Compiling with NWChem-6.6 with Intel MPI-5.0.3


Here is a write-up of my computing platform and applications:

  1. NWChem 6.6 (Oct 2015)
  2. Intel Compilers 2015 XE (version 15.0.6)
  3. Intel MPI (5.0.3)
  4. Intel MKL (11.2.4)
  5. Infiniband Inteconnect (OFED 1.5.3)
  6. CentOS 6.3 (x86_64)

Step 1: First thing first, source the intel components setting from

source /usr/local/intel_2015/parallel_studio_xe_2015/bin/psxevars.sh intel64
source /usr/local/intel_2015/impi/5.0.3.049/bin64/mpivars.sh intel64
source /usr/local/intel_2015/composerxe/bin/compilervars.sh intel64
source /usr/local/intel_2015/mkl/bin/mklvars.sh intel64

Step 2: Assuming you are done, you may want to download the NWChem 6.6 from NWChem Website. You may also want to take a look at instruction set for Compiling NWChem.

I have less problem running NWCHEM when the installation and the compiling directories are the same. If you recompile, do untar from source. Somehow the “make clean” does not clean the directories properly.

# tar -zxvf Nwchem-6.6.revision27746-src.2015-10-20.tar.gz
# cd nwchem-6.6

Step 3: Apply All the Patches for the 27746 revision of NWChem 6.6

cd $NWCHEM_TOP
wget http://www.nwchem-sw.org/download.php?f=Xccvs98.patch.gz
gzip -d Xccvs98.patch.gz
patch -p0 < Xccvs98.patch

Here is my nwchem_script_Feb2017.sh. For more details information, see Compiling NWChem for details on some of the parameters

export TCGRSH=/usr/bin/ssh
export NWCHEM_TOP=/home/melvin/Downloads/nwchem-6.6
export NWCHEM_TARGET=LINUX64
export NWCHEM_MODULES=all
export LARGE_FILES=TRUE

export ARMCI_NETWORK=OPENIB
export IB_INCLUDE=/usr/include
export IB_LIB=/usr/lib64
export IB_LIB_NAME="-libumad -libverbs -lpthread"

export MSG_COMMS=MPI
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MPI_LOC=/usr/local/RH6_apps/intel_2015/impi_5.0.3/intel64
export MPI_LIB=$MPI_LOC/lib
export MPI_INCLUDE=$MPI_LOC/include
export LIBMPI="-lmpigf -lmpigi -lmpi_ilp64 -lmpi"

export FC=ifort
export CC=icc

export MKLLIB=/usr/local/RH6_apps/intel_2015/mkl/lib/intel64
export MKLINC=/usr/local/RH6_apps/intel_2015/mkl/include

export PYTHONHOME=/usr
export PYTHONVERSION=2.6
export USE_PYTHON64=y
export PYTHONLIBTYPE=so
sed -i 's/libpython$(PYTHONVERSION).a/libpython$(PYTHONVERSION).$(PYTHONLIBTYPE)/g' config/makefile.h

export HAS_BLAS=yes
export BLAS_SIZE=8 
export BLASOPT="-L$MKLLIB -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm"
export LAPACK_LIBS="-L$MKLLIB -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm"
export SCALAPACK_SIZE=8
export SCALAPACK="-L$MKLLIB -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lmkl_blacs_intelmpi_ilp64 -lpthread -lm"
export USE_64TO32=y

echo "cd $NWCHEM_TOP/src"
cd $NWCHEM_TOP/src

echo "BEGIN --- make realclean "
make realclean
echo "END --- make realclean "

echo "BEGIN --- make nwchem_config "
make nwchem_config
echo "END --- make nwchem_config "

echo "BEGIN --- make"
make CC=icc FC=ifort FOPTIMIZE=-O3 -j4
echo "END --- make "

cd $NWCHEM_TOP/src/util
make CC=icc FC=ifort FOPTIMIZE=-O3 version
make CC=icc FC=ifort FOPTIMIZE=-O3
cd $NWCHEM_TOP/src
make CC=icc FC=ifort FOPTIMIZE=-O3  link

General Site Installation

Determine the local storage path for the install files. (e.g., /usr/local/NWChem).
Make directories

# mkdir /usr/local/nwchem-6.6
# mkdir /usr/local/nwchem-6.6/bin
# mkdir /usr/local/nwchem-6.6/data

Copy binary

# cp $NWCHEM_TOP/bin/ /usr/local/nwchem-6.6/bin
# cd /usr/local/nwchem-6.6/bin
# chmod 755 nwchem

Copy libraries

# cd $NWCHEM_TOP/src/basis
# cp -r libraries /usr/local/nwchem-6.6/data

# cd $NWCHEM_TOP/src/
# cp -r data /usr/local/nwchem-6.6

# cd $NWCHEM_TOP/src/nwpw
# cp -r libraryps /usr/local/nwchem-6.6/data

The Final Lap (From Compiling NWChem)

Each user will need a .nwchemrc file to point to these default data files. A global one could be put in /usr/local/nwchem-6.6/data and a symbolic link made in each users $HOME directory is probably the best plan for new installs. Users would have to issue the following command prior to using NWChem: ln -s /usr/local/nwchem-6.6/data/default.nwchemrc $HOME/.nwchemrc

Contents of the default.nwchemrc file based on the above information should be:

nwchem_basis_library /usr/local/nwchem-6.6/data/libraries/
nwchem_nwpw_library /usr/local/nwchem-6.6/data/libraryps/
ffield amber
amber_1 /usr/local/nwchem-6.6/data/amber_s/
amber_2 /usr/local/nwchem-6.6/data/amber_q/
amber_3 /usr/local/nwchem-6.6/data/amber_x/
amber_4 /usr/local/nwchem-6.6/data/amber_u/
spce    /usr/local/nwchem-6.6/data/solvents/spce.rst
charmm_s /usr/local/nwchem-6.6/data/charmm_s/
charmm_x /usr/local/nwchem-6.6/data/charmm_x/

References:

  1. 470. Very briefly: compiling nwchem 6.3 with ifort and mkl
  2. Compiling NWChem from source
  3. Problem building NWChem version 6.5 on IB cluster with MKL & IntelMPI
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One thought on “Compiling with NWChem-6.6 with Intel MPI-5.0.3

  1. Hello kittycool,
    I found your guide very useful during my first attempt to compile NWChem. May I suggest you to have a look to the following page?

    http://www.nwchem-sw.org/index.php/Special:AWCforum/st/id2370/Compile_NWChem_with_Intel_2017_%28….html

    In there, I’m reporting the setting that I used to successfully compile this code using Intel 2017 (MPI & OpenMP + MKL). I hope this could help many other people to have an awesome experience while using this software.

    Have you a nice day!!!!

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