Revision as of 21:27, 22 January 2016 by Jhammond (talk | contribs) (Phase 3)

(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to: navigation, search

NWChem with ARMCI-MPI3

You must use an implementation of MPI that supports MPI-3. These are listed on the front page of this website.

Phase 1 (6.3 release)

wget http://www.nwchem-sw.org/download.php?f=Nwchem-6.3.revision2-src.2013-10-17.tar.gz -O nwchem-6.3.tgz
tar -xzf nwchem-6.3.tgz
cd nwchem-6.3.revision2-src.2013-10-17
git clone git://git.mpich.org/armci-mpi.git || git clone http://git.mpich.org/armci-mpi.git
cd armci-mpi
git checkout mpi3rma

If ./autogen.sh fails due to lack of sufficiently recent versions, please see https://wiki.alcf.anl.gov/parts/index.php/Autotools and run the script there to install them. You will need to prepend $HOME/TOOLS/bin to PATH prior to running this script for it to succeed.

Phase 1 (6.6)

wget http://www.nwchem-sw.org/download.php?f=Nwchem-6.6.revision27746-src.2015-10-20.tar.bz2 -O nwchem-6.6.tbz
tar -xjf nwchem-6.6.tbz
cd nwchem-6.6
cd $NWCHEM_TOP/src/tools

The output of ./install-armci-mpi is important. In particular, it will tell you something like this:

Please set the following environment variables when you build NWChem:

You will use these in phase 2.

Phase 1 (Github)

Only use these instructions if you are collaborating with Jeff using his Github fork of NWChem...

You need to fork https://github.com/jeffhammond/nwchem before the next step.

git clone https://github.com/$YOUR_GITHUB_USERNAME/nwchem.git nwchem-git
cd nwchem-git
cd $NWCHEM_TOP/src/tools

The output of ./install-armci-mpi is important. In particular, it will tell you something like this:

Please set the following environment variables when you build NWChem:

You will use these in phase 2.

Phase 2

mkdir build
cd build
../configure CC=mpicc --prefix=$NWCHEM_TOP/external-armci
make -j12
make install
export EXTERNAL_ARMCI_PATH=$NWCHEM_TOP/external-armci

At this point, you should be done with anything related to ARMCI-MPI. The rest of the build is identical to how one builds NWChem normally. However, for completeness, we include this below.

Phase 3

The MPICH, MPICH-GLEX and MVAPICH options are commented out. You need to uncomment the one that is right for your system. For CrayMPI, just set MPI_DIR to /usr so that it is valid. It will not be used since cc and ftn are MPI wrappers already.

export USE_MPI=yes

There are implementation-specific options for different MPIs:

MPI_DIR=`which mpicc | sed "s/\/bin\/mpicc//g"`
export MPI_LIB="${MPI_DIR}/lib"
export MPI_INCLUDE="${MPI_DIR}/include"
MPICH_LIBS="-lmpifort -lmpi"
GLEX_LIBS="-L/usr/local/glex/lib64 -L/usr/local/glex/lib -lglex"
MVAPICH_LIBS="-lmpich -lopa -lmpl -libmad -lrdmacm -libumad -libverbs -lrt -lhwloc -lhwloc"
#MPICH# export LIBMPI="-L${MPI_DIR}/lib -Wl,-rpath -Wl,${MPI_DIR}/lib ${MPICH_LIBS} -lpthread"
#GLEX# export LIBMPI="-L${MPI_DIR}/lib -Wl,-rpath -Wl,${MPI_DIR}/lib ${MPICH_LIBS} ${GLEX_LIBS} -lpthread"
#MVAPICH# export LIBMPI="-L${MPI_DIR}/lib -Wl,-rpath -Wl,${MPI_DIR}/lib ${MVAPICH_LIBS} -lpthread"

These options change frequently. The best way to determine what should go in LIBMPI is via mpicc -show.


On a Cray XC30 system like NERSC Edison, you need to load the following modules:

module load PrgEnv-intel cray-mpich torque
module load craype-ivybridge

Then your MPI settings are trivial:

export MPI_LIB="."
export MPI_INCLUDE="."
export LIBMPI=""

Phase 4

These are compiler and library settings. The Intel compilers are recommended because Intel Fortran appears to be the best compiler for NWChem. It appears that some versions of gfortran create bugs. The other advantage is that Intel compilers link against MKL trivially.

export FC=ifort
export CC=icc
export BLASOPT="-mkl=sequential"

If you want to use a different BLAS library, just read the documentation and figure it out. You should always be able to use CC=gcc but it is perhaps simpler in some environments (e.g. Cray, where modules makes it hard to mix and match compiler toolchains) to use matched pairs.


In order to automatically include MPI on a Cray system, you need to use the Cray compiler wrappers (with the Intel compilers under the hood, per the modules noted above):

export FC=ftn
export CC=cc

Phase 5

Now you should be ready to blast your login nodes with the build.

cd $NWCHEM_TOP/src
gmake nwchem_config
gmake -j8

If this doesn't work, please email Jeff for assistance.