NAMD

Software Summary

Mesabi

Default Module: 

2.7-ompi

Other Modules Available: 

2.12-ibverbs-smp-CUDA, 2.12-multicore-CUDA, 2.13-ibverbs-smp-CUDA, 2.10-ibverbs, 2.11-ibverbs, 2.12-ibverbs, 2.13-ompi, 2.9-libverbs-CUDA, 2.9b1-libverbs, 2.7-ompi, 2.9-impi, 2.8-ompi

Last Updated On: 

Thursday, February 21, 2019

Mesabi K40

Default Module: 

2.7-ompi
Other Modules Available: 

2.12-ibverbs-smp-CUDA, 2.12-multicore-CUDA, 2.13-ibverbs-smp-CUDA, 2.10-ibverbs, 2.11-ibverbs, 2.12-ibverbs, 2.13-ompi, 2.9-libverbs-CUDA, 2.9b1-libverbs, 2.7-ompi, 2.9-impi, 2.8-ompi

Last Updated On: 

Thursday, February 21, 2019

Mangi

Default Module: 
2.7-ompi
Other Modules Available: 

2.10-ibverbs, 2.11-ibverbs, 2.12-ibverbs, 2.13-ompi, 2.9-libverbs-CUDA, 2.9b1-libverbs, 2.7-ompi, 2.9-impi, 2.8-ompi

Last Updated On: 

Thursday, November 15, 2018

Mangi v100

Default Module: 

2.7-ompi
Other Modules Available: 

2.10-ibverbs, 2.11-ibverbs, 2.12-ibverbs, 2.13-ompi, 2.9-libverbs-CUDA, 2.9b1-libverbs, 2.7-ompi, 2.9-impi, 2.8-ompi

Last Updated On: 

Thursday, November 15, 2018

NICE

Default Module: 
Other Versions Available: 
Last Updated On: 
Last Updated On: 

Thursday, February 21, 2019

Support Level: 
Primary Support
Software Access Level: 
Open Access
Software Categories: 
Drug Discovery
Structural Biology
Molecular Modeling and Simulation
Software Description

NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms. NAMD is best run on the high performance systems where it has been compiled with the latest Intel compilers and recent MPI parallel libraries. There are different compiled versions of NAMD, which use different parallelization methods.

Software Documentation

Software Documentation Tabs

Mangi v100
Mangi v100 Documentation: 

GPU-enabled NAMD on V100

To run this version of software in a Linux environment run the commands:
#!/bin/bash -l
#PBS -l walltime=0:10:0
#PBS -l pmem=1GB
#PBS -l nodes=1:ppn=24
#PBS -q v100
module load namd/2.13-ibverbs-smp-CUDA
cd $PBS_O_WORKDIR
rm namd.hostfile
for node in `cat $PBS_NODEFILE | sort | uniq`
do
  echo "host ${node}" >> namd.hostfile
done
# Please note there is no line break
# in the following charmrun ++remote-shell ssh ++p 24 ++ppn 24 ++nodelist \ 
namd.hostfile `which namd2` apoa1.namd > apoa1.out