Compiling 6.5. Erorr

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Threads 6
Posts 29
1:47:40 AM PDT - Wed, Sep 30th 2015
Hi all users

I use this instruction http://www.attaccalite.com/install-nwchem-6-5-on-linux-mint-17-1-64bit/
And i have trouble
...........

/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(dntmc_input.o): In function `dntmc_input_':
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_input.F:65: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_input.F:69: undefined reference to `ma_pop_stack_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_input.F:77: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_input.F:81: undefined reference to `ma_pop_stack_'
/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(gibbs.o): In function `dntmc_deallocate_arrays_':
gibbs.F:(.text+0x217): undefined reference to `ma_chop_stack_'
/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(gibbs.o): In function `dntmc_restart_post_':
gibbs.F:(.text+0x17e67): undefined reference to `ma_chop_stack_'
/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(gibbs.o): In function `dntmc_allocate_arrays_':
gibbs.F:(.text+0x17ff6): undefined reference to `ma_push_get_'
gibbs.F:(.text+0x180e8): undefined reference to `ma_push_get_'
gibbs.F:(.text+0x1812a): undefined reference to `ma_push_get_'
gibbs.F:(.text+0x18172): undefined reference to `ma_push_get_'
gibbs.F:(.text+0x181be): undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(gibbs.o):gibbs.F:(.text+0x181f1): more undefined references to `ma_push_get_' follow
/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(gibbs.o): In function `dntmc_gibbs_':
gibbs.F:(.text+0x1957d): undefined reference to `ma_chop_stack_'
/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(dntmc_setgeom.o): In function `dntmc_getspecgeom_':
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:201: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:205: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:209: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:217: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:220: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(dntmc_setgeom.o):/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:223: more undefined references to `ma_push_get_' follow
/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(dntmc_setgeom.o): In function `dntmc_getspecgeom_':
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:288: undefined reference to `ma_chop_stack_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:306: undefined reference to `ma_chop_stack_'
/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(dntmc_setgeom.o): In function `dntmc_getspecinfo_':
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:54: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:58: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:63: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:81: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:98: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(dntmc_setgeom.o):/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:465: more undefined references to `ma_push_get_' follow
/MD/azat/NWCHEM-6.5/lib/LINUX64/libdntmc.a(dntmc_setgeom.o): In function `dntmc_setcoords_':
/MD/azat/NWCHEM-6.5/src/dntmc/dntmc_setgeom.F:479: undefined reference to `ma_chop_stack_'
/MD/azat/NWCHEM-6.5/lib/LINUX64/libccca.a(ccca_utils.o): In function `ccca_setup_basis_':
/MD/azat/NWCHEM-6.5/src/ccca/ccca_utils.F:71: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/ccca/ccca_utils.F:97: undefined reference to `ma_pop_stack_'
/MD/azat/NWCHEM-6.5/lib/LINUX64/libnwcutil.a(geom_fragment.o): In function `geom_fragment_':
/MD/azat/NWCHEM-6.5/src/geom/geom_fragment.F:91: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/geom/geom_fragment.F:145: undefined reference to `ma_pop_stack_'
/MD/azat/NWCHEM-6.5/lib/LINUX64/libnwcutil.a(corr_mk_ref.o): In function `corr_mk_ref_':
/MD/azat/NWCHEM-6.5/src/util/corr_mk_ref.F:240: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/util/corr_mk_ref.F:244: undefined reference to `ma_push_get_'
/MD/azat/NWCHEM-6.5/src/util/corr_mk_ref.F:445: undefined reference to `ma_alloc_get_'
/MD/azat/NWCHEM-6.5/src/util/corr_mk_ref.F:449: undefined reference to `ma_alloc_get_'
/MD/azat/NWCHEM-6.5/src/util/corr_mk_ref.F:520: undefined reference to `ma_pop_stack_'
/MD/azat/NWCHEM-6.5/src/util/corr_mk_ref.F:522: undefined reference to `ma_pop_stack_'
collect2: error: ld returned 1 exit status
make: *** [all] Error 1
Edited On 3:01:32 AM PDT - Wed, Sep 30th 2015 by KAZat

