Skip to main content

Code-Migration-Handson

Source repo: sdsc-summer-institute-2025 | Branch: main | Last synced: 2026-04-24 10:27:17.425 UTC

Command Set #1​

Lets start with using module commands to search for the MATLAB software available. We can then check which environment variables are changed when one of these modules is loaded.

module spider matlab
module show matlab/2022b

Next we look for the ADIOS2 IO library and check for the dependencies that are needed to be loaded and the check the module dependencies that are automatically loaded.

module spider adios2
module reset
module load cpu/0.17.3b  gcc/10.2.0/npcyll4  openmpi/4.1.3/oq3qvsv
module load adios2/2.7.1
module list
module show adios2/2.7.1

Command Set #2​

In this part of the hands on section, we will copy over a PyTorch example from the Expanse examples directory and run it. This example uses a PyTorch Singularity image for the software environment.

cp -r /cm/shared/examples/sdsc/pytorch .
cd pytorch
sbatch --res=si25cpu -A gue998 run-pytorch-cpu-shared.sh

Once this job runs, check the output file!

Command Set #3​

In this example we first get interactive access to a compute node:

module reset
srun --pty --reservation=si25cpu --partition=shared --nodes=1 --ntasks-per-node=1 --cpus-per-task=8 --mem=16G -A gue998 -t 00:30:00 --wait 0 /bin/bash

Next we set the temporary directory to the node local NVMe scratch directory and change to that directory.

export TMPDIR=/scratch/$USER/job_$SLURM_JOBID
cd /scratch/$USER/job_$SLURM_JOBID

We next load the Singularity module, and build the Singularity image of the ExceRpt R application based on a docker image.

module load singularitypro
singularity build excerpt.sif docker://rkitchen/excerpt

Finally we copy over an example input and run the job using Singularity.

cp -r /cm/shared/examples/sdsc/excerpt/input .
mkdir output
singularity run --bind ./input:/exceRptInput --bind ./output:/exceRptOutput --bind /expanse/projects/qstore/data/excerpt/hg38:/exceRpt_DB/hg38 --bind /scratch:/scratch /cm/shared/apps/containers/singularity/excerpt/excerpt.sif INPUT_FILE_PATH=/exceRptInput/SRR026761.sra

Command Set #4​

In our final example we will download the source of the RAxML application and build it using a Makefile. First we set up our MPI compiler environment:

module reset
module load gcc/10.2.0
module load openmpi/4.1.3

Next we clone the code repository

git clone --branch v8.2.13 https://github.com/stamatak/standard-RAxML.git
cd standard-RAxML/

Inspect the Makefiles. In particular Makefile.AVX2.MPI.gcc. Then build!

make -f Makefile.AVX2.MPI.gcc