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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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