Compiling NWChem from source

On this page, a step-by-step description of the build process and necessary and optional environment variables is outlined. In addition, based on the experiences of developers and users how-to’s for various platforms have been created. These how-to’s will be updated with additional platforms and better environment variables over time.

Download of the NWChem source is a step needed before compilation. Details for downloading as well as instructions for installing pre-compiled version of NWChem are available at the Download page.

Setting up the proper environment variables

  • $NWCHEM_TOP defines the top directory of the NWChem source tree, e.g.

When dealing with source from a NWChem release (6.8 in this example)

export NWCHEM_TOP=<your path>/nwchem-6.8
  • $NWCHEM_TARGET defines your target platform, e.g.
export NWCHEM_TARGET=LINUX64

The following platforms are available:

NWCHEM_TARGET Platform OS Compilers
LINUX x86 Linux GNU, Intel, PGI
ppc Linux GNU, IBM
arm Linux GNU, flang
LINUX64 x86_64 Linux GNU, Intel, PGI, Flang
ppc64le Linux GNU, IBM
aarch64 Linux GNU, flang
MACX x86 Darwin GNU, Intel
MACX64 x86_64 Darwin GNU, Intel
BGL Blue Gene/L IBM
BGP Blue Gene/P IBM
BGQ Blue Gene/Q IBM


  • $ARMCI_NETWORK must be defined in order to achieve best performance on high performance networks, e.g.
export ARMCI_NETWORK=MPI-PR

For a single processor system, this environment variable does not have to be defined. Supported combination of ARMCI_NETWORK and NWCHEM_TARGET variables:

ARMCI_NETWORK NWCHEM_TARGET Network Protocol
OPENIB LINUX, LINUX64 Mellanox InfiniBand Verbs
MPI-PR LINUX64 Any network MPI
MPI-MT
MPI-SPAWN
LINUX64 MPI supporting
multi-threading multiple
MPI-2
MPI-TS
MPI-PT
any any network with MPI MPI
BGMLMPI BGL IBM Blue Gene/L BGLMPI
DC MFMPI BGP IBM Blue Gene/P DCMF,MPI


Please see Choosing the ARMCI Library for additional information on choosing the right network options.

MPI variables

Variable Description
USE_MPI Set to “y” to indicate that NWChem should be compiled with MPI
USE_MPIF Set to “y” for the NWPW module to use fortran-bindings of MPI.
(Generally set when USE_MPI is set)
USE_MPIF4 Set to “y” for the NWPW module to use Integer*4 fortran-bindings of MPI.
(Generally set when USE_MPI is set on most platforms)
LIBMPI Name of the MPI library that should be linked with -l (eg. -lmpich)
MPI_LIB Directory where the MPI library resides
MPI_INCLUDE Directory where the MPI include files reside


Automatic detection of MPI variables with mpif90

New in NWChem 6.6: If the location of the mpif90 command is part of your PATH env. variable, NWChem will figure out the values of LIBMPI, MPI_LIB and MPI_INCLUDE (if they are not set). Therefore, we do NOT recommend to set LIBMPI, MPI_LIB and MPI_INCLUDE and add the location of mpif90 to the PATH variable, instead. Therefore, the next section can be considered obsolete in the most common cases.

Obsolete: How to se the MPI variables

The output of the command

mpif90 -show

can be used to extract the values of LIBMPI, MPI_LIB and MPI_INCLUDE

E.g. for MPICH2, this might look like:

$ mpif90 -show
f95 -I/usr/local/mpich2.141p1/include -I/usr/local/mpich2.141p1/include -L/usr/local/mpich2.141p1/lib \
-lmpichf90 -lmpichf90 -lmpich -lopa -lmpl -lrt -lpthread

The corresponding environment variables are

  % export USE_MPI=y
  % export LIBMPI="-lmpich -lopa -lmpl -lpthread -lmpichf90 -lfmpich -lmpich"
  % export MPI_LIB=/usr/local/mpich2.141p1/lib 
  % export MPI_INCLUDE='/usr/local/mpich2.141p1/include

Note: a script is available since NWChem 6.5 to extract the environment variables listed above

$NWCHEM_TOP/contrib/distro-tools/getmpidefs_nwchem

For some specific implementations the settings for MPI_LIB, MPI_INCLUDE, and LIBMPI look like:
MPI Implementation Environment variables
MPICH export MPI_LOC=/usr/local #location of mpich installation
export MPI_LIB=$MPI_LOC/lib
export MPI_INCLUDE=$MPI_LOC/include
export LIBMPI="-lfmpich -lmpich -lpmpich"
MPICH2 export MPI_LOC=/usr/local #location of mpich2 installation
export MPI_LIB=$MPI_LOC/lib
export MPI_INCLUDE=$MPI_LOC/include
export LIBMPI="-lmpich -lopa -lmpl -lrt -lpthread"
OPENMPI export MPI_LOC=/usr/local #location of openmpi installation
export MPI_LIB=$MPI_LOC/lib
export MPI_INCLUDE=$MPI_LOC/include
export LIBMPI="-lmpi_f90 -lmpi_f77 -lmpi -ldl -Wl,--export-dynamic -lnsl -lutil"


How to start NWChem

When MPI is used, the appropriate MPI run command should be used to start an NWChem calculation, e.g.

