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November 30, 2017 01:23
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Example Singularity image with help for binding to typical HPC data directories on Comet
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Bootstrap: docker | |
From: python:2.7.13 | |
%help | |
This container creates internal directories to bind HPC system locations to as | |
follows... | |
/pfs_data - The location of your high performance parallel file system data | |
/pfs_scratch - The location of your high performance parallel file system scratch | |
/local_scratch - The location of you node-local scratch | |
Assuming the following ENV vars exist as would typically be the case in a Slurm | |
batch job on Comet... | |
SLURM_JOB_USER, SLURM_JOB_ACCOUNT, SLURM_JOB_ID | |
You would run this container inside your Slurm job on Comet with... | |
$ singularity shell \ | |
--bind /oasis/projects/nsf/$SLURM_JOB_ACCOUNT/$SLURM_JOB_USER:/pfs_data \ | |
--bind /oasis/scratch/comet/$SLURM_JOB_USER/temp_project:/pfs_scratch | |
--bind /scratch/$SLURM_JOB_USER/$SLURM_JOB_ID:/local_scratch | |
<container_img> $OPTS | |
%labels | |
Maintainer HPCDevOps | |
Version v1.0 | |
%post | |
# Creating Comet compatible mount points | |
mkdir -p /pfs_data /pfs_scratch /local_scratch | |
%test | |
python --version | |
/bin/ls /pfs_data /pfs_scratch /local_scratch |
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