Healthtech cluster - Revision history

Gabre at 12:47, 22 November 2024

2024-11-22T12:47:04Z

← Older revision		Revision as of 14:47, 22 November 2024
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	== Running things in parallel ==		== Running things in parallel versus interactive ==

	You can login to node07, node10, node12 and compute01 directly. The rest are non-interactive meaning you need to use slurm (see below).		'''You can login to node07, node10, node12 and compute01 directly. The rest are non-interactive meaning you need to use slurm (see below)'''.
	On the iterative nodes, you can use parallel. First, write a file with the commands, let's call it "list_cmds". We need full paths, no relative paths.		On the iterative nodes, you can use parallel. First, write a file with the commands, let's call it "list_cmds". We need full paths, no relative paths.

	Then pick an interative server to run the commands and you write:		Then pick an interative server to run the commands and you write:

2024-11-04T10:57:39Z

@@ Line 179: / Line 179: @@
 == Running things in parallel ==
-There is no queuing system on the cluster. But that can be simulated using parallel. First, write a file with the commands, let's call it "list_cmds". We need full paths, no relative paths.
+     cat list_cmds | parallel
 == General considerations ==

2024-10-25T13:07:09Z

← Older revision		Revision as of 15:07, 25 October 2024
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	scancel -u gabre		scancel -u gabre


			=== get info on jobs ===


			To get info on the nodes:

			sinfo -N -l


			=== submit jobs using sbatch ===

			We will launch 100 jobs of generating random numbers and check if they are prime. First make sure that you have a directory called ~/slurm_out/ and then run:

			for i in `seq 100`; do echo " /home/ctools/bin//python3 /home/projects/MAAG/FileDescriptors/random_int_generator.py --min 1000000000000 --max 100000000000000 1000 \| /home/ctools/bin//python3 /home/projects/MAAG/FileDescriptors/prime_checker.py"; done \| xargs -I CMD sbatch --job-name=gabriel_job --mem=2G --time=00:10:00 --cpus-per-task=1 --output=~/slurm_out/slurm_output_%j.out --error=~/slurm_out/slurm_error_%j.err --wrap="CMD"

			=== checking jobs ===

			Either use:

			squeue

			or:


			watch -n1 "squeue"

			to refresh every 1s. You can limit to a user using -u [username]

2024-10-25T10:41:47Z

← Older revision		Revision as of 12:41, 25 October 2024
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	'''Do not forget''' to nice -19 your commands.		'''Do not forget''' to nice -19 your commands.



			== Using SLURM ==


			=== cancel your jobs ===

			For a specific job:

			scancel JOBID

			For all your jobs:


			scancel -u gabre

2024-09-05T13:29:53Z