Forum Vet
Threads 10
Posts 1626
4:34:44 PM PDT - Wed, Sep 30th 2015
Please follow the instructions at
http://www.nwchem-sw.org/index.php/Compiling_NWChem#How-to:_Linux_platforms

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Threads 6
Posts 29
6:50:57 AM PDT - Thu, Oct 1st 2015
Edoapra, thankyou for you answer. I used your instructions, compiling making, but after long time i have next error
gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/MD/azat/NWCHEM-6.5/src/include -I/MD/azat/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="'/MD/azat/NWCHEM-6.5'" -DNWCHEM_BRANCH="'6.5'" -c -o nwchem.o nwchem.F
gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/MD/azat/NWCHEM-6.5/src/include -I/MD/azat/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="'/MD/azat/NWCHEM-6.5'" -DNWCHEM_BRANCH="'6.5'" -c -o stubs.o stubs.F
gfortran -L/MD/azat/NWCHEM-6.5/lib/LINUX64 -L/MD/azat/NWCHEM-6.5/src/tools/install/lib -o /MD/azat/NWCHEM-6.5/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 -lnwxc -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -llapack -lblas -L/usr/lib64/mpi/gcc/openmpi/lib64 -lmpi_f90 -lmpi_f77 -lmpi -lpthread
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lmpi_f90
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lmpi_f77
collect2: error: ld returned 1 exit status
make: *** [all] Error 1
Im not understand, why he is search in other directory?
declare -x PATH="/usr/lib64/mpi/gcc/openmpi/bin
declare -x MPI_INCLUDE="/usr/lib64/mpi/gcc/openmpi/include"
declare -x MPI_LIB="/usr/lib64/mpi/gcc/openmpi/lib64"
declare -x MPI_LOC="/usr/lib64/mpi/gcc/openmpi"
declare -x LIBMPI="-lmpi_f90 -lmpi_f77 -lmpi -lpthread"
Maybe version 1.7 is not supported?
mpif90: Open MPI 1.7.2 (Language: Fortran)
which mpif90 /usr/lib64/mpi/gcc/openmpi/bin/mpif90
more information
gcc -I/usr/lib64/mpi/gcc/openmpi/include/openmpi/opal/mca/hwloc/hwloc152/hwloc/include -I/usr/lib64/mpi/gcc/openmpi/include/openmpi/opal/mca/event/libevent2019/libevent -I/usr/lib64/mpi/gcc/openmpi/include/openmpi/opal/mca/event/libevent2019/libevent/include -I/usr/lib64/mpi/gcc/openmpi/include -I/usr/lib64/mpi/gcc/openmpi/include/openmpi -pthread -L/usr/lib64/mpi/gcc/openmpi/lib64 -lmpi
gfortran -I/usr/lib64/mpi/gcc/openmpi/include -pthread -I/usr/lib64/mpi/gcc/openmpi/lib64 -L/usr/lib64/mpi/gcc/openmpi/lib64 -lmpi_usempi -lmpi_mpifh -lmpi

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Threads 10
Posts 1626
6:10:28 PM PDT - Thu, Oct 1st 2015
Could you please try the 6.6 beta version since the MPI part of the installation has been simplified?
http://www.nwchem-sw.org/index.php/Compiling_NWChem#How-to:_Linux_platforms

Download instructions at
http://www.nwchem-sw.org/index.php/Download#Download_the_beta_version_of_the_NWChem_6.6_Re...

