Can anybody help me with compile NWCHEM?

Clicked A Few Times

12:47:33 AM PDT - Mon, Sep 28th 2015

install openmpi

shell$ gunzip -c openmpi-1.10.0.tar.gz | tar xf -
shell$ cd openmpi-1.10.0
shell$ ./configure --prefix=/usr/local/openmpi
<...lots of output...>
shell$ make all install

export PATH="....:/usr/local/openmpi/bin"
export LD_LIBRARY_PATH="/usr/local/openmpi/lib"

export NWCHEM_TOP="/diskB/bulat/Downloads/Nwchem-6.5"
export NWCHEM_TARGET="LINUX64"
export NWCHEM_MODULES="all"

export USE_MPI="y"
export USE_MPIF="y"
export USE_MPIF4="y"
export MPI_LIB="/usr/local/openmpi/lib"
export MPI_LOC="/usr/local/openmpi/"
export MPI_INCLUDE="/usr/local/openmpi/include"
export LIBMPI="-lmpi_f90 -lmpi_f77 -lmpi_usempi -lmpi_mpifh -lmpi
-lopen-rte -lopen-pal-ldl -Wl,--export-dynamic -lm -lpthread -lrt -lnsl -lutil"

mpicc -show
gcc -I/usr/local/openmpi/include -pthread -Wl,-rpath -Wl,/usr/local/openmpi/lib
-Wl,--enable-new-dtags -L/usr/local/openmpi/lib -lmpi

mpif90 -show
gfortran -I/usr/local/openmpi/include -pthread -I/usr/local/openmpi/lib -Wl,-rpath -Wl,/usr/local/openmpi/lib
-Wl,--enable-new-dtags -L/usr/local/openmpi/lib -lmpi_usempi -lmpi_mpifh -lmpi

cd $NWCHEM_TOP/src
make nwchem_config

make -C config -f make_nwchem_config NWCHEM_MODULES="all"
echo \# This configuration generated automatically on \

     `hostname` at `date` > nwchem_config.h

echo \# This configuration generated automatically on \

    `hostname` at `date` > NWCHEM_CONFIG

echo "# Request modules from user: all" >> NWCHEM_CONFIG
echo "# Request modules from user: all" >> nwchem_config.h
echo The following subdirectories are built: >> NWCHEM_CONFIG
echo "NW_MODULE_SUBDIRS = NWints atomscf ddscf gradients moints nwdft nwxc rimp2 stepper driver optim cphf ccsd vib mcscf prepar esp hessian selci dplot mp2_grad qhop property solvation nwpw fft analyz nwmd cafe space drdy vscf qmmm qmd etrans tce bq cons perfm dntmc dangchang ccca" >> nwchem_config.h
echo NWints analyz atomscf bq cafe ccca ccsd cons cphf dangchang ddscf dntmc dplot drdy driver esp etrans fft gradients hessian mcscf moints mp2_grad nwdft nwmd nwpw nwxc optim perfm prepar property qhop qmd qmmm rimp2 selci solvation space stepper symmetry tce vib vscf >> NWCHEM_CONFIG
echo "NW_MODULE_LIBS = -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 -lnwxc -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lcons -lperfm -ldntmc -lccca" >> nwchem_config.h
echo corresponding to these libraries: >> NWCHEM_CONFIG
echo "EXCLUDED_SUBDIRS = develop scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia" >> nwchem_config.h
echo -lnwints -lanalyze -lguess -lbq -lcafe -lccca -lccsd -lcons -lcphf -ldangchang -lddscf -ldntmc -ldplot -ldrdy -ldriver -lesp -letrans -lpfft -lgradients -lhessian -lmcscf -lmoints -lmp2 -lnwdft -lnwxc -lnwmd -lnwpw -lofpw -lpaw -lpspw -lband -lnwpwlib -lnwxc -lnwxc -loptim -lperfm -lprepar -lproperty -lqhop -lqmd -lqmmm -lrimp2 -lselci -lsolvation -lspace -lstepper -lnwcutil -ltce -lvib -lvscf >> NWCHEM_CONFIG
echo "CONFIG_LIBS = " >> nwchem_config.h
echo >> NWCHEM_CONFIG
cp census.skeleton ../stubs.F
echo The following directories are excluded from the build: >> NWCHEM_CONFIG
echo develop scfaux rimp2_grad python argos diana uccsdt rism geninterface smd nbo leps lucia >> NWCHEM_CONFIG
echo and these routines will be replaced by stubs: >> NWCHEM_CONFIG
echo argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand >> NWCHEM_CONFIG
echo "No extra configuration libraries were added " >> NWCHEM_CONFIG
for routine in argos argos_input crossing debtest dia_input diana gasdev geninterface jantest jvltest jvltest2 kgdtest leps_energy leps_gradient lucia mc_data mc_driver mc_init mc_main md_data md_driver md_set moints_screen mymc_input mymd_input nbo_input python_input raktest rimp2g rism_input rjhtest smd_input task_fragment_energy task_nbo task_python task_rism task_smd task_smd_dynamics task_smd_energy task_smd_fragment uccsdt uccsdtest urand; do \

