All my slurm jobs fail with exit code 0:53 within two seconds of starting. When I look at job details with scontrol show jobid <JOBID> it doesn't say anything suspicious. When I look at the f...

I have a simple test.ksh that I am running with the command: sbatch test.ksh I keep getting "JobState=FAILED Reason=NonZeroExitCode" (using "scontrol show job") I have already made sure of the f...

#!/bin/bash #SBATCH -N 1 # nodes requested #SBATCH -n 1 # tasks requested #SBATCH -c 4 # cores requested #SBATCH --mem=10 # memory in Mb #SBATCH -o outfile # send stdout to outfile #SBATCH -e errfi...

I was trying to run slurm jobs with srun on the background. Unfortunately, right now due to the fact I have to run things through docker its a bit annoying to use sbatch so I am trying to find out ...

I would like to let the slurm system send myprogram output via email when the computing is done. So I wrote the SBATCH as following #!/bin/bash -l #SBATCH -J MyModel #SBATCH -n 1 # Number of cores...

I created some slurm scripts and then tried to execute them with sbatch. But the output file is updated not frequently (once a minute maybe). Is there a way to change the output buffering latency...

I am trying to submit a large number of jobs (several hundred) to a Slurm server and was hoping to avoid having to submit a new shell script for each job I wanted to run. The code submitted is a Py...

When I submit a SLURM job with the option --gres=gpu:1 to a node with two GPUs, how can I get the ID of the GPU which is allocated for the job? Is there an environment variable for this purpose? Th...

I was provided two sbatch scripts to submit and run. The input of the second one is based on the output of the first one. The assignment I need to do this for simply tells us to check on the first ...

I am running a snakemake pipeline on a HPC that uses slurm. The pipeline is rather long, consisting of ~22 steps. Periodically, snakemake will encounted a problem when attempting to submit a job. T...

I have set of an array job as follows: sbatch --array=1:100%5 ... which will limit the number of simultaneously running tasks to 5. The job is now running, and I would like to change this number...

According to the answers here What does the --ntasks or -n tasks does in SLURM? one can run multiple jobs in parallel via ntasks parameter for sbatch followed by srun. To ask a follow up question -...

I want to run a script on cluster (SBATCH file). How can activate my virtual environment (path/to/env_name/bin/activate). Does I need only to add the following code to my_script.sh file? module l...

With SBATCH you can use the job-id in automatically generated output files using the following syntax with %j: #!/bin/bash # omitting some other sbatch commands here ... #SBATCH -o slurm-%j.out-...

with PBS scheduler is possible launch a batch command without script in this way: qsub -l select=1:ncpus=12:mem=112GB -l walltime=00:30:00 -- /usr/bin/bash -c "mpirun -np 12 sleep 10" Is it poss...

I am running a pipeline on a SLURM-cluster, and for some reason a lot of smaller files (between 500 and 2000 bytes in size) named along the lines of slurm-XXXXXX.out (where XXXXXX is a number). I'v...

I have a python submission script that I run with sbatch using slurm: sbatch batch.py when I do this things do not work properly because I assume, the batch.py process does not inherit the right...

I found some very similar questions which helped me arrive at a script which seems to work however I'm still unsure if I fully understand why, hence this question.. My problem (example): On 3 node...

I have a problem where I need to launch the same script but with different input arguments. Say I have a script myscript.py -p <par_Val> -i <num_trial>, where I need to consider N diff...

I am trying to understand what the difference is between SLURM's srun and sbatch commands. I will be happy with a general explanation, rather than specific answers to the following questions, but h...

Can I submit "one-liners" to SLURM? Using bsub from LSF and the standard Linux utility xargs, I can easily submit a separate job for uncompressing all of the files in a directory: ls *.gz | sed '...

I’m trying to align 168 sequence files on our HPC using slurm version 14.03.0. I’m only allowed to use a maximum of 9 compute nodes at once to keep some nodes open for other people. I changed the ...

I have a couple of thousand jobs to run on a SLURM cluster with 16 nodes. These jobs should run only on a subset of the available nodes of size 7. Some of the tasks are parallelized, hence use all ...