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Threads 6
Posts 29
6:51:36 AM PDT - Mon, Oct 5th 2015
Install 6.6
Im sorry, I have some problem with openblas
make[1]: Entering directory `/MD/azat/nwchem-6.6/src'
gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -march=native -mtune=native -finline-functions -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/MD/azat/nwchem-6.6/src/include -I/MD/azat/nwchem-6.6/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="'/MD/azat/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o nwchem.o nwchem.F
gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -march=native -mtune=native -finline-functions -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/MD/azat/nwchem-6.6/src/include -I/MD/azat/nwchem-6.6/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="'/MD/azat/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o stubs.o stubs.F
make[1]: Leaving directory `/MD/azat/nwchem-6.6/src'
gfortran -Wl,--export-dynamic -L/MD/azat/nwchem-6.6/lib/LINUX64 -L/MD/azat/nwchem-6.6/src/tools/install/lib -o /MD/azat/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 -lnwxc -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -L/MD/azat/Openblas/lib -lopenblas64 -lnwclapack -lnwcblas -L/usr/lib64/mpi/gcc/openmpi/lib64 -lmpi_usempi -lmpi_mpifh -lmpi -lrt -lm -lnwcutil
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lopenblas64
collect2: error: ld returned 1 exit status
make: *** [all] Error 1
My install steps:
type "make" to detect the CPU automatically.
make DEBUG=1
make install PREFIX=your_installation_directory
Link with libopenblas.a or -lopenblas for shared library.
Or for -lopenblas64 I need download another program? (zypper cant find)
Thank you
Edited On 6:52:58 AM PDT - Mon, Oct 5th 2015 by KAZat

Forum Vet
Threads 10
Posts 1626
9:18:20 AM PDT - Mon, Oct 5th 2015
Kazat
What linux distribution are you using (e.g. Ubuntu, Debian, Centos, RedHat, Suse, etc..)?
Have you installed OpenBlas?
What is the output of the command
ls -l /MD/azat/Openblas/lib

Could you try to install -- as a first baseline -- NWChem with the internal BLAS library by defining USE_INTERNALBLAS=y
?

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Threads 6
Posts 29
4:20:45 AM PDT - Tue, Oct 6th 2015
Im use OpenSuse
///////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
'Yes, Im install OpenBlas, I think ( Sorry, Im new user in Linux)
 last outputs installing openblas'
 cblas_zher2 PASSED THE COMPUTATIONAL TESTS ( 577 CALLS)
cblas_zher2 PASSED THE COMPUTATIONAL TESTS ( 577 CALLS)
cblas_zhpr2 PASSED THE TESTS OF ERROR-EXITS
cblas_zhpr2 PASSED THE COMPUTATIONAL TESTS ( 577 CALLS)
cblas_zhpr2 PASSED THE COMPUTATIONAL TESTS ( 577 CALLS)

END OF TESTS
make[1]: Leaving directory `/MD/azat/xianyi-OpenBLAS-d0c51c4/ctest'
make[1]: Entering directory `/MD/azat/xianyi-OpenBLAS-d0c51c4/exports'
gcc -O2 -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=4 -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\" -DNO_AFFINITY -I.. -shared -o ../libopenblas_core2p-r0.2.14.so \
-Wl,--whole-archive ../libopenblas_core2p-r0.2.14.a -Wl,--no-whole-archive \
-Wl,-soname,libopenblas.so.0 -lm -lpthread -lgfortran -lm -lpthread -lgfortran
gcc -O2 -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=4 -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\" -DNO_AFFINITY -I.. -w -o linktest linktest.c ../libopenblas_core2p-r0.2.14.so -L/usr/lib64/gcc/x86_64-suse-linux/4.8 -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/lib -L/usr/lib64/gcc/x86_64-suse-linux/4.8/../../.. -lgfortran -lm -lquadmath -lm -lc && echo OK.
OK.
rm -f linktest
make[1]: Leaving directory `/MD/azat/xianyi-OpenBLAS-d0c51c4/exports'

OpenBLAS build complete. (BLAS CBLAS LAPACK LAPACKE)

OS ... Linux
Architecture ... x86_64
BINARY ... 64bit
C compiler ... GCC (command line : gcc)
Fortran compiler ... GFORTRAN (command line : gfortran)
Library Name ... libopenblas_core2p-r0.2.14.a (Multi threaded; Max num-threads is 4)