  % mpirun -np 8 $NWCHEM_TOP/bin/$NWCHEM_TARGET/nwchem h2o.nw

NWCHEM_MODULES

  • $NWCHEM_MODULES defines the modules to be compiled, e.g.
export NWCHEM_MODULES="all python"

The following modules are available:

Module Description
all Everything useful
all python Everything useful plus python
qm All quantum mechanics modules
md MD only build


Note that additional environment variables need to be defined to specify the location of the Python libraries, when the python module is compiled. See the optional environmental variables section for specifics.

Adding optional environmental variables

USE_NOFSCHECK can be set to avoid NWChem creating files for each process when testing the size of the scratch directory (a.k.a. creation of junk files), e.g.

export USE_NOFSCHECK=TRUE

USE_NOIO can be set to avoid NWChem 6.5 doing I/O for the ddscf, mp2 and ccsd modules (it automatically sets USE_NOFSCHECK, too). It is strongly recommended on large clusters or supercomputers or any computer lacking any fast and large local filesystem.

export USE_NOIO=TRUE

LIB_DEFINES can be set to pass additional defines to the C preprocessor (for both Fortran and C), e.g.

export LIB_DEFINES=-DDFLT_TOT_MEM=16777216

Note: -DDFLT_TOT_MEM sets the default dynamic memory available for NWChem to run, where the units are in doubles. Instead of manually defining this environment variable, one can use the getmem.nwchem script in the $NWCHEM_TOP/contrib directory. This script should be run after an initial build of the binary has been completed. The script will choose the default memory settings based on the available physical memory, recompile the appropriate files and relink.

MRCC_METHODS can be set to request the multireference coupled cluster capability to be included in the code, e.g.

export MRCC_METHODS=TRUE

CCSDTQ can be set to request the CCSDTQ method and its derivatives to be included in the code, e.g.

export CCSDTQ=TRUE

Setting Python environment variables

Python programs may be embedded into the NWChem input and used to control the execution of NWChem. To build with Python, Python needs to be available on your machine. The software can be download from https://www.python.org . Follow the Python instructions for installation and testing. NWChem has been tested with Python versions up to 3.10

The following environment variables need to be set when compiling with Python, together with having the location of your installed python binary part of the PATH environment variable:

export PYTHONVERSION=2.7

Note that the third number in the version should not be kept: 2.7.3 should be set as 2.7

You will also need to set PYTHONPATH to include any modules that you are using in your input. Examples of Python within NWChem are in the $NWCHEM_TOP/QA/tests/pyqa3 and $NWCHEM_TOP/contrib/python directories.

Optimized math libraries

By default NWChem uses its own basic linear algebra subroutines (BLAS). To include faster BLAS routines, the environment variable BLASOPT needs to be set before building the code. For example, with OpenBLAS

export BLASOPT="-lopenblas"

Good choices of optimized BLAS libraries on x86 (e.g. LINUX and LINUX64) hardware include:

BLIS https://github.com/flame/blis
OpenBLAS https://github.com/xianyi/OpenBLAS
GotoBLAS http://www.tacc.utexas.edu/tacc-projects/gotoblas2
Intel MKL http://www.intel.com/software/products/mkl
Cray LibSci Available only on Cray hardware, it is automatically linked when compiling on Cray computers.
IBM ESSL Available only on IBM hardware https://www.ibm.com/support/knowledgecenter/en/SSFHY8_6.3/navigation/welcome.html


New since release 7.0.0 (after commit 6b0a971): If BLASOPT is defined, the LAPACK_LIB environment variable must be set up, too. LAPACK_LIB must provide the location of the library containing the LAPACK routines. For example, OpenBLAS provides the full suite of LAPACK routines, therefore, in this case, LAPACK_LIB can be set to the same value as BLASOPT

export BLASOPT=-lopenblas
export LAPACK_LIB=-lopenblas

NWChem can also take advantage of the ScaLAPACK library if it is installed on your system. The following environment variables need to be set:

export USE_SCALAPACK=y

export SCALAPACK="location of Scalapack and BLACS library"

How to deal with integer size of Linear Algebra libraries

In the case of 64-bit platforms, most vendors optimized BLAS libraries cannot be used. This is due to the fact that while NWChem uses 64-bit integers (i.e. integer*8) on 64-bit platforms, most of the vendors optimized BLAS libraries used 32-bit integers. The same holds for the ScaLAPACK libraries, which internally use 32-bit integers.
The BLAS_SIZE environment variable is used at compile time to set the size of integer arguments in BLAS calls.

