IT-Bereich des Instituts für Chemie - hpc

Interactive srun jobs

kraus (kraus@undisclosed.example.com) — 2022-10-06T15:38:20+00:00

Interactive srun jobs Standard nodes: srun -pstandard -t20:00 --mem=2G -n2 -N1 --hint=nomultithread --pty /bin/bash -il SMP nodes: srun -psmp -t20:00 --mem=2G -n2 -N1 --hint=nomultithread

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 …

Login

kraus (kraus@undisclosed.example.com) — 2020-04-25T12:59:43+00:00

Login Works only within the TU intranet or VPN: * ssh -2 -e none -p 22 <TU_Account_Name>@gateway.hpc.tu-berlin.de (130.149.243.190) date of revision: 04-25-2020 © kraus

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

Common terms in SLURM language

kraus (kraus@undisclosed.example.com) — 2020-02-26T13:07:04+00:00

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

NAMD

kraus (kraus@undisclosed.example.com) — 2020-02-26T13:02:59+00:00

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…

Batch Jobs

kraus (kraus@undisclosed.example.com) — 2020-02-26T09:56:46+00:00

Batch Jobs * Equeueing of scripts launched via: sbatch job_script * Please DO NOT employ the parameter --ntasks-per-core= unless you really know what you do. Erroneous usage of this flag
(especially in combination with the parameter

ORCA

kraus (kraus@undisclosed.example.com) — 2020-02-19T19:04:56+00:00

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…

Intranode jobs (SMP)

kraus (kraus@undisclosed.example.com) — 2020-02-19T19:04:26+00:00

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…

Internode jobs using parallel Linda (for experts)

kraus (kraus@undisclosed.example.com) — 2020-02-19T19:04:09+00:00

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…

- gelöscht

kraus (kraus@undisclosed.example.com) — 2020-02-19T19:02:31+00:00

Packages Group Biomodeling - angelegt

kraus (kraus@undisclosed.example.com) — 2020-02-19T19:01:42+00:00

Packages Group Biomodeling biomodeling index

- gelöscht

kraus (kraus@undisclosed.example.com) — 2020-02-19T19:00:47+00:00

Packages Group Quantenchemie - angelegt

kraus (kraus@undisclosed.example.com) — 2020-02-19T19:00:33+00:00

Packages Group Quantenchemie quantenchemie index

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…