View source for Code:libnwchem

Libnwchem is a patch to the [http://www.nwchem-sw.org/index.php/Download#Patches_for_the_26243_revision_of_NWChem_6.5 6.5 Revision of NWChem] that adds three useful features.

# push_inp_string and pop_inp_string (nw_inp_from_file.F) to fake string input as input from an nwchem parameter file
#* push_inp_cstring (push_inp_cstring.c) to provide a 0-terminated c-string interface to same
# an nwchem_init function (libnwchem.F) to perform just the start-up tasks of nwchem.F and return its runtime database handle
#* a libnwchem target to the GNUMakefile (sorry, no cygwin right now)
# nwchem.py, rtdb.py and related python wrappers to call nwchem's top-level functions and handle io from the rtdb
#* various fixes to error handling in rtdb

Warning: I've observed some strangeness with the test for a "movecs" file during SCF.  If the python script changes the geometry, but the movecs file from a previous SCF calc. is left unchanged, SCF may be skipped.  This results in similar property output for (actually) different structures.

== Obtaining ==

You can download the patch [http://predictivestatmech.org/libnwchem-6.5.patch here].  Next, get the nwchem sources from the link at the top of the page.  To unpack and patch them, use

<source lang="bash">
tar xjf Nwchem-6.5.revision26243-src.2014-09-10.tar.bz2
mv Nwchem-6.5.revision26243-src nwchem-6.5
cd nwchem-6.5/src
for i in Util_md_sockets Hbar Tcenxtask Parallelmpi Makefile_gcc4x Bcast_ccsd Elpa_syncs; do
  wget http://www.nwchem-sw.org/images/$i.patch.gz
  zcat $i.patch.gz | patch -p0
  rm -f $i.patch.gz
done
i=Hnd_giaxyz_noinline # there's always that one.
wget http://www.nwchem-sw.org/images/$i.patch.gz
zcat $i.patch.gz | (cd NWints/hondo && patch -p0)
rm -f $i.patch.gz

# Finally, apply the libnwchem patch.
zcat ../../libnwchem-6.5.patch.gz | patch -p1
cd ..
bash ../build-6.5.sh # the build-6.5.sh script is at the bottom of this page.
</source>
The mv line is really required, since nwchem's build can fail if the path to the path to the source directory is too long!

== Compilation ==

For most Linux systems (but not BSD-based OSX), the -fPIC flag is required.  This is such a PITA to add to nwchem's compilation that my solution is an ugly hack.  Replace the real compiler with a shell script in your $HOME/bin directory, and make sure your path has $HOME/bin in front of all other directories.

(for icc)
<source lang="bash">
#!/bin/sh
# file $HOME/bin/icc
/opt/intel/bin/icc -fPIC $@
</source>

(or gcc)
<source lang="bash">
#!/bin/sh
# file $HOME/bin/gcc
/usr/bin/gcc -fPIC $@
</source>

I use the following script for compiling NWChem:

(on 64-bit Linux with icc)
<source lang="bash">
#!/bin/bash
# file build-6.5.sh
export NWCHEM_TOP=$HOME/build/nwchem-6.5
export NWCHEM_TARGET=LINUX64

export NWCHEM_MODULES=all

export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LIB=/apps/openmpi/1.4.5/lib
export MPI_INCLUDE=/apps/openmpi/1.4.5/include
export LIBMPI="-lpthread -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -lrdmacm -libverbs
-lpsm_infinipath -lnuma -ldl -Wl,--export-dynamic -lnsl -lutil -lm -ldl"

export ARMCI_NETWORK=OPENIB
# export IB_INCLUDE <Location of Infiniband libraries>/include
export MSG_COMMS=MPI
export CC=icc
export FCC=ifort
export FOPTIMIZE="-O2 -fPIC"
export FFLAGS="-O2 -fPIC"
export CFLAGS="-O2 -fPIC"
export MKLROOT=/apps/intel/mkl
# see intel's link-line advisor for generating the next line.  Use the options for single dynamic library.
# (the following is for MKL 10.3.6 with icc 11.1)
export BLASOPT="-i8 -I$MKLROOT/include/intel64/ilp64 -I$MKLROOT/include $MKLROOT/lib/intel64/libmkl_blas95_ilp64.a
$MKLROOT/lib/intel64/libmkl_lapack95_ilp64.a -Wl,--start-group $MKLROOT/lib/intel64/libmkl_intel_ilp64.a
$MKLROOT/lib/intel64/libmkl_core.a $MKLROOT/lib/intel64/libmkl_sequential.a -Wl,--end-group -lpthread -lm"

# These may be helpful for compiling with CUDA, but beware - the resulting program no longer loads without cuda libraries!
#export TCE_CUDA=n
#export CUDA=$CUDA_HOME/bin/nvcc
#export CUDA_FLAGS="-arch=sm_35"
#export CUDA_INCLUDE="-I$CUDA_HOME/include"
#export CUDA_LIBS="-L$CUDA_HOME/lib64 -lcudart -lcufft"
# -L/usr/X11R6/lib -lGL -lGLU -lX11 -lXi -lXmu -lglut -lGLEW

cd $NWCHEM_TOP/src

#make realclean # These two lines let you start again (theoretically).
#find . -name dependencies -exec rm {} \; -print

make nwchem_config
make nwchem
#make -B -C ddscf # in case you just changed something in the ddscf directory
cp util/cfileprefix.fh include/
make libnwchem
</source>
The line: '''cp util/cfileprefix.fh include/''' is required since nwchem has a really strange way of finding dependencies that works when compiling $(MAKE) stubs.o inside nwchem's target, but doesn't work when compiling $(MAKE) stubs.o inside libnwchem's target in the ''same makefile''!

(on 64/32 OSX with gcc)

 to appear!

== Testing ==

Inspecting the patch file, you will notice that the python wrapper was added into the src/python directory.  It also includes a simple test (test.py), which opens libnwchem.so from its compiled location and does geometry optimization on a water molecule.  To use it yourself,
# cd to nwchem-6.5/src/python
# export PYTHONPATH=$PWD:$PYTHONPATH
# edit nwchem.py to make sure the CDLL() command has the right path to libnwchem.so (in a pinch, just move libnwchem.so to the current dir, and change the CDLL line to CDLL("libnwchem.so"))
# run: mkdir scratch; mkdir perm
#* these two dirs are the nwchem.py default scratch and perm directories 
# run: python test.py
# if all goes well, you should see normal nwchem output (listing basis functions, showing geometry convergence, and ending with a citation note)

== Help ==
The patch is released without any warranty or indeed any guarantee of working at all.  If you have lots of ($$$) around, shoot me an email.