  sed s/STUBROUTINE/$routine/g stub.skeleton >> ../stubs.F ; \

done

make FC=gfortran >& make.log

make.log:
test \! -f 64_to_32 -o \! -f 32_to_64 || rm -f 64_to_32 32_to_64
test -d /diskB/bulat/Downloads/Nwchem-6.5/lib/LINUX64 || mkdir -p /diskB/bulat/Downloads/Nwchem-6.5/lib/LINUX64
Making libraries in tools
test -d /diskB/bulat/Downloads/Nwchem-6.5/bin/LINUX64 || mkdir -p /diskB/bulat/Downloads/Nwchem-6.5/bin/LINUX64
./util/util_nwchem_version.bash
which: no svn in (/usr/local/phenix-1.9-1690/build/intel-linux-2.6-x86_64/bin:/diskB/bulat/bin:/usr/local/bin:/usr/bin:/sbin:/usr/sbin:/bin:/usr/games:/usr/X11R6/bin:/usr/bin/X11:/usr/local/openmpi/bin)
make[1]: warning: -jN forced in submake: disabling jobserver mode.

- - Building Parallel Tools ****

make all-recursive
Making all in comex
make[4]: *** No rule to make target `all'. Stop.
make[3]: *** [all-recursive] Error 1
make[2]: *** [all] Error 2
make[1]: *** [build/.libs/libga.a] Error 1
make: *** [libraries] Error 1

