I have made the changes you have suggested, and everything runs smoothly (i.e. no discernable error messages). Here is the setup script I used, with your modifications for clarification purposes:
!#/bin/bash
export NWCHEM_TARGET=LINUX64
export NWCHEM_TOP=/work/zacharyw/recompile_nwchem6_6/nwchem-6.6
export ARMCI_NETWORK=OPENIB
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export PATH=/usr/local/intel-2015.2/impi/5.0.3.048/bin64/mpif90:$PATH #location of 'which mpif90'
export PYTHONHOME=/usr/local/python #defined in manual online
export PYTHONVERSION=2.7
export USE_PYTHONCONFIG=y
export USE_64TO32=y
export ARMCI_OPENIB_DEVICE=mlx4_0
export IB_HOME="/usr"
export IB_INCLUDE="$IB_HOME/include/infiniband"
export IB_LIB="$IB_HOME/lib64"
export IB_LIB_NAME="-libverbs -libumad -lpthread -lrt"
export MIC_LIBRARY_PATH=/usr/linux-k1om-4.7/linux-k1om/lib64:$MIC_LIBRARY_PATH
export MIC_LD_LIBRARY_PATH=/usr/linux-k1om-4.7/linux-k1om/lib64:$MIC_LD_LIBRARY_PATH
export ARMCI_OPENIB_DEVICE=mlx4_0
export USE_MPI=y
export USE_MPIF=y
export USE_MPIF4=y
export MKLROOT=/usr/local/intel-2017/compilers_and_libraries_2017.0.098/linux/mkl
export USE_OPENMP=1
export SCALAPACK="-mkl -qopenmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64"
export BLASOPT="-mkl -qopenmp"
export SCALAPACK_SIZE=4
export BLAS_SIZE=8
export OMP_NUM_THREADS=4
export MIC_USE_2MB_BUFFER=16k
export USE_INTERNALBLAS=y
unset USE_F90_ALLOCATABLE
unset USE_FASTMEM
cd $NWCHEM_TOP/src
make nwchem_config NWCHEM_MODULES="all"
make FC=ifort link
cd $NWCHEM_TOP/src/64to32blas
make clean
make FC=ifort
cd ../tools
make clean
make FC=ifort
cd ..
make FC=ifort link
The last few lines of output looks something like:
Libraries have been installed in:
/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the `-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the `LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the `LD_RUN_PATH' environment variable
during linking
- use the `-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to `/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
/bin/mkdir -p '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin'
/bin/sh ./libtool --mode=install /usr/bin/install -c global/trace/adjust.x global/trace/collisions.x '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin'
libtool: install: /usr/bin/install -c global/trace/adjust.x /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin/adjust.x
libtool: install: /usr/bin/install -c global/trace/collisions.x /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin/collisions.x
/bin/mkdir -p '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin'
/usr/bin/install -c tools/ga-config '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/bin'
/bin/mkdir -p '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include'
/usr/bin/install -c -m 644 ../ga-5-4/ma/error.h ../ga-5-4/ma/macdecls.h ../ga-5-4/ma/macommon.h ../ga-5-4/ma/maf2c.fh ma/mafdecls.fh ma/matypes.h ../ga-5-4/ma/scope.h ../ga-5-4/ma/string-util.h ../ga-5-4/ma/table.h ../ga-5-4/global/src/gacommon.h ../ga-5-4/global/src/ga.h global/src/global.fh ../ga-5-4/global/src/ga-papi.h ../ga-5-4/global/src/ga-mpi.h ../ga-5-4/global/src/ga-mpi.fh ../ga-5-4/pario/dra/dra.fh ../ga-5-4/pario/dra/dra.h ../ga-5-4/pario/eaf/eaf.fh ../ga-5-4/pario/eaf/eaf.h ../ga-5-4/pario/elio/chemio.h ../ga-5-4/pario/elio/elio.h ../ga-5-4/pario/sf/coms.h ../ga-5-4/pario/sf/sf.fh ../ga-5-4/pario/sf/sf.h gaf2c/typesf2c.h gaf2c/farg.h ../ga-5-4/tcgmsg/tcgmsg.fh ../ga-5-4/tcgmsg/tcgmsg.h ../ga-5-4/tcgmsg/tcgmsg-mpi/msgtypesc.h ../ga-5-4/tcgmsg/tcgmsg-mpi/msgtypesf.h '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include'
/bin/mkdir -p '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include'
/usr/bin/install -c -m 644 global/src/ga-wapi.h '/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include'
make[4]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/build'
make[3]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/build'
make[2]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/build'
make[1]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/build'
+ cd ..
+ make FC=ifort link
make nwchem.o stubs.o
make[1]: Entering directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -I. -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/work/zacharyw/recompile_nwchem6_6/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o nwchem.o nwchem.F
ifort -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -I. -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/include -I/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/include -DEXT_INT -DLINUX -DLINUX64 -DUSE_OPENMP -DIFCV8 -DIFCLINUX -DSCALAPACK -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/work/zacharyw/recompile_nwchem6_6/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o stubs.o stubs.F
make[1]: Leaving directory `/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -qopenmp -qopt-report-phase=openmp -qno-openmp-offload -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -L/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/lib/LINUX64 -L/work/zacharyw/recompile_nwchem6_6/nwchem-6.6/src/tools/install/lib -o /work/zacharyw/recompile_nwchem6_6/nwchem-6.6/bin/LINUX64/nwchem nwchem.o stubs.o -lnwctask -lccsd -lmcscf -lselci -lmp2 -lmoints -lstepper -ldriver -loptim -lnwdft -lgradients -lcphf -lesp -lddscf -ldangchang -lguess -lhessian -lvib -lnwcutil -lrimp2 -lproperty -lsolvation -lnwints -lprepar -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -mkl -qopenmp -lmkl_scalapack_ilp64 -lmkl_blacs_intelmpi_ilp64 -l64to32 -mkl -qopenmp -lnwclapack -lnwcblas -L/usr/local/intel-2015.2//impi/5.0.3.048/intel64/lib/release_mt -L/usr/local/intel-2015.2//impi/5.0.3.048/intel64/lib -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread -libverbs -libumad -lpthread -lrt -L/usr/lib64 -lrt -lm -lpthread
This leads us to assume that, providing my corrections to 'BLAS_SIZE' env variable and omitting references to openMPI, the python env variables I used in earlier setup scripts are the issue. How should I proceed?
Curiously, there is no specific reference to nwchem-6.6 in my /usr/local directory. I was going to see if the executable linked successfully using 'ldd' command; but as the directory is not present this is not possible. There is, however, a directory to nwchem-6.5 (containing an executable that is not completely linked), as well as a 'nwchem' symbolic link to the path '/usr/local/server/x86_64-RedHat6/nwchem' which also contains an executable that is not completely linked. I find this odd; any thoughts?
Thanks
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