azurehpc/apps/namd

Install and run NAMD

Prerequisites

Cluster is built with the desired configuration for networking, storage, compute etc. You can see the tutorial or examples folder in this repo for how to set this up. Spack is installed (See here for details).

Dependencies for binary version:

• None

First copy the apps directory to the cluster in a shared directory. The azhpc-scp can be used to do this:

azhpc-scp -r $azhpc_dir/apps/. hpcuser@headnode:.

Alternatively you can checkout the azurehpc repository but you will need to update the paths according to where you put it.

Connect to the headnode

azhpc-connect -u hpcuser headnode

Installation

Run namd install script

apps/namd/install_namd_openmpi.sh 

Note: Set SKU_TYPE environmental to the type of sku you are using (e.h hb, hbv2 or hc). NAMD_SOURE_TAR_GZ_LOC to the location of the namd source code (e.g NAMD_2.14_Source.tar.gz). Set NAMD_SMP to "smp" if you want to build the smp version. Set NAMD_MEMOPT to "--with-memopt" if you want to built the memopt version of namd.

Running

Now, you can run namd on hbv2 as follows:

qsub -l select=2:ncpus=120:mpiprocs=120 -v SKU_TYPE=hbv2,INPUTDIR=/path/to/inputfiles apps/namd/run_namd_openmpi.pbs

Where SKU_TYPE is the sku type you are running on and INPUTDIR contains the location of namd input files.