BLAS_SIZE size of integer arguments in BLAS routines
4 32-bit (most common default)
8 64-bit

A method is available to link against the libraries mentioned above, using the following procedure:

   cd $NWCHEM_TOP/src
   make clean
   make 64_to_32
   make USE_64TO32=y  BLAS_SIZE=4 BLASOPT=" optimized BLAS" SCALAPACK="location of Scalapack and BLACS library"

E.g., for IBM64 this looks like

  % make USE_64TO32=y BLAS_SIZE=4 BLASOPT="-lessl -lmass"

Notes:

  • GotoBLAS2 (or OpenBLAS) can be installed with 64bit integers. This is accomplished by compiling the GotoBLAS2 library after having edited the GotoBLAS2 Makefile.rule file and un-commenting the line containing the INTERFACE64 definition. In other words, the line
          #INTERFACE64 = 1

needs to be changed to

          INTERFACE64 = 1
  • ACML and MKL can support 64-bit integers if the appropriate library is chosen. For MKL, one can choose the ILP64 Version of IntelĀ® MKL and the correct recipe can be extracted from the website https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor. For ACML the int64 libraries should be chosen, e.g. in the case of ACML 4.4.0 using a PGI compiler /opt/acml/4.4.0/pgi64_int64/lib/libacml.a

New in NWChem 7.0.2: 1. The environment variable BUILD_OPENBLAS can be used to automatically build the OpenBLAS library during a NWChem compilation (either using BLAS_SIZE=8 or BLAS_SIZE=4) 2. The environment variable BUILD_SCALAPACK can be used to automatically build the ScaLapack library during a NWChem compilation (either using SCALAPACK_SIZE=8 or SCALAPACK_SIZE=4)

Linking in NBO

The 5.0 (obsolete) version of NBO provides a utility to generate source code that can be linked into computational chemistry packages such as NWChem. To utilize this functionality, follow the instructions in the NBO 5 package to generate an nwnbo.f file. Linking NBO into NWChem can be done using the following procedure:

  % cd $NWCHEM_TOP/src 
  % cp nwnbo.f $NWCHEM_TOP/src/nbo/.  
  % make nwchem_config NWCHEM_MODULES="all nbo" 
  % make

One can now use “task nbo” and incorporate NBO input into the NWChem input file directly:

 nbo  
   $NBO NRT $END  
   ... 
 end  

 task nbo

Building the NWChem binary

Once all required and optional environment variables have been set, NWChem can be compiled:

  % cd $NWCHEM_TOP/src  

  % make nwchem_config 

  % make >& make.log

The make above will use the standard compilers available on your system. To use compilers different from the default one can either set environment variables:

  % export FC=<fortran compiler>  
  % export CC=<c compiler>

Or one can supply the compiler options to the make command (recommended option), e.g:

  % make FC=ifort 

For example, on Linux FC could be set either equal to ifort, gfortran or pgf90

Nota bene: NWChem does NOT support usage of the full path in FC and CC variables. Please provide filenames only as in the examples above!

Note 1: If in a Linux environment, FC is set equal to anything other than the tested compilers, there is no guarantee of a successful installation, since the makefile structure has not been tested to process other settings. In other words, please avoid make FC=”ifort -O3 -xhost” and stick to make FC=”ifort”, instead

Note 2: It’s better to avoid redefining CC, since a) NWChem does not have C source that is a computational bottleneck and b) we typically test just the default C compiler. In other words, the recommendation is to compile with make FC=ifort

Note 3: It’s better to avoid modifying the values of the FOPTIMIZE and COPTIMIZE variables. The reason is that the default values for FOPTIMIZE and COPTIMIZE have been tested by the NWChem developers (using the internal QA suites, among others), while any modification might produce incorrect results.

How-to: Linux platforms

  • Common environmental variables for building in serial or in parallel with MPI
 % export NWCHEM_TOP=<your path>/nwchem  
 % export NWCHEM_TARGET=LINUX64  
 % export NWCHEM_MODULES =all
  • Common environmental variables for building with MPI

The following environment variables need to be set when NWChem is compiled with MPI:

% export USE_MPI=y
% export USE_MPIF=y
% export USE_MPIF4=y

% export MPI_LOC=<your path>/openmpi-1.4.3  (for example, if you are using OpenMPI)
% export MPI_LIB=<your path>/openmpi-1.4.3/lib
% export MPI_INCLUDE=<your path>/openmpi-1.4.3/include
% export LIBMPI="-lmpi_f90 -lmpi_f77 -lmpi -lpthread"

New in NWChem 6.6: If the location of the mpif90 command is part of your PATH env. variable, NWChem will figure out the values of LIBMPI, MPI_LIB and MPI_INCLUDE (if they are not set). Therefore, we recommend not to set LIBMPI, MPI_LIB and MPI_INCLUDE and add the location of mpif90 to the PATH variable, instead.

  • Compiling the code once all variables are set
% cd $NWCHEM_TOP/src
% make nwchem_config
% make FC=gfortran >& make.log

NWChem 6.6 on Ubuntu 14.04 (Trusty Tahr)

These instruction are likely to work (with minor modifications) on all Debian based distributions

  • Packages required:
python-dev gfortran libopenblas-dev libopenmpi-dev openmpi-bin tcsh make
  • Settings
export USE_MPI=y
export NWCHEM_TARGET=LINUX64
export USE_PYTHONCONFIG=y
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export BLASOPT="-lopenblas -lpthread -lrt"
export LAPACK_LIB=$BLASOPT
export BLAS_SIZE=4
export USE_64TO32=y
  • Compilation steps
make nwchem_config NWCHEM_MODULES="all python"
make 64_to_32
make

