SLURM Array Job BASH scripting within python subprocess Question: Update: I was able to get a variable assignment from SLURM_JOB_ID with this line. JOBID=`echo ${SLURM_JOB_ID}` However, I haven’t yet gotten SLURM_ARRAY_JOB_ID to assign itself to JOBID. Due to needing to support existing HPC workflows. I have a need to pass a bash script within a …
Catching the output of scontrol show job ID with python subprocess Question: I’m trying to return the output of the slurm command scontrol show job ID where ID is the ID number of the slurm job, to python as a string. I’m trying to use python’s subprocess command by trying x = subprocess.check_output("scontrol show job …
AWS ParallelCluster Graviton Rest API Connection Refused Question: I am trying to follow a tutorial using AWS ParallelCluster (AWS Research Workshop) and once I get CloudFormation up and running, I cannot connect to the cluster via the Rest API. I am using Slurm 21.08.8 and ParallelCluster 3.1.4. I am able to SSH into the head …
How can I start Tensorboard dev from within Python as a subprocess parallel to the Python session? Question: I want to monitor training progress of a CNN which is trained via a slurm process on a server (i.e., the Python script is executed through a bash script whenever the server has resources available; the session …
AllenNLP predictor object loading before it is called — rest of the script hangs Question: Background I am working on a project where I need to do coreference resolution on a lot of text. In doing so I’ve dipped my toe into the NLP world and found AllenNLP’s coref model. In general I have a …
No module named certifi Question: When executing python3 (Python 3.6.8) script on a local directory, it works well, but when running sbatch job in slurm, complains about certifi. python3 -m pip install certifi Defaulting to user installation because normal site-packages is not writeable Requirement already satisfied: certifi in /usr/local/lib/python3.6/site-packages (2020.12.5) After adding to the python …
How to change the working directory on Slurm Question: I am working on a slurm cluster where I am running couple of jobs. It is hard for me to check the jobs one by one in each directory. I could manage to check in which directory the jobs are running using scontrol show job JOB_ID …
How do I save print statements when running a program in SLURM? Question: I am running a Python code that contains print statements via SLURM. Normally when I run the Python code directly via “python program.py” the print statements appear in the terminal. When I run my program via SLURM, as expected the print statements …
