https://it.chem.wiki.tu-berlin.de/ 2026-10-18T06:16:34+00:00 https://it.chem.wiki.tu-berlin.de/ https://it.chem.wiki.tu-berlin.de/lib/tpl/bootstrap3/images/favicon.ico text/html 2022-10-06T15:38:20+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:interactive_jobs&rev=1665070700&do=diff Interactive srun jobs <html> Standard nodes: </html> <html> srun -pstandard -t20:00 --mem=2G -n2 -N1 --hint=nomultithread --pty /bin/bash -il </html> <html> SMP nodes: </html> <html> srun -psmp -t20:00 --mem=2G -n2 -N1 --hint=nomultithread text/html 2020-02-26T13:07:04+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:common_terms&rev=1582722424&do=diff Common terms in SLURM language * cpu: hardware processor, generally termed core (not logical CPU entity, no hyperthreading) * node: computing host * queue: scheduling of jobs on a partition/group of nodes * partition: a group of nodes with similar computing capabilities text/html 2020-02-26T13:02:59+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:biomodeling:namd&rev=1582722179&do=diff NAMD #!/bin/bash --login ################################################################################################### # WARNING: Please adapt all relevant parameters so that they fit the requirements of your job(s). # ################################################################################################### # #SBATCH -o %x.%j.%N.out # for debugging purposes: redirect SLURM's stdout (p… text/html 2020-02-26T09:56:46+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:batch_jobs&rev=1582711006&do=diff Batch Jobs * <html> Equeueing of scripts launched via: sbatch job_script </html> * <html> Please DO NOT employ the parameter --ntasks-per-core= unless you really know what you do. Erroneous usage of this flag </br>(especially in combination with the parameter text/html 2020-02-19T19:04:56+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:orca&rev=1582139096&do=diff ORCA #!/bin/bash --login ################################################################################################### # WARNING: Please adapt all relevant parameters so that they fit the requirements of your job(s). # ################################################################################################### # #SBATCH -o %x.%j.%N.out # for debugging purposes: redirect SLURM's stdout (p… text/html 2020-02-19T19:04:26+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:gaussian:intranode&rev=1582139066&do=diff Intranode jobs (SMP) #!/bin/bash --login ################################################################################################### # WARNING: Please adapt all relevant parameters so that they fit the requirements of your job(s). # ################################################################################################### # #SBATCH -o %x.%j.%N.out # for debugging purposes: redirect S… text/html 2020-02-19T19:04:09+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:gaussian:linda&rev=1582139049&do=diff Internode jobs using parallel Linda (for experts) #!/bin/bash --login ################################################################################################### # WARNING: Please adapt all relevant parameters so that they fit the requirements of your job(s). # ################################################################################################### # #SBATCH -o %x.%j.%N.out # for d… text/html 2020-02-19T19:02:31+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:namd&rev=1582138951&do=diff text/html 2020-02-19T19:01:42+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:biomodeling:start&rev=1582138902&do=diff Packages Group Biomodeling biomodeling index text/html 2020-02-19T19:00:47+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:quantenchemie&rev=1582138847&do=diff text/html 2020-02-19T19:00:33+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:quantenchemie:start&rev=1582138833&do=diff Packages Group Quantenchemie quantenchemie index text/html 2019-08-26T18:01:26+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:quantenchemie:cfour&rev=1566842486&do=diff CFOUR #!/bin/bash --login ################################################################################################### # WARNING: Please adapt all relevant parameters so that they fit the requirements of your job(s). # ################################################################################################### # #SBATCH -o %x.%j.%N.out # for debugging purposes: redirect SLURM's stdout (please see man 1 sbatch for explanation of replacement symbols) # #SBATCH -e %x.%j.%N.err … text/html 2019-06-24T11:18:31+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:cheatsheet&rev=1561375111&do=diff Useful commands * Showing information about status and resources of each host within the cluster: sinfo -Nel * Showing your own job queue: sqeueue -u$USER * Showing the queue's status on a specific partition: squeue -p[partition] * Sending a SLURM script to the queue: text/html 2019-06-24T11:07:51+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:memory_limit&rev=1561374471&do=diff Memory Limits Type of Memory Limits * Resident memory (RSS): amount real memory in use by process * Virtual memory (VMem): amount of virtual memory pages allocated by process * In the current cluster setup, only the limit for the real memory has to be taken into consideration for jobs (by parameter <html> text/html 2019-05-02T14:00:31+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:gaussian:start&rev=1556805631&do=diff Gaussian gaussian index text/html 2019-05-02T13:57:13+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:turbomole&rev=1556805433&do=diff Turbomole text/html 2019-05-02T13:56:56+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:gaussian&rev=1556805416&do=diff Gaussian text/html 2019-05-02T13:56:27+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript:start&rev=1556805387&do=diff Example batch job scripts for program packages packages_jobscript index text/html 2019-05-02T13:56:14+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:packages_jobscript&rev=1556805374&do=diff Example batch job scripts for program packages packages_jobscript index text/html 2019-05-02T13:52:26+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:slurm_usage:start&rev=1556805146&do=diff Using SLURM batch job facility slurm_usage index