nwchem

We do not use the Ubuntu provided package since it depends on mpi and we block the system mpi packages from being installed.

7.0.2

Trying to adapt from the 6.8.1 steps took hours to build and left me with a program that failed our workstation tests (:0:geom_binvr: ysyev failed:Received an Error in Communication).

But fortunately anaconda has packaged a version of this, which works fine:

# from wales01 (a [real] box running focal)
module load anaconda/python3
conda create -n nwchem -c conda-forge nwchem
# from styx (so I can both use my ssh keys and mount /shared/shared rw)
sudo ~/work/hold_shared_w_lock.py &
time sudo rsync -rvl -e "sudo -u ajh221 ssh" wales01:/home/ajh221/.conda/envs/nwchem/ /shared/shared/ubuntu-20.04/x86_64/nwchem/7.0.2
sudo mkdir /shared/shared/ubuntu-20.04/x86_64/nwchem/7.0.2/data/
# then provide the /shared/shared/ubuntu-20.04/x86_64/nwchem/7.0.2/data/default.nwchemrc file
# now, from an actual download of the nwchem source code, put in place the contrib directory (used for the python script nwgeom.py at least)
sudo cp -r nwchem-7.0.2-release/contrib /usr/local/shared/ubuntu-20.04/x86_64/nwchem/7.0.2/
# now, back on wales01
cd ~/work/linux-workstation-tests
mpirun -n 2 /usr/local/shared/ubuntu-20.04/x86_64/nwchem/7.0.2/bin/nwchem tests/data/nwchem.nw | less
# or module load nwchem && mpirun -n 2 nwchem tests/data/nwchem.nw | less
nosetests3 -v tests/test_nwchem.py |& less

6.8.1

See /usr/local/shared/ubuntu-18.04/x86_64/nwchem/6.8.1/build-nwchem-atlas.sh and /usr/local/shared/ubuntu-18.04/x86_64/nwchem/6.8.1/test-nwchem.sh . The QA suite that ships with nwchem contains many, many failing tests but the test script used here contains only the ones the nwchem developers use themselves.

Focal: Global Arrays (GA) needs a patch to work with MPI 4. I used that suggested at https://nwchemgit.github.io/Special_AWCforum/sp/id10351.html  However, I still had problems (it was complaining about unresolved Python symbols at the linking stage - perhaps I should have followed the following for 6.6 in full?).

6.6

export NWCHEM_TOP=`pwd`
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES='all python'
export USE_MPI=y

module purge
#module add mpi/openmpi/64/gnu/1.6.5
module add mpi/openmpi/64/gnu/1.8

$NWCHEM_TOP/contrib/distro-tools/getmpidefs_nwchem # and then execute the result
# You may need to add -Wl,-rpath -Wl,/path/to/your/openmpi/lib too MPI_LIB too
#export LIBMPI="-lmpi_f90 -lmpi_f77 -lmpi -ldl -Wl,--export-dynamic -lnsl -lutil"
#export LIBMPI='-lmpi'
#echo $MPI_LIB
#echo $MPI_INCLUDE
export FC=mpif90
export CC=mpicc
export PYTHONHOME=/usr
export PYTHONVERSION=2.7
export USE_PYTHON64=y
export PYTHONLIBTYPE=so
export PYTHON_SYSLIB=/usr/lib
export PYTHONCONFIGDIR=config-x86_64-linux-gnu
vim src/config/makefile.h

find the PYTHON64 bit and change $(PYTHONHOME)/lib64/python$(PYTHONVERSION)/config-x86_64-linux-gnu/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE) to $(PYTHONHOME)/lib/python$(PYTHONVERSION)/config-x86_64-linux-gnu/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)

cd $NWCHEM_TOP/src
make nwchem_config
make

export NWCINS=/whereever
mkdir $NWCINS
mkdir $NWCINS/bin
mkdir $NWCINS/data
mkdir $NWCINS/contrib

cd $NWCHEM_TOP
cp -r contrib/python $NWCINS/contrib
cp bin/$NWCHEM_TARGET/nwchem $NWCINS/bin
chmod 755 $NWCINS/bin 
cd $NWCHEM_TOP/src/basis
cp -r libraries $NWCINS/data
cd $NWCHEM_TOP/src/
cp -r data $NWCINS
cd $NWCHEM_TOP/src/nwpw
cp -r libraryps $NWCINS/data
chmod -R go+rX $NWCINS

Make a $NWCINS/data/default.nwchemrc file containing this (expand the vars)

nwchem_basis_library $NWCINS/data/libraries/
nwchem_nwpw_library $NWCINS/data/libraryps/
ffield amber
amber_1 $NWCINS/data/amber_s/
amber_2 $NWCINS/data/amber_q/
amber_3 $NWCINS/data/amber_x/
amber_4 $NWCINS/data/amber_u/
spce $NWCINS/data/solvents/spce.rst
charmm_s $NWCINS/data/charmm_s/
charmm_x $NWCINS/data/charmm_x/

You need the module for nwchem to link the default.nwchemrc to ~/.nwchemrc