NWChem 6.6 on Fedora 22

  • Packages required:
python-devel gcc-gfortran openblas-devel openblas-serial64 openmpi-devel tcsh make patch
  • Settings
export USE_MPI=y
export NWCHEM_TARGET=LINUX64
export USE_PYTHONCONFIG=y
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export BLASOPT="-lnwclapack -lopenblas64"
export BLAS_SIZE=8
export PATH=/usr/lib64/openmpi/bin:$PATH
export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:$LD_LIBRARY_PATH
export USE_ARUR=y
  • Compilation steps
make nwchem_config NWCHEM_MODULES="all python"
make

NWChem 6.8 on Centos 7.1/Fedora 27

Once you have added the EPEL repository to your Centos/Fedora/RedHat installation, you can have a more efficient NWChem build.

sudo rpm -Uvh http://download.fedoraproject.org/pub/epel/7/x86_64/Packages/e/epel-release-7-11.noarch.rpm
  • Packages required:
python-devel gcc-gfortran openblas-devel openblas-serial64 openmpi-devel scalapack-openmpi-devel \
elpa-openmpi-devel tcsh openssh-clients which tar bzip2
  • Settings
export USE_MPI=y
export NWCHEM_TARGET=LINUX64
export USE_PYTHONCONFIG=y
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export USE_64TO32=y
export BLAS_SIZE=4
export BLASOPT="-lopenblas -lpthread -lrt"
export LAPACK_LIB=$BLASOPT
export SCALAPACK_SIZE=4
export SCALAPACK="-L/usr/lib64/openmpi/lib -lscalapack"
export ELPA="-I/usr/lib64/gfortran/modules/openmpi -L/usr/lib64/openmpi/lib -lelpa"
export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/:$LD_LIBRARY_PATH
export PATH=/usr/lib64/openmpi/bin/:$PATH
  • Compilation steps
cd $NWCHEM_TOP/src  
make nwchem_config NWCHEM_MODULES="all python"  
make 64_to_32  
make

NWChem 6.6 on RedHat 6

  • Packages required:
python-devel gcc-gfortran openmpi-devel tcsh make
  • Settings
export USE_MPI=y
export NWCHEM_TARGET=LINUX64
export USE_PYTHONCONFIG=y
export PYTHONVERSION=2.6
export PYTHONHOME=/usr
export USE_INTERNALBLAS
export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib/:$LD_LIBRARY_PATH
export PATH=/usr/lib64/openmpi/bin/:$PATH
  • Compilation steps
make nwchem_config NWCHEM_MODULES="all python"
make

NWChem 6.6 on RedHat 6 & EPEL repository

Once you have added the EPEL repository to you RedHat 6 installation, you can have a more efficient NWChem build. The settings are exactly the same as Centos 7.1

NWChem 6.6 on OpenSuse 13

  • Packages required:
gcc-fortran make python-devel openblas-devel openmpi-devel tcsh
  • Settings
export USE_MPI=y
export NWCHEM_TARGET=LINUX64
export USE_PYTHONCONFIG=y
export PYTHONVERSION=2.7
export PYTHONHOME=/usr
export USE_64TO32=y
export BLAS_SIZE=4
export BLASOPT="-lopenblas -lpthread -lrt"
export PATH=/usr/lib64/mpi/gcc/openmpi/bin:$PATH
export LD_LIBRARY_PATH=/usr/lib64/mpi/gcc/openmpi/lib64:$LD_LIBRARY_PATH
export PATH=/usr/lib64/openmpi/bin/:$PATH
  • Compilation steps
make nwchem_config NWCHEM_MODULES="all python"
make 64_to_32
make

How to: Mac platforms

Compilation of NWChem 6.5 release on Mac OS X 10.9 x86_64

  • Download and unpack latest NWChem tarball to the directory of your choosing, say /Users/johndoe/nwchem
  • Install Homebrew as described at http://brew.sh
ruby -e "$(curl -fsSL https://raw.github.com/Homebrew/homebrew/go/install)"
  • Use Homebrew to install mpich2
brew install mpich2
  • As usual, set the env. variables
export USE_MPI=y
export NWCHEM_MODULES=all
export NWCHEM_TARGET=MACX64
export NWCHEM_TOP=/Users/johndoe/nwchem
  • Important: set the following env. variable (GA will not compile otherwise)
export CFLAGS_FORGA="-DMPICH_NO_ATTR_TYPE_TAGS"
  • Go to your source directory, configure, and compile
cd /Users/johndoe/nwchem/src
make nwchem_config
make

Compilation of NWChem 6.6 on Mac OS X 10.10 (Yosemite) x86_64

Method #1: using gfortran from hpc.sf.net and mpich from macports

  • Install mpi (e.g. using macports)
sudo port install mpich
sudo port select mpi mpich-mp-fortran
  • Set environmental variables
export NWCHEM_TOP=/Users/johndoe/nwchem/
export NWCHEM_TARGET=MACX64
export USE_MPI="y"
export USE_MPIF="y"
export USE_MPIF4="y"
export CFLAGS_FORGA="-DMPICH_NO_ATTR_TYPE_TAGS"
export LIBMPI="-lmpifort -lmpi -lpmpi -lpthread"
export BLASOPT=" "
  • Go to your source directory, configure, and compile
cd /Users/johndoe/nwchem/src
make nwchem_config
make

