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Only members of the namd user group have access to NAMD executables provided by HLRN. To have their user ID included in this group, users can send a message to their consultant or to HLRN our support.
Modules
The environment modules shown in the table below are available to include NAMD executables in the directory search path. To see what is installed and what is the current default version of NAMD at HLRN, a corresponding overview can be obtained by saying module avail namd.
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For Intel Skylake compute nodes (Phase 1, Göttingen only) – simple case of a NAMD job using a total of 200 CPU cores distributed over 5 nodes running 40 tasks each
Codeblock linenumbers true #!/bin/bash #SBATCH --timet 12:00:00 #SBATCH --nodesp medium40 #SBATCH -N 5 #SBATCH --tasks-per-node 40 export SLURM_CPU_BIND=none module load impi/2019.5 module load namd/2.13 mpirun namd2 inputfile > outputfile
For Intel Cascade Lake compute nodes (Phase 2) – – simple case of a NAMD job using a total of 960 CPU cores distributed over 10 nodes running 96 tasks each
Codeblock linenumbers true #!/bin/bash #SBATCH --timet 12:00:00 #SBATCH --nodesp standard96 #SBATCH -N 10 #SBATCH --tasks-per-node 96 export SLURM_CPU_BIND=none module load impi/2019.5 module load namd/2.13 mpirun namd2 inputfile > outputfile
A set of input files for a small and short replica-exchange simulation is included with the NAMD installation. A description can be found in the NAMD User's Guide. The following job script executes this replica-exchange simulation on 2 nodes using 8 replicas (i.e., 10 24 tasks per replica)
Codeblock linenumbers true #!/bin/bash #SBATCH --timet 0:20:00 #SBATCH --nodesp standard96 #SBATCH -N 2 #SBATCH --tasks-per-node 4096 export SLURM_CPU_BIND=none module load impi/2019.5 module load namd/2.13 cp -r /sw/chem/namd/2.13/skl/lib/replica . cd replica/example/ mkdir output (cd output; mkdir 0 1 2 3 4 5 6 7) mpirun namd2 +replicas 8 job0.conf +stdout output/%d/job0.%d.log
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