thakyou

Clicked A Few Times

2:23:35 AM PDT - Mon, Sep 28th 2015
I missed export CC=gcc export FC=gfortran Now I have make.log: configure: Aggregate Remote Memory Copy Interface (ARMCI) configured as follows: configure: ************************************************************ configure: configure: TARGET=LINUX64 configure: MSG_COMMS=MPI configure: GA_MP_LIBS= -lmpi_f90 -lmpi_f77 -lmpi_usempi -lmpi_mpifh -lmpi -lopen-rte -lopen-pal-ldl -lm -lpthread -lrt -lnsl -lutil configure: GA_MP_LDFLAGS= -L/usr/local/openmpi/lib -Wl,--export-dynamic -L/usr/local/openmpi//lib configure: GA_MP_CPPFLAGS= -I/usr/local/openmpi/include -I/usr/local/openmpi//include configure: ARMCI_NETWORK=MPI_TS configure: ARMCI_NETWORK_LDFLAGS= configure: ARMCI_NETWORK_LIBS= configure: ARMCI_NETWORK_CPPFLAGS= configure: CC=gcc configure: CFLAGS= configure: ARMCI_COPT=-O3 -funroll-loops configure: CPP=gcc -E configure: CPPFLAGS= configure: LDFLAGS= configure: LIBS=-lm configure: FLIBS= configure: AR=ar configure: AR_FLAGS=cru configure: CCAS=gcc configure: CCAS_FLAGS= configure: DEFS=-DHAVE_CONFIG_H configure: SHELL=/bin/sh configure: MPIEXEC=/usr/local/bin/mpirun -n %NP% configure: NPROCS=4 configure: === configuring in comex (/diskB/bulat/Downloads/Nwchem-6.5/src/tools/build/comex) configure: running /bin/sh ../../ga-5-3/comex/configure --disable-option-checking '--prefix=/diskB/bulat/Downloads/Nwchem-6.5/src/tools/install' '--with-tcgmsg' '--with-mpi=-I/usr/local/openmpi/include -L/usr/local/openmpi/lib -lmpi_f90 -lmpi_f77 -lmpi_usempi -lmpi_mpifh -lmpi -lopen-rte -lopen-pal-ldl -Wl,--export-dynamic -lm -lpthread -lrt -lnsl -lutil /usr/local/openmpi/' '--enable-peigs' '--enable-underscoring' '--disable-mpi-tests' '--without-scalapack' '--without-lapack' '--without-blas' '--with-mpi-ts' 'CC=gcc' 'F77=gfortran' 'ARMCI_DEFAULT_SHMMAX_UBOUND=131072' --cache-file=/dev/null --srcdir=../../ga-5-3/comex checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for a thread-safe mkdir -p... /usr/bin/mkdir -p checking for gawk... gawk checking whether make sets $(MAKE)... yes checking whether make supports nested variables... yes checking whether to enable maintainer-specific portions of Makefiles... no configure: Detected VPATH build configure: configure: C compiler configure: checking for style of include used by make... GNU checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for grep that handles long lines and -e... /usr/bin/grep checking for egrep... /usr/bin/grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking minix/config.h usability... no checking minix/config.h presence... no checking for minix/config.h... no checking whether it is safe to define __EXTENSIONS__... yes checking whether a simple C MPI program compiles... yes configure: searching for MPI_TS... checking mpi.h usability... yes checking mpi.h presence... yes checking for mpi.h... yes checking for library containing MPI_Init... no configure: error: test for COMEX_NETWORK=MPI_TS failed configure: error: ../../ga-5-3/comex/configure failed for comex make[1]: * [build/config.status] Error 1 make: *** [libraries] Error 1

Clicked A Few Times

2:44:19 AM PDT - Mon, Sep 28th 2015
add export ARMCI_NETWORK=MPI-TS now make.log again: test \! -f 64_to_32 -o \! -f 32_to_64 \|\| rm -f 64_to_32 32_to_64 test -d /diskB/bulat/Downloads/Nwchem-6.5/lib/LINUX64 \|\| mkdir -p /diskB/bulat/Downloads/Nwchem-6.5/lib/LINUX64 test -d /diskB/bulat/Downloads/Nwchem-6.5/bin/LINUX64 \|\| mkdir -p /diskB/bulat/Downloads/Nwchem-6.5/bin/LINUX64 ./util/util_nwchem_version.bash which: no svn in (/usr/local/phenix-1.9-1690/build/intel-linux-2.6-x86_64/bin:/diskB/bulat/bin:/usr/local/bin:/usr/bin:/sbin:/usr/sbin:/bin:/usr/games:/usr/X11R6/bin:/usr/bin/X11:/usr/local/openmpi/bin) make[1]: warning: -jN forced in submake: disabling jobserver mode. Building Parallel Tools ** make all-recursive Making all in comex make[4]: * No rule to make target `all'. Stop. make[3]: * [all-recursive] Error 1 make[2]: * [all] Error 2 make[1]: * [build/.libs/libga.a] Error 1 make: * [libraries] Error 1 Whats wrong?

Forum Vet

10:08:59 AM PDT - Mon, Sep 28th 2015

I just tried to use Openmpi 1.10.0 and I got an mpipf90 -show output different from yours (and I have eventually manage to build nwchem).
What is the output you get for
mpif90 -showme:version

This is what I am getting

$ mpif90 -showme:version
mpif90: Open MPI 1.10.0 (Language: Fortran)
$ mpif90 -show
ifort -I/home/edo/apps/ompi1100.ifort/include -I/home/edo/apps/ompi1100.ifort/lib -Wl,-rpath -Wl,/home/edo/apps/ompi1100.ifort/lib -Wl,--enable-new-dtags -L/home/edo/apps/ompi1100.ifort/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi

This is what I used to build NWChem. Please notice the LIBMPI value, that seems very different from yours

MPI_INCLUDE=/home/edo/apps/ompi1100.ifort/include
MPI_LIB=/home/edo/apps/ompi1100.ifort/lib
LIBMPI="-lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi"

Clicked A Few Times

12:49:22 AM PDT - Tue, Sep 29th 2015
version is the same: mpif90: Open MPI 1.10.0 (Language: Fortran ) I took your offer LIBMPI, but log is not changed.

