IT-Bereich des Instituts für Chemie - hpc:numericserveruser

NAMD with CUDA

kraus (kraus@undisclosed.example.com) — 2020-11-06T19:56:58+00:00

NAMD with CUDA Launch the script shown below by typing: qsub jobscript_namd-2.13_cuda-smp.sh #!/bin/bash --login ##### example for an NAMD OpenMP run with 4 CPU #$ -cwd ##### please define your own job resources # time in hh:mm:ss #$ -l h_rt=00:30:00 #$ -l mem_free=1G #$ -pe mp 2 # GPU resources and CUDA Compute Capability #$ -l gpus=1 # select from node pool comprising node batches node[560-565] (GeForce GTX 1080), node[730-739] (Quadro RTX 6000) and node[740-741] (GeForce RTX 2080 …

Storage Guidelines HPC

kraus (kraus@undisclosed.example.com) — 2020-03-24T16:43:04+00:00

Storage Guidelines HPC Storage Types Storage type Where/Mount Mount type Purpose Quota Capacity HOME /[homes|homes2]/[your_faculty|extern]/[username] network Program application data; only small files (very precious data) ~ 2.5 GiB

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] ]

- gelöscht

kraus (kraus@undisclosed.example.com) — 2020-02-18T14:20:02+00:00

Schrödinger MS Jaguar

kraus (kraus@undisclosed.example.com) — 2020-02-17T20:08:41+00:00

Schrödinger MS Jaguar Documentation module add schrodinger/2016.4 $SCHRODINGER/docs/Documentation.htm Example batch job script Do not be confused: MS Jaguar itself launches a second batch job (see remark within the script below) #!/bin/bash # remark: The jobcontrol tool (located at root of Schrödinger installation) allows to manage your MS Jaguar jobs # ******** EDIT HERE ******** # input file name input=input.in # job resource parameters name=ms-jaguar-job mem_free=4G procno=8 paren…

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…

CHARMM c41b2 serial (built with Intel compiler)

kraus (kraus@undisclosed.example.com) — 2020-02-14T17:12:07+00:00

CHARMM c41b2 serial (built with Intel compiler) Launch this script shown below by typing: qsub jobscript_charmm-c41b2.sh Remark: Might be that individual jobs crash with illegal CPU instructions on the computing node (will be probably fixed).

CHARMM c41b2 MPI (built with Intel compiler)

kraus (kraus@undisclosed.example.com) — 2020-02-14T17:11:51+00:00

CHARMM c41b2 MPI (built with Intel compiler) Launch this script shown below by typing: qsub jobscript_charmm-c41b2_mpi.sh Remark: Evtl. jobs could crash with illegal CPU instructions on some old computing nodes (will be fixed in the future).

Gaussian

kraus (kraus@undisclosed.example.com) — 2020-02-14T17:08:10+00:00

Gaussian Launch this script shown below by typing: qsub jobscript_gaussian16.sh [name_of_your_job] OR substitute NAME=$1 by NAME=[name_of_your_job] and launch as: qsub jobscript_gaussian16.sh Remark: Please ensure the value for NProcShared

Good Practice - Available parameters

kraus (kraus@undisclosed.example.com) — 2020-02-14T17:05:10+00:00

Good Practice - Available parameters (please also cf. man qsub) Example header for a batch job script: #!/bin/bash --login #$ -N [jobname] # job resources #$ -l mem_free=[xxxM]|[yyyG] #$ -l h_rt=HH:MM:SS #$ -q [name_of_job_queue] #$ -pe [name_of_parallel_env] [no_of_cpu_cores] # cd to execution path #$ -cwd # mail stuff #$ -o stdout.out #$ -e stderr.out #$ -j [no|yes] #$ -m [n|b|e|e,b,...] #$ -M [name_of_your_mailbox]

- 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

Numericserver - User Documentation

kraus (kraus@undisclosed.example.com) — 2019-11-29T12:03:05+00:00

Numericserver - User Documentation numericserveruser index Allgemeines * Das /work Verzeichnis des Numerikservers lokal mounten Anwendungen * Schrödinger Software

Usage of Modules package

kraus (kraus@undisclosed.example.com) — 2019-11-27T21:09:22+00:00

Usage of Modules package * List all available/installed modules: module avail * Load a module: module add/load [module_name] * Unload a module: module rm/unload [module_name] * Add/Remove path containing modules: module use/unuse [module_path_to_add]