrid.org/wiki/sbgrid-gui

BRB cluster(i.e., scu-login01/02)

Access is managed via modules. To see what’s available: 

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

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

  1. Run the following modules command to selectively view SBGrid-provisioned software:

module avail sbgrid

Software is loaded using standard modules commands, e.g., 

module load sbgrid/relion/4.0.1_cu11.6

 

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

SBGRID membership is centered around a PI and their lab with an annual membership fee.

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 

      [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 run

    • 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

      #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

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