Method #2: using gfortran and openmpi from brew

 /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" 
  • Use Homebrew to install open-mpi
brew install open-mpi
  • As usual, set the env. variables
export USE_MPI=y  
export NWCHEM_TARGET=MACX64  
export NWCHEM_TOP=/Users/johndoe/nwchem  
export USE_INTERNALBLAS=y
  • Important: set the following env. variable (GA will not compile otherwise)
export CFLAGS_FORGA "-DMPICH_NO_ATTR_TYPE_TAGS"
  • Go to your source directory, configure, and compile
 cd /Users/johndoe/nwchem/src  
 make nwchem_config`  
 make

WARNING: Please do not use the Mac OS X default BLAS and LAPACK libraries available (or brew’s veclibfort), since they are causing NWChem to produce erroneous results

Method #3: using Intel compilers and MKL

The Intel compilers and MKL work just fine on Mac with the following options:

NWCHEM_TARGET=MACX64
CC=icc
FC=ifort
BLASOPT="-mkl -openmp"
USE_OPENMP=T

MPICH and ARMCI-MPI work reliably on Mac. See Choosing the ARMCI Library for details on ARMCI-MPI

How-to: Cray platforms

Common environmental variables for building and running on the Cray XT, XE, XC and XK:

  % export NWCHEM_TOP=<your path>/nwchem  
  % export NWCHEM_TARGET=LINUX64  
  % export NWCHEM_MODULES=all  
  % export USE_MPI=y
  % export USE_MPIF=y 
  % export USE_MPIF4=y 
  % export USE_SCALAPACK=y 
  % export USE_64TO32=y  
  % export LIBMPI=" "
  • Compiling the code on Cray once all variables (described below) are set
  % cd $NWCHEM_TOP/src
  % make nwchem_config
  % make 64_to_32
  % make FC=ftn >& make.log

The step make 64_to_32 is required only if either SCALAPACK_SIZE or BLAS_SIZE are set equal to 4.

Method #2: ARMCI_NETWORK=MPI-PR

This is a new option available in NWChem 6.6.

Set the environmental variables for compilation:

  % export ARMCI_NETWORK=MPI-PR

Example: OLCF Titan

These are variables used for compilation on the OLCF Titan, a Cray XK7 We assume use of Portland Group compilers programming environment (module load PrgEnv-pgi)

NWCHEM_TARGET=LINUX64  
ARMCI_NETWORK=MPI-PR  
USE_64TO32=y  
USE_MPI=y  
BLAS_SIZE=4 
LAPACK_SIZE=4  
SCALAPACK_SIZE=4  
SCALAPACK=-lsci_pgi_mp  
BLASOPT=-lsci_pgi_mp

To enable the GPU part, set

TCE_CUDA=y

and load the cudatoolkit module

module load cudatoolkit

Aries, e.g. XC30/XC40

Method #1: ARMCI_NETWORK=MPI-PR

This is a new option available in NWChem 6.6.

Set the environmental variables for compilation:

% export ARMCI_NETWORK=MPI-PR

Example: NERSC Edison

These are variables used for compilation on NERSC Edison, a Cray XC30, as of October 23rd 2015, when using Intel compilers (i.e. after issuing the commands module swap PrgEnv-gnu PrgEnv-intel). Very similar settings can be applied to other Cray XC30 computers, such as the UK ARCHER computer

CRAY_CPU_TARGET=sandybridge 
NWCHEM_TARGET=LINUX64  
ARMCI_NETWORK=MPI-PR  
USE_MPI=y
SCALAPACK="-L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential \\  
-lmkl_blacs_intelmpi_ilp64 -lpthread -lm"  
SCALAPACK_SIZE=8  
BLAS_SIZE=8  
BLASOPT="-L$MKLROOT/lib/intel64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lpthread -lm"  
LD_LIBRARY_PATH=/opt/gcc/4.9.2/snos/lib64:$LD_LIBRARY_PATH 
PATH=/opt/gcc/4.9.2/bin:$PATH  
CRAYPE_LINK_TYPE=dynamic 

To compile

make nwchem_config 
make FC=ftn

The following env. variables needs to added to the batch queue submission script

MPICH_GNI_MAX_VSHORT_MSG_SIZE=8192
MPICH_GNI_MAX_EAGER_MSG_SIZE=131027   
MPICH_GNI_NUM_BUFS=300   
MPICH_GNI_NDREG_MAXSIZE=16777216  
MPICH_GNI_MBOX_PLACEMENT=nic    
COMEX_MAX_NB_OUTSTANDING=6

Example: NERSC Cori

These are variables used for compilation on the Haswell partition of NERSC Edison, a Cray XC40, as of November 6th 2016, when using Intel compilers (i.e. after issuing the commands module swap PrgEnv-gnu PrgEnv-intel).

export NWCHEM_TARGET=LINUX64  
export USE_MPI=y  
export NWCHEM_TARGET=LINUX64  
export ARMCI_NETWORK=MPI-PR  
export USE_MPI=y  
export USE_SCALAPACK=y  
export SCALAPACK="-L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential \  
-lmkl_blacs_intelmpi_ilp64 -lpthread -lm"  
export SCALAPACK_SIZE=8  
export SCALAPACK_LIB="$SCALAPACK" 
export BLAS_SIZE=8
export BLASOPT="-L$MKLROOT/lib/intel64 -lmkl_intel_ilp64 -lmkl_core -lmkl_sequential -lmkl_core -liomp5 -lpthread -ldmapp -lm"  
export USE_NOIO=y  
export CRAYPE_LINK_TYPE=dynamic

To compile

make nwchem_config
make FC=ftn

The following env. variables needs to added to the batch queue submission script

MPICH_GNI_MAX_VSHORT_MSG_SIZE=10000  
MPICH_GNI_MAX_EAGER_MSG_SIZE=98304  
MPICH_GNI_NUM_BUFS=300  
MPICH_GNI_NDREG_MAXSIZE=16777216 
MPICH_GNI_MBOX_PLACEMENT=nic
COMEX_MAX_NB_OUTSTANDING=6

How-to: Intel Xeon Phi

This section describes both the newer KNL and older KNC hardware, in reverse chronological order.

  • Compiling NWChem on self-hosted Intel Xeon Phi Knights Landing processors

NWChem 6.6 (and later versions) support OpenMP threading, which is essential to obtaining good performance with NWChem on Intel Xeon Phi many-core processors.
As of November 2016, the development version of NWChem contains threading support in the TCE coupled-cluster codes (primarily non-iterative triples in e.g. CCSD(T)), semi-direct CCSD(T), and plane-wave DFT (i.e. NWPW).

Required for compilation: Intel compilers, version 16+ (17+ is strongly recommended).

Environmental variables required for compilation:

% export USE_KNL=1 
% export USE_OPENMP=1  
% export USE_F90_ALLOCATABLE=T  
% export USE_FASTMEM=T

The latter two options are required to allocate temporaries in MCDRAM when running in flat mode. Please do not use cache mode for NWChem CCSD(T) codes. Note that using Fortran heap allocations means the memory statistics generated by MA are no longer accurate, but we doubt that anyone has been relying on these anyways.

USE_FASTMEM requires the memkind library to be installed. An open source version of the memkind library can be downloaded from Github

Side note: With the exception of USE_FASTMEM, all of the options in the KNL section apply to Intel Xeon processors as well. OpenMP is certainly useful on multicore processors as a way to reduce the communication overhead and memory footprint of NWChem.

When using MKL and Intel 16+, please use the following settings

% export BLASOPT  ="-mkl -qopenmp" 
% export SCALAPACK="-mkl -qopenmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64"

The command require for compilation is

$ make FC=ifort CC=icc

Environmental variables recommended at runtime (assuming Intel OpenMP and MPI):

% export I_MPI_PIN=1  
% export I_MPI_DEBUG=4  
% export KMP_BLOCKTIME=1 
% export KMP_AFFINITY=scatter,verbose

Once you are comfortable with the affinity settings, you can use these instead:

% export I_MPI_PIN=1
% export KMP_BLOCKTIME=1  
% export KMP_AFFINITY=scatter

Please consult the Intel or similar documentation regarding MPI+OpenMP affinity on your system. This is a complicated issue that depends on the software you use; it is impossible to document all the different combinations of MPI and OpenMP implementations that may be used with NWChem.

If you encounter segfaults not related to ARMCI, you may need to set the following or recompile with -heap-arrays. Please create thread in the Forum if you observe this.

% ulimit -s unlimited  
% export OMP_STACKSIZE=32M
  • Compiling NWChem on hosts equipped with Intel Xeon Phi Knights Corner coprocessors

NWChem 6.5 (and later versions) offers the possibility of using Intel Xeon Phi hardware to perform the most computationally intensive part of the CCSD(T) calculations (non-iterative triples corrections).

Required for compilation: Intel Composer XE version 14.0.3 (or later versions)

Environmental variables required for compilation:

% export USE_OPENMP=1 
% export USE_OFFLOAD=1

When using MKL and Intel Composer XE version 14 (or later versions), please use the following settings

% export BLASOPT  ="-mkl -openmp   -lpthread -lm"  
% export SCALAPACK="-mkl -openmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -lpthread -lm"

The command require for compilation is

$ make FC=ifort 
  • Examples of recommended configurations

From our experience using the CCSD(T) TCE module, we have determined that the optimal configuration is to use a single Global Arrays ranks for offloading work to each Xeon Phi card.

On the EMSL cascade system, each node is equipped with two coprocessors, and NWChem can allocate one GA ranks per coprocessor. In the job scripts, we recommend spawning just 6 GA ranks for each node, instead of 16 (number that would match the number of physical cores). Therefore, 2 out 6 GA ranks assigned to a particular compute node will offload to the coprocessors, while the remaining 6 cores while be used for traditional CPU processing duties. Since during offload the host core is idle, we can double the number of OpenMP threads for the host (OMP_NUM_THREADS=4) in order to fill the idle core with work from another GA rank (4 process with 4 threads each will total 16 threads on each node).

NWChem itself automatically detects the available coprocessors in the system and properly partitions them for optimal use, therefore no action is required other than specifying the number of processes on each node (using the appropriate mpirun/mpiexec options) and setting the value of OMP_NUM_THREADS as in the example above.