To install the library, you can run "make PREFIX=/path/to/your/installation install".

 linux432:/MD/azat/xianyi-OpenBLAS-d0c51c4 # make install PREFIX=/MD/azat/Openblas
make -j 4 -f Makefile.install install
make[1]: Entering directory `/MD/azat/xianyi-OpenBLAS-d0c51c4'
Generating openblas_config.h in /MD/azat/Openblas/include
Generating f77blas.h in /MD/azat/Openblas/include
Generating cblas.h in /MD/azat/Openblas/include
Copying LAPACKE header files to /MD/azat/Openblas/include
Copying the static library to /MD/azat/Openblas/lib
Copying the shared library to /MD/azat/Openblas/lib
Generating OpenBLASConfig.cmake in /MD/azat/Openblas/lib/cmake/openblas
Install OK!
make[1]: Leaving directory `/MD/azat/xianyi-OpenBLAS-d0c51c4'
/////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
linux432:/MD/azat/xianyi-OpenBLAS-d0c51c4 # ls -l /MD/azat/Openblas/lib
total 36808
drwxr-xr-x 3 root root 4096 Oct 5 16:27 cmake
lrwxrwxrwx 1 root root 28 Oct 5 18:25 libopenblas.a -> libopenblas_core2p-r0.2.14.a
-rw-r--r-- 1 root root 25233830 Oct 5 18:25 libopenblas_core2p-r0.2.14.a
-rwxr-xr-x 1 root root 12449355 Oct 5 18:25 libopenblas_core2p-r0.2.14.so
lrwxrwxrwx 1 root root 29 Oct 5 18:25 libopenblas.so -> libopenblas_core2p-r0.2.14.so
lrwxrwxrwx 1 root root 29 Oct 5 18:25 libopenblas.so.0 -> libopenblas_core2p-r0.2.14.so
////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
Installing with internal BLAS library

/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:804: undefined reference to `PyErr_SetString'
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:809: undefined reference to `PyErr_SetString'
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:814: undefined reference to `PyErr_SetString'
/MD/azat/NWTRY/nwchem-6.6/lib/LINUX64/libnwpython.a(nwchem_wrap.o):/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:818: more undefined references to `PyErr_SetString' follow
/MD/azat/NWTRY/nwchem-6.6/lib/LINUX64/libnwpython.a(nwchem_wrap.o): In function `initnwchem':
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:1725: undefined reference to `Py_InitModule4_64'
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:1726: undefined reference to `PyModule_GetDict'
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:1727: undefined reference to `PyErr_NewException'
/MD/azat/NWTRY/nwchem-6.6/lib/LINUX64/libnwpython.a(nwchem_wrap.o): In function `nwwrap_integers':
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:68: undefined reference to `PyInt_FromLong'
/MD/azat/NWTRY/nwchem-6.6/lib/LINUX64/libnwpython.a(nwchem_wrap.o): In function `nwwrap_doubles':
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:92: undefined reference to `PyFloat_FromDouble'
/MD/azat/NWTRY/nwchem-6.6/lib/LINUX64/libnwpython.a(nwchem_wrap.o): In function `do_pgroup_ngroups':
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:1646: undefined reference to `Py_BuildValue'
/MD/azat/NWTRY/nwchem-6.6/lib/LINUX64/libnwpython.a(nwchem_wrap.o): In function `do_pgroup_groupid':
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:1657: undefined reference to `Py_BuildValue'
/MD/azat/NWTRY/nwchem-6.6/lib/LINUX64/libnwpython.a(nwchem_wrap.o): In function `do_ga_groupid':
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:1668: undefined reference to `Py_BuildValue'
/MD/azat/NWTRY/nwchem-6.6/lib/LINUX64/libnwpython.a(nwchem_wrap.o): In function `do_pgroup_nnodes':
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:1621: undefined reference to `Py_BuildValue'
/MD/azat/NWTRY/nwchem-6.6/lib/LINUX64/libnwpython.a(nwchem_wrap.o): In function `do_pgroup_nodeid':
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:1635: undefined reference to `Py_BuildValue'
/MD/azat/NWTRY/nwchem-6.6/lib/LINUX64/libnwpython.a(nwchem_wrap.o): In function `initnwchem':
/MD/azat/NWTRY/nwchem-6.6/src/python/nwchem_wrap.c:1728: undefined reference to `PyDict_SetItemString'
collect2: error: ld returned 1 exit status
make: *** [all] Error 1
//////////////////////////////////////////////////////////////////////////////////////////////////////////////
Edited On 4:25:14 AM PDT - Tue, Oct 6th 2015 by KAZat

