Python

Using Python Interactively on command line

[test@login31 ~]$ srun --pty bash
srun: job 3168742 queued and waiting for resources
srun: job 3168742 has been allocated resources
[test@compute-100 ~]$ module load python
[test@compute-100 ~]$ module list

Currently Loaded Modules:
  1) JHPCE_ROCKY9_DEFAULT_ENV   2) JHPCE_tools/3.0   3) python/3.9.14

[test@compute-100 ~]$ python3
Python 3.9.14 (main, May 16 2023, 14:32:18) 
[GCC 11.3.1 20220421 (Red Hat 11.3.1-2)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> 

Running Python program in batch mode

1. Write your python source in a file with .py extension (e.g. python_example.py)

   values = [88, 47, 96, 85, 72]
   for i in values:
       print('Example number = ', i)
   

2. Write a submit job script (e.g. python_example.sh)

   #!/bin/bash
   
   #SBATCH --mem=2G
   #SBATCH --time=2:00
   
   #SBATCH -o slurm.%N.%J.%u.out   # STDOUT
   #SBATCH -e slurm.%N.%J.%u.err   # STDERR
   
   module load python
   python3 python_example.py
   

3. Submit your python job

   [test@login31 ~]$ sbatch python_example.sh 
   Submitted batch job 3169570
   

4. Monitor the job status

   [test@login31 ~]$ squeue --me
                JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
              3169570    shared python_e    test R       0:01      1 compute-153
   

5. When the job is finished, the output files are created in your Current Working Directory

   -rw-r--r-- 1 test test   0 Mar 13 12:45 slurm.compute-153.3169570.test.err
   -rw-r--r-- 1 test test 105 Mar 13 12:45 slurm.compute-153.3169570.test.out
   

6. Look at the results from output file, file with stderr is empty(job without errors):

   [test@login31 ~]$ cat slurm.compute-153.3169570.test.out
   Example number =  88
   Example number =  47
   Example number =  96
   Example number =  85
   Example number =  72
   

Installing Your Own Packages

Please see this document