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install-nwchem-openmpi.md

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Install NWChem with OpenMPI

Prerequisites

  1. Ubuntu (version 14.04 or higher)
  2. NWChem source code (6.8.1 or higher)
  3. GNU compiler (gcc and gfortran)
  4. OpenBLAS
  5. OpenMPI (version 1.6.x - 3.x.x)
  6. Python (version 2.6 or 2.7)
  7. root or sudo permission (needed for installation at global directory)

Step-by-step installation instruction

  1. Install all dependencies
sudo apt -y install gfortran libgfortran4 mpi-default-bin libopenblas-base \
libopenmpi2 libscalapack-openmpi2.0 openmpi-bin libquadmath0 \
libfabric1 libhwloc5 libibverbs1 libpsm-infinipath1 \
openmpi-common libhwloc-plugins libnl-route-3-200 \
ocl-icd-libopencl1  librdmacm1 \
python-dev tcsh make

Note that the above command will install OpenMPI version 2.1.1 (on the day of writing).

  1. Download the tarball of the source of NWChem from official Github repository https://github.com/nwchemgit/nwchem/releases/latest, for example, to your home directory
cd $HOME
wget https://github.com/nwchemgit/nwchem/releases/download/6.8.1-release/nwchem-6.8.1-release.revision-v6.8-133-ge032219-src.2018-06-14.tar.bz2
  1. Uncompress the tarball
tar -xvf nwchem-6.8.1-release.revision-v6.8-133-ge032219-src.2018-06-14.tar.bz2
  1. As MPI_LIB, MPI_INCLUDE, and LIBMPI parameters are not fixed (it depends on the environment of the system). Execute $HOME/nwchem-6.8.1/src/tools/guess-mpidefs shell script to get the suitable MPI libraries.
./home/ubuntu/nwchem-6.8.1/src/tools/guess-mpidefs
export MPI_INCLUDE="/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/lib"
export MPI_LIB="/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib"
export LIBMPI="-I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi"

In case guess-mpidefs cannot find the MPI libraries, maybe mpif90 command is not yet installed on your system. So you can use the following command to install mpif90

sudo apt -y install libopenmpi-dev
  1. Create a bash (or tcsh) script called, e.g., install-nwchem-openmpi.sh
vi install-nwchem-openmpi.sh
  1. Add the following commands to the newly created script. However, you can tweak the script as you need.
#!/bin/bash

# Install NWChem with parallel method on AWS EC2 system.
# Ubuntu OS
# Compile with GNU compiler and OpenMPI v.4.0.
# GNU BLAS
 
export NWCHEM_TOP=/home/ubuntu/nwchem-6.8.1/

## ---------------------- NWChem comfiguration ------------------------
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES="all python"
export MAKE=/usr/bin/make
export USE_NOFSCHECK=TRUE
## ---------------------- Python --------------------------------------
export PYTHONHOME=/usr
export PYTHONVERSION=2.7
export USE_PYTHONCONFIG=y
export USE_PYTHON64=y
## ---------------------- CC & FC compilers ---------------------------
export CC="gcc"
export FC="gfortran"
## ---------------------- Special method compilation ------------------
export MRCC_METHODS=TRUE
export CCSDTQ=y
export CCSDTLR=y
export IPCCSD=y
export EACCSD=y
## ---------------------- MPI Libraries box ---------------------------
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
# output of guess-mpidefs script.
export MPI_INCLUDE="/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/lib"
export MPI_LIB="/usr//lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib"
export LIBMPI="-I/usr/lib/x86_64-linux-gnu/openmpi/include -I/usr/lib/x86_64-linux-gnu/openmpi/lib -L/usr/lib/x86_64-linux-gnu/openmpi/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi"
## ---------------------- Math library --------------------------------
export HAS_BLAS=yes
export BLASOPT="-lopenblas -lpthread -lrt"
export BLAS_SIZE=4
#------------------------ Convert 64 to 32 bit ------------------------
export USE_64TO32=y
## --------------------------------------------------------------------

cd $NWCHEM_TOP/src

make nwchem_config
make 64_to_32 >& make_64to32.log
make FC=gfortran >& make.log

Very important note for OpenMPI version 4.0 or higher

As OpenMPI 4.0 changed the name of the functions, we have to tweak the name in the following files before compiling the program. e.g.

#!/bin/bash

export NWCHEM_TOP=/home/ubuntu/nwchem-6.8.1/

sed -i "s/MPI_Errhandler_set/MPI_Comm_set_errhandler/g" $NWCHEM_TOP/src/tools/ga-5.6.5/tcgmsg/tcgmsg-mpi/misc.c
sed -i "s/MPI_Type_struct/MPI_Type_create_struct/g" $NWCHEM_TOP/src/tools/ga-5.6.5/comex/src-armci/message.c

...
Configuration parameters snipped off
...

make nwchem_config
make 64_to_32
make

For more information please visit https://www-lb.open-mpi.org/faq/?category=mpi-removed.

  1. Execute the script to start installation.
./install-nwchem-openmpi.sh

This can take 20 - 30 minutes depending on the performance of compiler and system.

  1. If it is done without any error, the executable binary file can be found at $NWCHEM_TOP/bin/LINUX64/nwchem. For example,
/home/ubuntu/nwchem-6.8.1/bin/LINUX64/nwchem
  1. Create a hidden NWChem resource file called .nwchemrc and put it at your home directory.
vi $HOME/.nwchemrc

Add the following commands to .nwchemrc file:

nwchem_basis_library <location of NWChem installation>/src/basis/libraries/
nwchem_nwpw_library <location of NWChem installation>/src/nwpw/libraryps/
ffield amber
amber_1 <location of NWChem installation>/src/data/amber_s/
amber_2 <location of NWChem installation>/src/data/amber_q/
amber_3 <location of NWChem installation>/src/data/amber_x/
amber_4 <location of NWChem installation>/src/data/amber_u/
spce   <location of NWChem installation>/src/data/solvents/spce.rst
charmm_s <location of NWChem installation>/src/data/charmm_s/
charmm_x <location of NWChem installation>/src/data/charmm_x/

where <location of NWChem installation> is $NWCHEM_TOP.

  1. All test files are available at $NWCHEM_TOP/QA/tests.