Clicked A Few Times
Threads 6
Posts 29
4:25:41 AM PDT - Tue, Oct 6th 2015
I tried install with UBUNTU instruction, but same problem with openblas

ar r /MD/azat/nwchem-6.6/lib/LINUX64/libccca.a task_ccca.o ccca_utils.o
echo /MD/azat/nwchem-6.6/lib/LINUX64/libccca.a
/MD/azat/nwchem-6.6/lib/LINUX64/libccca.a
make[2]: Leaving directory `/MD/azat/nwchem-6.6/src/ccca'
make[1]: Leaving directory `/MD/azat/nwchem-6.6/src/ccca'
Making libraries in 64to32blas
make[1]: Entering directory `/MD/azat/nwchem-6.6/src/64to32blas'
make[2]: Entering directory `/MD/azat/nwchem-6.6/src/64to32blas'
make[2]: `/MD/azat/nwchem-6.6/lib/LINUX64/lib64to32.a' is up to date.
make[2]: Leaving directory `/MD/azat/nwchem-6.6/src/64to32blas'
make[2]: Entering directory `/MD/azat/nwchem-6.6/src/64to32blas'
make[2]: Leaving directory `/MD/azat/nwchem-6.6/src/64to32blas'
make[1]: Leaving directory `/MD/azat/nwchem-6.6/src/64to32blas'
make: /usr/local/bin/destination/ccp4mg/pythondist//bin/python-config: Command not found
make: /usr/local/bin/destination/ccp4mg/pythondist//bin/python-config: Command not found
make nwchem.o stubs.o
make[1]: Entering directory `/MD/azat/nwchem-6.6/src'
gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -march=native -mtune=native -finline-functions -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/MD/azat/nwchem-6.6/src/include -I/MD/azat/nwchem-6.6/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="'/MD/azat/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o nwchem.o nwchem.F
gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -march=native -mtune=native -finline-functions -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/MD/azat/nwchem-6.6/src/include -I/MD/azat/nwchem-6.6/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="'/MD/azat/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o stubs.o stubs.F
make[1]: Leaving directory `/MD/azat/nwchem-6.6/src'
gfortran -Wl,--export-dynamic -L/MD/azat/nwchem-6.6/lib/LINUX64 -L/MD/azat/nwchem-6.6/src/tools/install/lib -o /MD/azat/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 -lnwxc -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -l64to32 /MD/azat/OpenBlas/lib -lopenblas -lpthread -lrt -lnwclapack -lnwcblas -L/usr/lib64/mpi/gcc/openmpi/lib64 -lmpi_usempi -lmpi_mpifh -lmpi -lrt -lm -lnwcutil
gfortran: error: /MD/azat/OpenBlas/lib: No such file or directory
make: *** [all] Error 1

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9:10:34 AM PDT - Tue, Oct 6th 2015
1)
What is the value toy set for BLASOPT?
I believe you missed the -L

This is the value I would use

BLASOPT="-L/MD/azat/OpenBlas/lib -lopenblas"

2) You are missing python-config
Please install the RPM python-devel.
sudo yum install python-devel

Since you are using OpenSuse, please follow the CentOs instructions, not Ubuntu
Edited On 9:11:01 AM PDT - Tue, Oct 6th 2015 by Edoapra

