Great Lakes (UMich)

Great Lakes is the University of Michigan campus cluster.

Downloading

The glotzerlab-software image and the singularity cache are large, store them in your scratch directory:

$ cd /scratch/<your-account_root>/<your-account>/$USER
$ export SINGULARITY_CACHEDIR=/scratch/<your-account_root>/<your-account>/$USER/.singularity

Note

Replace <your-account> with your Great Lakes account name.

Download the image with support for Great Lakes:

$ singularity pull software.sif docker://glotzerlab/software:greatlakes

Using

Use the following commands in your job scripts or interactively to execute software inside the container:

Note

replace command arguments with the command and arguments you wish to run. For example: python3 script.py

Serial (or multithreaded) CPU jobs:

module load gcc/10.3.0 openmpi/4.1.4 singularity
mpirun -n 1 singularity exec --bind /scratch,/gpfs \
  /scratch/your-account_root/your-account/$USER/software.sif command arguments

Single GPU jobs:

module load gcc/10.3.0 openmpi/4.1.4 singularity
mpirun -n 1 singularity exec --bind /scratch,/gpfs --nv \
  /scratch/your-account_root/your-account/$USER/software.sif command arguments

MPI parallel CPU jobs:

module load gcc/10.3.0 openmpi/4.1.4 singularity
mpirun singularity exec --bind /scratch,/gpfs \
  /scratch/your-account_root/your-account/$USER/software.sif command arguments

MPI parallel GPU jobs:

module load gcc/10.3.0 openmpi/4.1.4 singularity
mpirun singularity exec --bind /scratch,/gpfs --nv \
  /scratch/your-account_root/your-account/$USER/software.sif command arguments