UVA CS Computing Environment

University of Virginia

UVA CS Project Directories

https://www.cs.virginia.edu/computing/doku.php?id=project_directories

Project directory /p/nmg5g

UVA CS Slurm cluster

https://www.cs.virginia.edu/computing/doku.php?id=compute_slurm#resource_limits

Create a project-scoped env

Pick a path under your project dir (example: /p/nmg5g/condaenvs/py312):

# on a login node (portal) or short salloc
module load miniforge
mkdir -p /p/nmg5g/condaenvs
 
# create the env *by path* so it lives in /p
conda create -y --prefix /p/nmg5g/condaenvs/py312 python=3.12

To use it interactively:

module load miniforge
# make 'conda activate' available in non-interactive shells
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate /p/nmg5g/condaenvs/py312
python -V

Keep caches out of /u (optional but recommended)

By default, Conda’s package cache and named envs live in your home. Redirect them to /p with a .condarc:

rhe9cf@portal03:~$ cd
rhe9cf@portal03:~$ pwd
/u/rhe9cf

# create/edit ~/.condarc
cat >> ~/.condarc <<'YAML'
envs_dirs:
  - /p/nmg5g/conda/envs
pkgs_dirs:
  - /p/nmg5g/conda/pkgs
YAML
 
mkdir -p /p/nmg5g/conda/envs /p/nmg5g/conda/pkgs

Conda reads .condarc to set envs_dirs and pkgs_dirs. You can also use conda config —add envs_dirs … / —add pkgs_dirs …

Use the env in Slurm jobs

create hello.py

import sys, multiprocessing as mp
print("Python:", sys.version)
print("CPUs visible:", mp.cpu_count())

create conda_example.slurm

#!/bin/bash
#SBATCH -p cpu
#SBATCH --cpus-per-task=4
#SBATCH --mem=8G
#SBATCH -t 01:00:00
#SBATCH -J conda-demo
#SBATCH --output=slurm-%A.out
 
set -euo pipefail
module --ignore_cache purge
module load miniforge
 
# make `conda activate` work in batch shells
source "$(conda info --base)/etc/profile.d/conda.sh"
conda activate /p/nmg5g/condaenvs/py312
 
echo "Python: $(python -V) @ $(which python)"
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
 
# use heredoc with the *activated* interpreter
srun python hello.py

run:

sbatch conda_example.slurm

squeue -u rhe9cf

Reference List

1. https://www.cs.virginia.edu/computing/doku.php?id=start