Bridges-2 (PSC)

Bridges-2 is an HPC cluster at PSC with GPU and CPU nodes. Apply for resources on Bridges through the ACCESS program.

Downloading

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

$ cd $PROJECT
$ export SINGULARITY_CACHEDIR=$PROJECT/.singularity

Download the image with support for Bridges-2:

$ singularity pull software.sif docker://glotzerlab/software:bridges2

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 (RM-shared partitions):

module load openmpi/4.0.5-gcc10.2.0
mpirun -n 1 singularity exec --bind /ocean $PROJECT/software.sif command arguments

Single GPU jobs (GPU-shared partition):

module load openmpi/4.0.5-gcc10.2.0
mpirun -n 1 singularity exec --bind /ocean --nv $PROJECT/software.sif command arguments

MPI parallel CPU jobs (RM partition, RM-shared partition with more than 1 core):

module load openmpi/4.0.5-gcc10.2.0
mpirun singularity exec --bind /ocean $PROJECT/software.sif command arguments

MPI parallel GPU jobs (GPU partition):

module load openmpi/4.0.5-gcc10.2.0
mpirun singularity exec --bind /ocean --nv $PROJECT/software.sif command arguments

Important

You must use mpirun to launch parallel jobs. srun is not compatible with the MPI library installed inside the container.