IT-Bereich des Instituts für Chemie - hpc:numericserveruser:software

MS Jaguar

kraus (kraus@undisclosed.example.com) — 2020-02-18T14:23:47+00:00

MS Jaguar Html Documentation module add schrodinger/2016.4 $SCHRODINGER/docs/Documentation.htm Batch job script Please refer to: Example SGE batch job script Job control module add schrodinger/2016.4 $SCHRODINGER/jobcontrol -list $SCHRODINGER/jobcontrol -[kill|pause|resume|stop|abort|show] ]

Running CFOUR

kraus (kraus@undisclosed.example.com) — 2020-02-17T19:53:22+00:00

Running CFOUR * module use /net/projects/kaupp/modules && module load cfour/1.2 * Basis file named GENBAS and input file named ZMAT must be present in current working directory: * ln -sr /projects/kaupp/prog/cfour/1.2/basis/GENBAS * In SGE batch jobs invoke via:

Schrödinger - angelegt

kraus (kraus@undisclosed.example.com) — 2020-02-17T19:11:38+00:00

Schrödinger schroedinger index

Example batch job script for NAMD runs

kraus (kraus@undisclosed.example.com) — 2020-02-14T17:13:20+00:00

Example batch job script for NAMD runs #!/bin/bash --login #$ -N jobname_namd # job resources in Mebibytes #$ -l mem_free=500M # wall clock time in HH:MM:SS #$ -l h_rt=00:10:00 # choose any host in cluster18 #$ -l cluster18 # use five CPU cores at all #$ -pe mp 5 # ask for one GPU adapter card #$ -l gpus=1 #$ -cwd # mail sending options #$ -o stdout.out #$ -e stderr.out #$ -j no #$ -m b,e #$ -M [name_of_your_mailbox] module load cuda/8.0 namd/2.12-cuda namd2 +p 5 inputfile > outputf…

- gelöscht

kraus (kraus@undisclosed.example.com) — 2020-01-23T20:32:24+00:00

Launching Gaussian Jobs - angelegt

kraus (kraus@undisclosed.example.com) — 2020-01-23T20:31:50+00:00

Launching Gaussian Jobs date of revision: 01-23-2020 © kraus

Usage - angelegt

kraus (kraus@undisclosed.example.com) — 2020-01-23T20:29:52+00:00

Usage usage index

Known problems

kraus (kraus@undisclosed.example.com) — 2020-01-23T20:26:39+00:00

Known problems Problem 1: Gaussview refuses to start with error output similar to the following: YYY@cluster-a#-bash_4.2:~:[4]$ gaussview libGL error: unable to load driver: swrast_dri.so libGL error: failed to load driver: swrast [xcb] Unknown sequence number while processing queue [xcb] Most likely this is a multi-threaded client and XInitThreads has not been called [xcb] Aborting, sorry about that. gview.exe: xcb_io.c:259: poll_for_event: Assertion `!xcb_xlib_threads_sequence_lost' failed…

Gaussview

kraus (kraus@undisclosed.example.com) — 2020-01-23T20:24:57+00:00

Gaussview gaussview index

Running Batch Jobs from within Gaussview 6 - angelegt

kraus (kraus@undisclosed.example.com) — 2019-12-09T09:00:44+00:00

Running Batch Jobs from within Gaussview 6

Group repositories

kraus (kraus@undisclosed.example.com) — 2019-07-23T10:38:38+00:00

Group repositories * /net/homes/extern/mrogin/Software: ChemShell 3.5 (built by Daria Tombolelli) and special versions of 3.2 (old builts; still runnable?) * /projects/biomodeling: Currently empty; under construction

Q-Chem 5.1

kraus (kraus@undisclosed.example.com) — 2019-02-05T19:07:03+00:00

Q-Chem 5.1 * Features of Q-Chem 5.x: [ presentation_features] date of revision: 02-05-2019 © kraus

Citing & Credits

kraus (kraus@undisclosed.example.com) — 2019-01-29T14:44:42+00:00

Citing & Credits * The users must be informed that any published work arising from use of “MRCC” must include the following citation: “Mrcc, a quantum chemical program suite written by M. Kállay, Z. Rolik, J. Csontos, P. Nagy, G. Samu, D. Mester, J. Csóka, B. Szabó, I. Ladjánszki, L. Szegedy, B. Ladóczki, K. Petrov, M. Farkas, P. D. Mezei, and B. Hégely. See also. Z. Rolik, L. Szegedy, I. Ladjánszki, B. Ladóczki, and M. Kállay, J. Chem. Phys. 139, 094105 (2013), as well as: …

Citing & Credits

kraus (kraus@undisclosed.example.com) — 2019-01-29T14:39:23+00:00

Citing & Credits The following citations are requested by the licensing agreement to be included in any publication including results based on calculations with CFOUR: * The users must be informed that any published work arising from use of ”CFOUR” must include the following citation: CFOUR, a quantum chemical program package written 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. Ber…

CFOUR - angelegt

kraus (kraus@undisclosed.example.com) — 2019-01-29T14:08:01+00:00

CFOUR cfour index

CFOUR - angelegt

kraus (kraus@undisclosed.example.com) — 2019-01-29T13:57:32+00:00

CFOUR cfour index

MRCC

kraus (kraus@undisclosed.example.com) — 2019-01-18T11:46:49+00:00

MRCC mrcc index

CHARMM

kraus (kraus@undisclosed.example.com) — 2019-01-18T11:46:25+00:00

CHARMM charmm index

Software for Biomodeling group

kraus (kraus@undisclosed.example.com) — 2019-01-18T11:46:04+00:00

Software for Biomodeling group biomodeling_group index

- gelöscht

kraus (kraus@undisclosed.example.com) — 2019-01-18T11:42:21+00:00