Environmental variables useful at run-time:

OMP_NUM_THREADS is needed for the thread-level parallelization on the Xeon CPU hosts

% export OMP_NUM_THREADS=4

MIC_USE_2MB_BUFFER greatly improve communication between host and Xeon Phi card

% export MIC_USE_2MB_BUFFER=16K

Very important: when running on clusters equipped with Xeon Phi and Infiniband network hardware (requiring ARMCI_NETWORK=OPENIB), the following env. variable is required, even in the case when the Xeon Phi hardware is not utilized.

% export ARMCI_OPENIB_DEVICE=mlx4_0

How-to: IBM platforms

  • Compiling NWChem on BLUEGENE/L

The following environment variables need to be set

% export NWCHEM_TOP=<your path>/nwchem
% export NWCHEM_TARGET=BGL
% export ARMCI_NETWORK=BGMLMPI
% export BGLSYS_DRIVER=/bgl/BlueLight/ppcfloor
% export BGLSYS_ROOT=${BGLSYS_DRIVER}/bglsys
% export BLRTS_GNU_ROOT=${BGLSYS_DRIVER}/blrts-gnu
% export BGDRIVER=${BGLSYS_DRIVER}
% export BGCOMPILERS=${BLRTS_GNU_ROOT}/bin
% export USE_MPI=y
% export LARGE_FILES=TRUE
% export MPI_LIB=${BGLSYS_ROOT}/lib
% export MPI_INCLUDE=${BGLSYS_ROOT}/include
% export LIBMPI="-lfmpich_.rts -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts"
% export BGMLMPI_INCLUDE=/bgl/BlueLight/ppcfloor/bglsys/include
% export BGMLLIBS=/bgl/BlueLight/ppcfloor/bglsys/lib

To compile, the following commands should be used:

% cd $NWCHEM_TOP/src
% make nwchem_config
% make FC=blrts_xlf >& make.log
  • Compiling NWChem on BLUEGENE/P

The following environment variables need to be set

% export NWCHEM_TARGET=BGP
% export ARMCI_NETWORK=DCMFMPI
% export MSG_COMMS=DCMFMPI
% export USE_MPI=y
% export LARGE_FILES=TRUE
% export BGP_INSTALLDIR=/bgsys/drivers/ppcfloor
% export BGCOMPILERS=/bgsys/drivers/ppcfloor/gnu-linux/bin
% export BGP_RUNTIMEPATH=/bgsys/drivers/ppcfloor/runtime
% export ARMCIDRV=${BGP_INSTALLDIR}
% export BGDRIVER=${ARMCIDRV}
% export MPI_LIB=${BGDRIVER}/comm/lib
% export MPI_INCLUDE=${BGDRIVER}/comm/include
% export LIBMPI="-L${MPI_LIB} -lfmpich_.cnk -lmpich.cnk -ldcmfcoll.cnk -ldcmf.cnk -lpthread -lrt -L${BGP_RUNTIMEPATH}/SPI -lSPI.cna"
% export BGMLMPI_INCLUDE=${MPI_INCLUDE}

To compile, the following commands should be used:

% cd $NWCHEM_TOP/src
% make nwchem_config
% make FC=bgxlf >& make.log
  • Compiling NWChem on BLUEGENE/Q

The following environment variables need to be set

% export NWCHEM_TARGET=BGQ
% export USE_MPI=y
% export USE_MPIF=y
% export USE_MPIF4=y
% export MPI_INCLUDE=/bgsys/drivers/ppcfloor/comm/xl/include
% export LIBMPI=" "
% export BLASOPT="/opt/ibmmath/essl/5.1/lib64/libesslbg.a -llapack -lblas -Wl,-zmuldefs "
% export BLAS_LIB="/opt/ibmmath/essl/5.1/lib64/libesslbg.a -zmuldefs "
% export BLAS_SIZE=4
% export USE_64TO32=y
% set path=(/bgsys/drivers/ppcfloor/gnu-linux/bin/ $path)
% export ARMCI_NETWORK=MPI-TS
% export DISABLE_GAMIRROR=y

To compile, the following commands should be used:

% module load bgq-xl
% make nwchem_config
% make 64_to_32 >& make6t3.log
% make >& make.log

WARNING: This is just a baseline port that we have tested and validated against our QA suite. There is large room for improvement both for serial performance (compiler options) and parallel performance (use of alternative ARMCI_NETWORKs other than MPI-TS)

  • Compiling NWChem on IBM PowerPC architectures

The following environment variables should be set:

% export NWCHEM_TOP=<your path>/nwchem
% export NWCHEM_TARGET=IBM64
% export ARMCI_NETWORK=MPI-MT
% export OBJECT_MODE=64
% export USE_MPI=y
% export LARGE_FILES=TRUE
% export MPI_LIB=/usr/lpp/ppe.poe/lib
% export MPI_INCLUDE=/usr/lpp/ppe.poe/include
% export LIBMPI="-lmpi -lpthreads"

To compile, the following commands should be used:

