Skip to content

Latest commit

 

History

History

nwchem

README.md

Installing NWChem

Getting Started

NWChem is a quantum chemistry and molecular dynamics software which provides comprehensive many methods such as Hartree-Fock (HF), post-Hartree-Fock (post-HF), Density Functional Theory (DFT), classical molecular dynamics (MD), and hybrid quantum mechanics/molecular mechanics (QM/MM) for computing the properties of molecule. NWChem is an open-source, fast, efficient, and powerful. The program algorithm is optimized and designed to run with distributed-memory parallel method on Linux cluster across multiple compute nodes.

Website: http://www.nwchem-sw.org Github: https://github.com/nwchemgit/nwchem Documentation: https://github.com/nwchemgit/nwchem/wiki

Specification of AWS EC2 instance I used for writing this page

  • I compiled and installed NWChem 6.8.1 and 7.0.0 beta 1 on Red Hat 8, CentOS 7, Ubuntu 16.04, and Ubuntu 18.04 with and without enabling GPU (CUDA).
  • Instance types
    • CPU instance: t2.micro (free tier)
    • CPU instance: c5.xlarge - 4 CPU cores
    • CPU instance: c5.4xlarge - 16 CPU cores
    • GPU instance: g3s.xlarge - 4 CPU cores + 1 GPU
  • Storage
    • SSD
    • 30 GiB (free tier)

1. General prerequisites for compiling program

  • C++ and Fortran compilers such as Intel or GNU compiler
  • MPI library such as Intel MPI or OpenMPI
  • Math library such as Intel MKL (BLAS, LAPACK, and ScaLAPACK) or GNU OpenBLAS and OpenScaLAPACK
  • Make
  • Python 2.6 or 2.7
  • ARMCI (optional)
  • Casper (optional)
  • root or sudo permission (needed for installing program at global space)

2. Creating Script containing all configuration parameters

NWChem documentation - Compiling NWChem

Look at the bottom of this page for example of Bash scripts

3. Starting compilation

Execute the script to start compilation using the following commands

chmod +x INSTALL_NWCHEM_SCRIPT.sh
./INSTALL_NWCHEM_SCRIPT.sh

4. During compilation

  1. Compilation and installation can take 20 - 60 min depending on configuration setting, compiler and system performance.
  2. If it is done successfully, the NWChem executable binary will be created at $NWCHEM_TOP/bin/$NWCHEM_TARGET/nwchem by default.

where $NWCHEM_TOP and $NWCHEM_TARGET are environment variables that define the top directory of nwchem-6.8.1 and platform of machine such as LINUX64.

5. Running NWChem

  • Normal running
mpirun -np N /$NWCHEM_TOP/bin/$NWCHEM_TARGET/nwchem input.nw >& output.out &
  • Normal running with specifying the number of processes per node
mpirun -np N -ppn M /$NWCHEM_TOP/bin/$NWCHEM_TARGET/nwchem input.nw >& output.out &
  • Running with Casper
export NWCHEM_CASLIB=/full/path/to/casper/lib

mpirun -np N -ppn M -genv CSP_NG 1 \
        -genv LD_PRELOAD $NWCHEM_CASLIB/libcasper.so \
        /$NWCHEM_TOP/bin/$NWCHEM_TARGET/nwchem input.nw >& output.out

where N is the total number of MPI processes and M is the total number of MPI processes per node.

Note that the Casper is used for enhancing the performance of ARMCI method especially on cross-node MPI calculation.

6. Submitting NWChem job to the cluster using job scheduler

  • SGE

SGE scripts for submitting NWChem jobs

  • SLURM

SLURM scripts for submitting NWChem jobs

Example of Bash script for automated compilation

Red Hat and CentOS

  • OpenMPI on Red Hat/CentOS
  • Intel MPI on Red Hat/CentOS
  • Intel MPI + GPU on Red Hat/CentOS
  • MPICH MPI on Red Hat/CentOS
  • MPICH MPI + GPU on Red Hat/CentOS
  • MVAPICH2 MPI on Red Hat/CentOS
  • MVAPICH2 MPI + GPU on Red Hat/CentOS

Ubuntu

Contact

Rangsiman Ketkaew - [email protected]