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9:46:09 AM PDT - Tue, Oct 6th 2015
Then which install I must use? Installing with internal BLAS library, Fedora or Ubuntu?
Edited On 9:58:54 AM PDT - Tue, Oct 6th 2015 by KAZat

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10:08:01 AM PDT - Tue, Oct 6th 2015
I use Fedora and again
make: /usr/local/bin/destination/ccp4mg/pythondist//bin/python-config: Command not found
make: /usr/local/bin/destination/ccp4mg/pythondist//bin/python-config: Command not found
make nwchem.o stubs.o
make[1]: Entering directory `/MD/azat/nwchem-6.6/src'
gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -march=native -mtune=native -finline-functions -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/MD/azat/nwchem-6.6/src/include -I/MD/azat/nwchem-6.6/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="'/MD/azat/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o nwchem.o nwchem.F
gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -march=native -mtune=native -finline-functions -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/MD/azat/nwchem-6.6/src/include -I/MD/azat/nwchem-6.6/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="'/MD/azat/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o stubs.o stubs.F
make[1]: Leaving directory `/MD/azat/nwchem-6.6/src'
gfortran -Wl,--export-dynamic -L/MD/azat/nwchem-6.6/lib/LINUX64 -L/MD/azat/nwchem-6.6/src/tools/install/lib -o /MD/azat/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 -lnwxc -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -l64to32 -L/MD/azat/OpenBlas/lib -lopenblas -lnwclapack -lnwcblas -L/usr/lib64/mpi/gcc/openmpi/lib64 -lmpi_usempi -lmpi_mpifh -lmpi -lrt -lm -lnwcutil
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: cannot find -lopenblas
collect2: error: ld returned 1 exit status
make: *** [all] Error 1
:(

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10:45:31 AM PDT - Tue, Oct 6th 2015
I am sorry but I am not able follow you since you seem to be constantly changing target

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10:59:02 AM PDT - Tue, Oct 6th 2015
Im sorry, I mean that in the last compilation use instructions for Fedora with your advice (BLASOPT="-L and install python-devel), because on site absent instruction for opensuse.
Edited On 10:59:24 AM PDT - Tue, Oct 6th 2015 by KAZat

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11:03:31 AM PDT - Tue, Oct 6th 2015
Quote:KAZat Oct 6th 9:59 am
Im sorry, I mean that in the last compilation use instructions for Fedora with your advice (BLASOPT="-L and install python-devel), because on site absent instruction for opensuse.


They have just been added

http://www.nwchem-sw.org/index.php/Compiling_NWChem#NWChem_6.6_on_OpenSuse_13

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9:19:38 AM PDT - Thu, Oct 8th 2015
ixamax.F:14: note: === vect_analyze_data_refs ===
ixamax.F:14: note: get vectype with 2 units of type integer(kind=8)
ixamax.F:14: note: vectype: vector(2) integer(kind=8)
ixamax.F:14: note: get vectype with 4 units of type integer(kind=4)
ixamax.F:14: note: vectype: vector(4) integer(kind=4)
ixamax.F:14: note: get vectype with 2 units of type integer(kind=8)
ixamax.F:14: note: vectype: vector(2) integer(kind=8)
ixamax.F:14: note: get vectype with 4 units of type integer(kind=4)
ixamax.F:14: note: vectype: vector(4) integer(kind=4)
ixamax.F:14: note: === vect_pattern_recog === ixamax.F:14: note: === vect_analyze_dependences === ixamax.F:14: note: === vect_analyze_data_refs_alignment === ixamax.F:14: note: vect_compute_data_ref_alignment:
ixamax.F:14: note: can't force alignment of ref: *incx_2(D)
ixamax.F:14: note: vect_compute_data_ref_alignment:
ixamax.F:14: note: force alignment of incx4
ixamax.F:14: note: misalign = 0 bytes of ref incx4
ixamax.F:14: note: vect_compute_data_ref_alignment:
ixamax.F:14: note: can't force alignment of ref: *n_6(D)
ixamax.F:14: note: vect_compute_data_ref_alignment:
ixamax.F:14: note: force alignment of n4
ixamax.F:14: note: misalign = 0 bytes of ref n4
ixamax.F:14: note: === vect_analyze_data_ref_accesses === ixamax.F:14: note: not consecutive access _3 = *incx_2(D);

