azurehpc/apps/nwchem

NWCHEM installation and running instructions

Prerequisites

Dependencies for binary version:

• None

Installation

First copy the apps directory to the cluster. 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.

Install from source

For this the headnode needs to be a HB or HC node with CentOS-HPC-7.6 upwards

azhpc-run -u hpcuser $azhpc_dir/apps/nwchem/build_install_nwchem.sh

Install binaries

None

Connect to the headnode

azhpc-connect -u hpcuser headnode

Run the NWCHEM h2o_freq scenario

To run on a single node with 4 cores run

qsub -l select=1:ncpus=60:mpiprocs=4 apps/nwchem/run_h2o_freq.sh

To run on two HB nodes with 8 total cores (4 cores on each node) run

qsub -l select=2:ncpus=60:mpiprocs=4 apps/nwchem/run_h2o_freq.sh

Install and run nwchem Benchmarks using Azure CycleCloud Cluster

Prerequisites

These steps require a Azure CycleCloud cluster with PBS. The cyclecloud_simple_pbs template in the examples directory a suitable choice.

Follow the steps in the examples/cyclecloud_simple_pbs/readme.md to setup cycle, import the template and start cluster.

Log in to the headnode of the cluster (from cycleserver):

    $ cyclecloud connect master -c <cyclecloud cluster name>

Installing nwchem

You will need to copy the apps/nwchem folder to the cyclecloud master.

Run the following to install nwchem on the cluster (in /scratch):

export APP_INSTALL_DIR=/scratch

apps/nwchem/build_install_nwchem.sh

Running nwchem

Copy apps/nwchem to the cyclecloud master node.

To run on two HB nodes with 8 total cores (4 cores on each node) run (nwchem installation and model are in /scratch)

qsub -l select=2:ncpus=60:mpiprocs=4 -v APP_INSTALL_DIR=/scratch,DATA_DIR=/scratch apps/nwchem/run_h2o_freq.sh