NWChem Compilation Issues in the Cluster Solved

From NWChem

Viewed 207 times, With a total of 0 Posts
Jump to: navigation, search

Just Got Here
Threads 1
Posts 1
Dear all:

I'm new in NWCHEM and a little bit struggling in compiling for a couple weeks.
This is my environment variable:
Quote:username
export NWCHEM_TOP="/home/tan294/NWCHEM6668/nwchem-6.8"
export NWCHEM_TARGET="LINUX64"
export ARMCI_NETWORK="MPI-PR"
export USE_MPI="y"
export USE_MPIF="y"
export USE_MPIF4="y"

export PATH="gfortran -I/apps/cent7/intel/impi/2017.1.132/intel64/include/gfortran/4.8.0 -I/apps/cent7/intel/impi/2017.1.132/intel64/include -L/apps/cent7/intel/impi/2\
017.1.132/intel64/lib/release_mt -L/apps/cent7/intel/impi/2017.1.132/intel64/lib -Xlinker --enable-new-dtags -Xlinker -rpath -Xlinker /apps/cent7/intel/impi/2017.1.132\
/intel64/lib/release_mt -Xlinker -rpath -Xlinker /apps/cent7/intel/impi/2017.1.132/intel64/lib -Xlinker -rpath -Xlinker /opt/intel/mpi-rt/2017.0.0/intel64/lib/release_\
mt -Xlinker -rpath -Xlinker /opt/intel/mpi-rt/2017.0.0/intel64/lib -lmpifort -lmpi -lmpigi -ldl -lrt -lpthread":$PATH

  1. export MPI_LOC="/apps/cent7/intel/impi/2017.1.132/intel64"
  2. export PATH="$MPI_LOC/bin":$PATH

export PATH="/apps/cent7/intel/impi/2017.1.132/intel64/include/gfortran/4.8.0":$PATH
export PATH="/apps/cent7/intel/impi/2017.1.132/intel64/include":$PATH
export PATH="/apps/cent7/intel/impi/2017.1.132/intel64/lib/release_mt":$PATH
export PATH="/apps/cent7/intel/impi/2017.1.132/intel64/lib":$PATH
export PATH="/opt/intel/mpi-rt/2017.0.0/intel64/lib/release_mt":$PATH
export PATH="/opt/intel/mpi-rt/2017.0.0/intel64/lib":$PATH
export PATH="/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/bin/intel64/ifort":$PATH

export LIBMPI="-lmpifort -lmpi -lmpigi -ldl -lrt -lpthread"

export LD_LIBRARY_PATH=$MPI_LOC/lib:$LD_LIBRARY_PATH

export NWCHEM_MODULES="all"
export USE_NOIO="TRUE"

export PATH=/home/tan294/anaconda2/bin:$PATH
export USE_PYTHONCONFIG=Y
export PYTHONVERSION=2.7


And this is the final few lines of the make.log file:

Quote:username
make[1]: Leaving directory `/home/tan294/NWCHEM68/nwchem-6.8/src'
ifort -i8 -align -fpp -qopt-report-file=stderr -qno-openmp -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -L/home/tan294/NWCHEM68/nwchem-6.8/\
lib/LINUX64 -L/home/tan294/NWCHEM68/nwchem-6.8/src/tools/install/lib -o /home/tan294/NWCHEM68/nwchem-6.8/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 -lsolvatio\
n -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 -ldimqm -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -L/apps/cent7/intel/compilers_and_libraries_2017.1.132/\
linux/mkl/lib/intel64 -Wl,--no-as-needed -lmkl_scalapack_ilp64 -lmkl_cdft_core -lmkl_gf_ilp64 -lmkl_gnu_thread -lmkl_core -lmkl_blacs_openmpi_ilp64 -lgomp -lpthread -l\
m -ldl -lnwclapack -lnwcblas -L/apps/cent7/intel/impi/2017.1.132/intel64/lib/release_mt -L/apps/cent7/intel/impi/2017.1.132/intel64/lib -lmpifort -lmpi -lmpigi -ld\
l -lrt -lpthread -lpthread
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_comm_null'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `MPI_Comm_f2c'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_double'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_dblcplex'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_packed'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_op_max'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_op_maxloc'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_op_min'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_byte'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_comm_world'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_float'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_request_null'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_cplex'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_unsigned_short'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `MPI_Comm_c2f'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_double_int'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_int'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_long_long_int'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_integer'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_dblprec'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `MPI_Type_f2c'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `MPI_Op_f2c'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_op_sum'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `MPI_Op_c2f'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `ompi_mpi_real'
/apps/cent7/intel/compilers_and_libraries_2017.1.132/linux/mkl/lib/intel64/libmkl_blacs_openmpi_ilp64.so: undefined reference to `MPI_Type_c2f'
/usr/bin/ld: link errors found, deleting executable `/home/tan294/NWCHEM68/nwchem-6.8/bin/LINUX64/nwchem'
/usr/bin/sha1sum: /home/tan294/NWCHEM68/nwchem-6.8/bin/LINUX64/nwchem: No such file or directory
make: *** [all] Error 1


I referred to the intel MKL_HOME setting website and my problem is solve now. Thanks!
https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor

tan294
Edited On 9:36:07 AM PST - Mon, Dec 2nd 2019 by Tan294


Forum >> NWChem's corner >> Compiling NWChem



Who's here now Members 0 Guests 1 Bots/Crawler 0


AWC's: 2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC