https://it.chem.wiki.tu-berlin.de/ 2026-10-18T09:45:17+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 2020-04-25T12:59:43+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:clust_conf:login&rev=1587819583&do=diff Login <html> Works only within the TU intranet or VPN: </html> * <html> ssh -2 -e none -p 22 &lt;TU_Account_Name&gt;@gateway.hpc.tu-berlin.de (130.149.243.190) </html> date of revision: 04-25-2020 © kraus 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 2019-12-07T15:56:14+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:module_package:quantenchemie_group:cfour&rev=1575734174&do=diff CFOUR Current installation * Version: 1 * Revision: 2 * Parallelization: process level for intra- and internode jobs Credits and Citation CFOUR, Coupled-Cluster techniques for Computational Chemistry, a quantum-chemical program package by J.F. Stanton, J. Gauss, L. Cheng, M.E. Harding, D.A. Matthews, P.G. Szalay with contributions from A.A. Auer, R.J. Bartlett, U. Benedikt, C. Berger, D.E. Bernholdt, Y.J. Bomble, O. Christiansen, F. Engel, R. Faber, M. Heckert, O. Heun, M. Hilgenber… text/html 2019-10-21T16:54:01+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:module_package:orca&rev=1571676841&do=diff ORCA Current installation * Versions: 4.2.0 and 4.1.2 * Parallelization: process level (OpenMPI) Credits and Citation Generic reference for ORCA: Neese, F. “The ORCA program system” Wiley Interdisciplinary Reviews: Computational Molecular Science, 2012, Vol. 2, Issue 1, Pages 73–78. 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 2019-07-26T17:26:43+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:module_package:quantenchemie_group:intel_parallel-studio-xe_composer&rev=1564162003&do=diff Parallel Studio XE Composer * Documentation will follow soon... date of revision: 07-26-2019 © kraus text/html 2019-07-25T13:15:39+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:module_package:quantenchemie_group:respect&rev=1564060539&do=diff ReSpect Current installation * Versions: 5.1.0 beta * Parallelization: OpenMP threads Credits and Citation ReSpect 5.1.0 (2019), relativistic spectroscopy DFT program. Authors M. Repisky, S. Komorovsky, V. G. Malkin, O. L. Malkina, M. Kaupp, K. Ruud, with contributions from R. Bast, R. Di Remigio, U. Ekstrom, M. Kadek, S. Knecht, L. Konecny, E. Malkin, I. Malkin Ondik. (see http://www.respectprogram.org) text/html 2019-07-25T13:15:00+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:module_package:gaussian&rev=1564060500&do=diff Gaussian 16 Current installation * Version: 16 * Revision: A03 * Parallelization: shared memory intranode (OpenMP) and process level internode (Linda, only for experts) Credits and Citation Gaussian 16, Revision C.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, G. A. Petersson, H. Nakatsuji, X. Li, M. Caricato, A. V. Marenich, J. Bloino, B. G. Janesko, R. Gomperts, B. Mennucci, H. P. Hratchian, J. V. Ortiz, A. F. Izm… text/html 2019-07-24T13:20:45+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:module_package:quantenchemie_group:start&rev=1563974445&do=diff Software for Quantenchemie Group quantenchemie_group index text/html 2019-07-23T14:53:20+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:hpc_tubit:clust_conf:docu&rev=1563893600&do=diff Further Cluster Information and Links * Official Cluster Wiki: HCP Homepage * ISIS learning course (including discussion forum and cluster annoumcements): ISIS HPC Course * [Talk] held by Sebastian Kraus at 10/31/2018 during group seminar of Quantum Chemistry group date of revision: 06-24-2019 © kraus