NAMD
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. More information can be found here
Available containers
| Name | sha256 | mpi | labels | descripion |
|---|---|---|---|---|
| Singularity.namd-2.14-intel-2021a-mpi.localimage.sif | 1f343b7b3c67228201efb0406b57048a644791e27479c1b7c60da8e421bccfa4 | IntelMPI 2021a | pmi2 | benchmark |
Running the container
Example invocation of NAMD benchmark
# Note: $PLCR is base path of container repository and $CONT is the container filename
export I_MPI_PMI_LIBRARY=$PLCR/local/pmi2/libpmi2.so
wget -q https://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz
tar xf apoa1.tar.gz
cd apoa1
wget https://www.ks.uiuc.edu/Research/namd/2.13/benchmarks/ns_per_day.py
srun --mpi=pmi2 --cpu-bind=cores singularity -s run -B $I_MPI_PMI_LIBRARY -B $PWD:/host_pwd --pwd /host_pwd $PLCR/images/$CONT namd2 apoa1.namd | tee apoa1.out