% cd $NWCHEM_TOP/src
% make nwchem_config
% make FC=xlf >& make.log

How-to: Commodity clusters with Infiniband

Common environmental variables for building and running on most Infiniband clusters are:

  export NWCHEM_TOP=<your path>/nwchem  
  export NWCHEM_TARGET=LINUX64 
  export NWCHEM_MODULES="all"  
  export USE_MPI=y 
  export USE_MPIF=y 
  export USE_MPIF4=y  
  • On Infiniband clusters with the OpenIB software stack, the following environment variables should be defined
  export ARMCI_NETWORK=OPENIB 
  export IB_INCLUDE=<Location of Infiniband libraries>/include  
  • Compiling the code on an Infiniband cluster once all variables are set
  cd $NWCHEM_TOP/src  

  make nwchem_config  

  make >& make.log

How-to: Commodity clusters with Intel Omni-Path

  • On clusters with the Intel Omni-Path network, the following environment variables should be defined
  export ARMCI_NETWORK=MPI-PR

The following setting is needed to avoid run-time errors

  export PSM2_MEMORY=large

More details on this topic discussed a

How-to: Windows Platforms

MingW

The current recommended approach for building a NWChem binary for a Windows platform is to build with the MinGW/Mingw32 environment. MinGW can be installed using a semi-automatic tool mingw-get-setup.exe (http://sourceforge.net/projects/mingw/files/Installer/). A basic MinGW installation is required (Basic Setup), plus pthreads-32, mingw32-gcc-fortran-dev of “All Packages” and the MSYS software.
More detailed MinGW/MSYS installation tips can be found in the following forum discussions

https://nwchemgit.github.io/Special_AWCforum/sp/id5124.html
https://nwchemgit.github.io/Special_AWCforum/sp/id6628.html

Another essential prerequisite step is to install Mpich, which can be found at the following URL

http://www.mpich.org/static/tarballs/1.4.1p1/mpich2-1.4.1p1-win-ia32.msi

Once Mpich is installed, you should copy the installation files to a different location to avoid the failure of the tools compilation. You can use the following command

% cp -rp /c/Program\ Files\ \(x86\)/MPICH2/ ~/

You might want to install Python, too, by using the following installation file

https://www.python.org/ftp/python/2.7.8/python-2.7.8.msi

Next, you need to set the env.

% export NWCHEM_TOP=~/nwchem-6.8  
% export NWCHEM_TARGET=LINUX
% export USE_MPI=y  
% export MPI_LOC=~/MPICH2  
% export MPI_INCLUDE=$MPI_LOC/include  
% export MPI_LIB=$MPI_LOC/lib  
% export LIBMPI="-lfmpich2g -lmpi"  
% export PYTHONVERSION=27  
% export DEPEND_CC=gcc
% export USE_INTERNALBLAS=y
% export NWCHEM_MODULES=all

Then, you can start the compilation by typing

% cd $NWCHEM_TOP/src  
% make nwchem_config  
% make FC=gfortran DEPEND_CC=gcc

MSYS2

https://github.com/msys2/msys2/wiki/MSYS2-installation

pacman -Syuu
pacman -S mingw32/mingw-w64-i686-gcc-fortran
pacman -S mingw32/mingw-w64-i686-python3
pacman -S msys/make

WSL on Windows 10

A good alternative only on Windows 10 is Windows Subsystem for Linux (WSL). This option gives the best performance on Windows when WLS 2 is used. WSL allows you to obtain a functional command line Linux 64-bit NWChem environment, either by compiling the NWChem code from scratch or by using the Ubuntu precompiled NWChem package. Here is a link to the install guide

https://msdn.microsoft.com/en-us/commandline/wsl/install_guide

Once Ubuntu is installed, the quickest method to install NWChem is by fetching the Ubuntu NWChem package by typing

sudo apt install nwchem

General site installation

The build procedures outlined above will allow use of NWChem within the NWChem directory structure. The code will look for the basis set library file in a default place within that directory structure. To install the code in a general, public place (e.g., /usr/local/NWChem) the following procedure can be applied:

  • Determine the local storage path for the install files. (e.g., /usr/local/NWChem).
  • Make directories
mkdir /usr/local/NWChem
mkdir /usr/local/NWChem/bin
mkdir /usr/local/NWChem/data
  • Copy binary
cp $NWCHEM_TOP/bin/${NWCHEM_TARGET}/nwchem /usr/local/NWChem/bin
cd /usr/local/NWChem/bin
chmod 755 nwchem
  • Set links to data files (basis sets, force fields, etc.)
cd $NWCHEM_TOP/src/basis
cp -r libraries /usr/local/NWChem/data
cd $NWCHEM_TOP/src/
cp -r data /usr/local/NWChem
cd $NWCHEM_TOP/src/nwpw
cp -r libraryps /usr/local/NWChem/data
  • Each user will need a .nwchemrc file to point to these default data files. A global one could be put in /usr/local/NWChem/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/data/default.nwchemrc $HOME/.nwchemrc

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

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

Of course users can copy this file instead of making the symbolic link described above and change these defaults at their discretion.

It is can also be useful to use the NWCHEM_BASIS_LIBRARY environment variable when testing a new installation when an old one exists. This will allow you to overwrite the value of nwchem_basis_library in your .nwchemrc file and point to the new basis library. For example:

% export NWCHEM_BASIS_LIBRARY="$NWCHEM/data-5.0/libraries/"

Do not forget the trailing “/”.