Forum Vet

9:55:26 AM PDT - Tue, Sep 29th 2015
Please send me the output of the following commands 1) cd $NWCHEM_TOP/src make FC=gfortran LIBMPI="-lmpi_usempi -lmpi_mpifh -lmpi" MPI_LIB=/usr/local/openmpi/lib link 2) mpif90 -showme 3) mpicc -showme 4) which mpif90

Clicked A Few Times

11:56:23 PM PDT - Tue, Sep 29th 2015
1) make nwchem.o stubs.o make[1]: warning: -jN forced in submake: disabling jobserver mode. gfortran -m64 -ffast-math -Wuninitialized -fdefault-integer-8 -g -g -O -I. -I/diskB/bulat/Downloads/Nwchem-6.5/src/include -I/diskB/bulat/Downloads/Nwchem-6.5/src/tools/install/include -DGFORTRAN -DCHKUNDFLW -DGCC4 -DGCC46 -DEXT_INT -DLINUX -DLINUX64 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/diskB/bulat/Downloads/Nwchem-6.5'" -DNWCHEM_BRANCH="'6.5'" -c -o nwchem.o nwchem.F gfortran -m64 -ffast-math -Wuninitialized -fdefault-integer-8 -g -g -O -I. -I/diskB/bulat/Downloads/Nwchem-6.5/src/include -I/diskB/bulat/Downloads/Nwchem-6.5/src/tools/install/include -DGFORTRAN -DCHKUNDFLW -DGCC4 -DGCC46 -DEXT_INT -DLINUX -DLINUX64 -DPARALLEL_DIAG -DCOMPILATION_DATE="'`date +%a_%b_%d_%H:%M:%S_%Y`'" -DCOMPILATION_DIR="'/diskB/bulat/Downloads/Nwchem-6.5'" -DNWCHEM_BRANCH="'6.5'" -c -o stubs.o stubs.F nwchem.F:3:0: fatal error: errquit.fh: No such file or directory compilation terminated. stubs.F:15:0: fatal error: errquit.fh: No such file or directory compilation terminated. make[1]: * [nwchem.o] Error 1 make[1]: * Waiting for unfinished jobs.... make[1]: * [stubs.o] Error 1 make: * [link] Error 2 2) gfortran -I/usr/local/openmpi/include -pthread -I/usr/local/openmpi/lib -Wl,-rpath -Wl,/usr/local/openmpi/lib -Wl,--enable-new-dtags -L/usr/local/openmpi/lib -lmpi_usempi -lmpi_mpifh -lmpi 3) gcc -I/usr/local/openmpi/include -pthread -Wl,-rpath -Wl,/usr/local/openmpi/lib -Wl,--enable-new-dtags -L/usr/local/openmpi/lib -lmpi 4) /usr/local/bin/mpif90

Forum Vet

4:37:11 PM PDT - Wed, Sep 30th 2015
Could you please try the 6.6 beta version since the MPI part of the installation has been simplified? http://nwchemgit.github.io/index.php/Compiling_NWChem#How-to:_Linux_platforms Download instructions at http://nwchemgit.github.io/index.php/Download#Download_the_beta_version_of_the_NWChem_6.6_Re...

Clicked A Few Times

8:26:24 AM PDT - Thu, Oct 1st 2015
Compiling successfull without any problems and errors! Thanks One question: I ll must compiling realise version in future or I may use beta for work?

Forum Vet

6:10:05 PM PDT - Thu, Oct 1st 2015
Quote:Bulat Oct 1st 7:26 am Compiling successfull without any problems and errors! Thanks One question: I ll must compiling realise version in future or I may use beta for work? I would suggest you to check some of the results your obtain from the beta version with run from the release (it will be out soon,m anyway) Another good (= suggested) practice is to run the QA tests as explained in the file $NWCHEM_TOP/QA/HOW-TO-RUN-TESTS

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