https://it.chem.wiki.tu-berlin.de/ 2026-10-18T07:07:38+00:00 https://it.chem.wiki.tu-berlin.de/ https://it.chem.wiki.tu-berlin.de/lib/tpl/bootstrap3/images/favicon.ico text/html 2020-11-06T19:56:58+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:numericserveruser:hpc_numericserver:batch_job_scripts:job_scripts_examples:namd&rev=1604692618&do=diff 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 … text/html 2020-02-17T20:08:41+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:numericserveruser:hpc_numericserver:batch_job_scripts:job_scripts_examples:ms_jaguar:start&rev=1581970121&do=diff 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… text/html 2020-02-14T17:12:07+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:numericserveruser:hpc_numericserver:batch_job_scripts:job_scripts_examples:charmm:c41b2_serial&rev=1581700327&do=diff CHARMM c41b2 serial (built with Intel compiler) Launch this script shown below by typing: qsub jobscript_charmm-c41b2.sh <html> Remark: Might be that individual jobs crash with illegal CPU instructions on the computing node (will be probably fixed). text/html 2020-02-14T17:11:51+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:numericserveruser:hpc_numericserver:batch_job_scripts:job_scripts_examples:charmm:c41b2_mpi&rev=1581700311&do=diff CHARMM c41b2 MPI (built with Intel compiler) Launch this script shown below by typing: qsub jobscript_charmm-c41b2_mpi.sh <html> Remark: Evtl. jobs could crash with illegal CPU instructions on some old computing nodes (will be fixed in the future). text/html 2020-02-14T17:08:10+00:00 kraus (kraus@undisclosed.example.com) https://it.chem.wiki.tu-berlin.de/doku.php?id=hpc:numericserveruser:hpc_numericserver:batch_job_scripts:job_scripts_examples:script_gaussian&rev=1581700090&do=diff 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: <html> Please ensure the value for NProcShared