https://it.chem.tu-berlin.de/wiki/ 2026-04-28T16:34:53+00:00 https://it.chem.tu-berlin.de/wiki/ https://it.chem.tu-berlin.de/wiki/lib/tpl/arctic/images/favicon.ico text/html 2020-02-14T18:13:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://it.chem.tu-berlin.de/wiki/doku.php?id=hpc:numericserveruser:software:namd:batch_job_script&rev=1581700400&do=diff 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… text/html 2018-08-24T16:16:10+00:00 Anonymous (anonymous@undisclosed.example.com) https://it.chem.tu-berlin.de/wiki/doku.php?id=hpc:numericserveruser:software:namd:benchmarking&rev=1535120170&do=diff Benchmarks Runtime/Scaling behaviour on GPU platforms The wall clock time of jobs is influenced by following factors: * Scaling with respect to each GPU: the number of threads (SMP) and/or processes (MPI,hybrid) determines the load on each GPU card text/html 2018-08-24T17:57:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://it.chem.tu-berlin.de/wiki/doku.php?id=hpc:numericserveruser:software:namd:start&rev=1535126263&do=diff NAMD namd index