ixamax.F:14: note: not consecutive access incx4 = incx4.0_4;

ixamax.F:14: note: not consecutive access _7 = *n_6(D);

ixamax.F:14: note: not consecutive access n4 = n4.1_8;

ixamax.F:14: note: === vect_analyze_slp === ixamax.F:14: note: Failed to SLP the basic block.
ixamax.F:14: note: not vectorized: failed to find SLP opportunities in basic block.
make[2]: Leaving directory `/MD/azat/nwchem-6.6/src/64to32blas'
make[2]: Entering directory `/MD/azat/nwchem-6.6/src/64to32blas'
Got lock on /MD/azat/nwchem-6.6/lib/LINUX64/lib64to32.lock
ar r /MD/azat/nwchem-6.6/lib/LINUX64/lib64to32.a yscal.o ycopy.o ydot.o ygemm.o ygemv.o iyamax.o ygesv.o ygesvd.o yaxpy.o yspsvx.o yposv.o ysyev.o yger.o yrot.o ylaset.o yswap.o ygebak.o ygebal.o ynrm2.o ylacpy.o ylascl.o ylange.o ytrevc.o yhseqr.o yorghr.o ygehrd.o ysterf.o ylarnv.o ylagtf.o ylagts.o yasum.o ypotri.o ypotrf.o ysygv.o ygeev.o ygeevx.o ifily.o xscal.o xaxpy.o xgemm.o xheev.o xcopy.o xdotc.o ixamax.o
ar: creating /MD/azat/nwchem-6.6/lib/LINUX64/lib64to32.a
echo /MD/azat/nwchem-6.6/lib/LINUX64/lib64to32.a
/MD/azat/nwchem-6.6/lib/LINUX64/lib64to32.a
make[2]: Leaving directory `/MD/azat/nwchem-6.6/src/64to32blas'
make[1]: Leaving directory `/MD/azat/nwchem-6.6/src/64to32blas'
make nwchem.o stubs.o
make[1]: Entering directory `/MD/azat/nwchem-6.6/src'
gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -march=native -mtune=native -finline-functions -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/MD/azat/nwchem-6.6/src/include -I/MD/azat/nwchem-6.6/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="'/MD/azat/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o nwchem.o nwchem.F
gfortran -m64 -ffast-math -Warray-bounds -fdefault-integer-8 -march=native -mtune=native -finline-functions -O2 -g -fno-aggressive-loop-optimizations -g -O -I. -I/MD/azat/nwchem-6.6/src/include -I/MD/azat/nwchem-6.6/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="'/MD/azat/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o stubs.o stubs.F
make[1]: Leaving directory `/MD/azat/nwchem-6.6/src'
gfortran -Wl,--export-dynamic -L/MD/azat/nwchem-6.6/lib/LINUX64 -L/MD/azat/nwchem-6.6/src/tools/install/lib -o /MD/azat/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 -lnwxc -lcafe -lspace -lanalyze -lqhop -lpfft -ldplot -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil -l64to32 -L/MD/azat/Openblas/lib -lopenblas -lpthread -lrt -lnwclapack -lnwcblas -L/usr/lib64/mpi/gcc/openmpi/lib64 -lmpi_usempi -lmpi_mpifh -lmpi -lrt -lm -lnwcutil -lpthread -ldl -lutil -lm -lpython2.7 -lpthread -ldl -lutil -lm -lpython2.7 -Xlinker -export-dynamic
/bin/rm -f nwchem.o stubs.o

I think compile is done. The problem with SLP is normal?

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9:41:33 AM PDT - Thu, Oct 8th 2015
Quote:KAZat Oct 8th 8:19 am


I think compile is done. The problem with SLP is normal?


Why should not it be?


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