Relion using SBGRID
Slurm Relion Docs
Submitting Slurm jobs via the Relion interface
Source the SBGRID software compilation and export required Relion variables by adding the following to your ~.bashrc. Be sure to either logout and back in or source the ~.bashrc after modification.
# Source SBGrid (Note, sourcing sbgrid in both bashrc and the Relion job submission template caused job failures) source /programs/sbgrid.shrc # RELION VARIABLES (these will show up in the Relion GUI) export RELION_QSUB_EXTRA_COUNT=3 export RELION_QSUB_EXTRA1="Walltime in hours" export RELION_QSUB_EXTRA2="Mem per CPU" export RELION_QSUB_EXTRA3="GRES"
Create default SBGRID preferences
Default software packages for SBGRID can be changed by creating and editing ~/.sbgrid.conf . Normally the defaults should work fine but changes can be made if required.
#RELION_X=3.1.0_cu10.2 #CUDA_X=10.2 #OPENMPI_X=3.1.6_slurm-20.02.03 #PYTHON_X=3.7.0
Create the Relion Slurm submission template
The submission template will be used to generate the actual Slurm submission script on a per-job basis. Be sure this script is being referenced in the Relion GUI.
#!/bin/bash #SBATCH --partition=any #SBATCH --nodes=1 # number of nodes #SBATCH --ntasks=XXXmpinodesXXX #SBATCH --cpus-per-task=XXXthreadsXXX #SBATCH --mem-per-cpu=XXXextra2XXX #SBATCH -t XXXextra1XXX:00:00 #SBATCH --gres=XXXextra3XXX #SBATCH --error=XXXerrfileXXX #SBATCH --output=XXXoutfileXXX # LOAD MODULES, INSERT CODE, AND RUN YOUR PROGRAMS HERE #Uncomment the cuda/opemmpi below if you need it.
#module load cuda/11.2 openmpi/4.1.1_cuda-11.2 #INFO echo "Starting at `date`" echo "Running on hosts:$SLURM_NODELIST" echo "Running on $SLURM_NNODES nodes." # Export shell variables to run environment. This will export the sbgrid environment that was originally sourced in the ~/.bashrc #SBATCH --export=ALL # RUN srun --export=ALL --mpi=pmi2 XXXcommandXXX
Error: An ORTE daemon has unexpectedly failed after launch and beforecommunicating back to mpirun. This could be caused by a number
of factors, including an inability to create a connection back
to mpirun due to a lack of common network interfaces and/or no
route found between them.
Other useful SBGRID commands
Verify information and version of an active package
sbgrid-info -l relion