Add additional libraries in linking

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8:06:53 AM PDT - Fri, Oct 9th 2015
Dear Developers I am compiling nwchem-6.6. In the last linking step, it stopped with an error message like "//lib/x86_64-linux-gnu/libz.so.1: error adding symbols: DSO missing from command line". it seems the linkage requires -lz. I think I need to modify LDFLAGS by adding this missing library, could you please point out the easiest way to do it? Or is there any other means? Thanks! best wishes john

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8:46:31 AM PDT - Fri, Oct 9th 2015
Could you please send 1) env. variables you have set 2) full output of the command cd $NWCHEM_TOP/src make link (or make FC=... link) 3) What linux distribution and version are you using?

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11:19:58 AM PDT - Fri, Oct 9th 2015
Quote:Edoapra Oct 9th 3:46 pm Could you please send 1) env. variables you have set 2) full output of the command cd $NWCHEM_TOP/src make link (or make FC=... link) 3) What linux distribution and version are you using? Here they are export CC=icc export FC=ifort export CXX=icpc export LARGE_FILES=TRUE export USE_NOFSCHECK=TRUE export LIB_DEFINES="-DDFLT_TOT_MEM=16777216" export CCSDTQ=y export CCSDTLR=y export MRCC_THEORY=TRUE export NWCHEM_TOP=/opt/apps/nwchem-6.6 export NWCHEM_TARGET=LINUX64 export NWCHEM_MODULES="all python" export USE_MPI=y export USE_MPIF=y export USE_MPIF4=y export MPI_LOC=/opt/apps//openmpi-1.10.0-intel-15.0.4-i4 export MPI_LIB=$MPI_LOC/lib export MPI_INCLUDE=$MPI_LOC/include export LIBMPI="-Wl,-rpath -Wl,/opt/apps//openmpi-1.10.0-intel-15.0.4-i4/lib -Wl,--enable-new-dtags -L/opt/apps/openmpi-1.10.0-intel-15.0.4-i4/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lpthread" export MSG_COMMS=MPI export ARMCI_NETWORK=OPENIB export IB_INCLUDE=/usr/include/infiniband export IB_LIB=/usr/lib export IB_LIB_NAME="-libverbs -libumad -lpthread" export PYTHONHOME=/usr export PYTHONVERSION=2.7 export PYTHON_EXE=/usr/bin/python export PYTHONCONFIGDIR=config-x86_64-linux-gnu export MKLROOT=/opt/apps/intel/Xe2015Update5/composer_xe_2015.5.223/mkl export MKLINCLUDE=/opt/apps/intel/Xe2015Update5/composer_xe_2015.5.223/mkl/include export HAS_BLAS=y export BLASOPT="$MKLROOT/lib/intel64/libmkl_scalapack_ilp64.a $MKLROOT/lib/intel64/libmkl_lapack95_ilp64.a $MKLROOT/lib/intel64/libmkl_blas95_ilp64.a -Wl,--start-group $MKLROOT/lib/intel64/libmkl_cdft_core.a $MKLROOT/lib/intel64/libmkl_intel_ilp64.a $MKLROOT/lib/intel64/libmkl_core.a $MKLROOT/lib/intel64/libmkl_sequential.a -Wl,--end-group $MKLROOT/lib/intel64/libmkl_blacs_intelmpi_ilp64.a -lpthread -lm" export BLAS_SIZE=8 export BLAS_I8=yes export SCALAPACK_SIZE=8 export SCALAPACK_LIB="$BLASOPT" export USE_SCALAPACK=y export LAPACK_SIZE=8 export LAPACK_LIB="$BLASOPT" Here is the linking part with error message ifort -i8 -align -fpp -qopt-report-file=stderr -fimf-arch-consistency=true -finline-limit=250 -O2 -g -fp-model source -Wl,--export-dynamic -L/opt/apps/nwchem-6.6/lib/LINUX64 -L/opt/apps/nwchem-6.6/src/tools/install/lib -o /opt/apps/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 /usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.a /opt/apps/intel/Xe2015Update5/composer_xe_2015.5.223/mkl/lib/intel64/libmkl_scalapack_ilp64.a /opt/apps/intel/Xe2015Update5/composer_xe_2015.5.223/mkl/lib/intel64/libmkl_lapack95_ilp64.a /opt/apps/intel/Xe2015Update5/composer_xe_2015.5.223/mkl/lib/intel64/libmkl_blas95_ilp64.a -Wl,--start-group /opt/apps/intel/Xe2015Update5/composer_xe_2015.5.223/mkl/lib/intel64/libmkl_cdft_core.a /opt/apps/intel/Xe2015Update5/composer_xe_2015.5.223/mkl/lib/intel64/libmkl_intel_ilp64.a /opt/apps/intel/Xe2015Update5/composer_xe_2015.5.223/mkl/lib/intel64/libmkl_core.a /opt/apps/intel/Xe2015Update5/composer_xe_2015.5.223/mkl/lib/intel64/libmkl_sequential.a -Wl,--end-group /opt/apps/intel/Xe2015Update5/composer_xe_2015.5.223/mkl/lib/intel64/libmkl_blacs_intelmpi_ilp64.a -lpthread -lm -lnwcblas -L/opt/apps/openmpi-1.10.0-intel-15.0.4-i4/lib -Wl,-rpath -Wl,/opt/apps/openmpi/openmpi-1.10.0-intel-15.0.4-i4/lib -Wl,--enable-new-dtags -L/opt/apps/openmpi-1.10.0-intel-15.0.4-i4/lib -lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lpthread -libverbs -libumad -lpthread -L/usr/lib -lrt -lnwcutil -lpython2.7 -lpthread -ldl -lutil -lm /usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.a(posixmodule.o): In function `posix_tmpnam': (.text.unlikely+0xff8): warning: the use of `tmpnam_r' is dangerous, better use `mkstemp' /usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.a(posixmodule.o): In function `posix_tempnam': (.text.unlikely+0xf01): warning: the use of `tempnam' is dangerous, better use `mkstemp' ld: /usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.a(zlibmodule.o): undefined reference to symbol 'inflateInit2_' //lib/x86_64-linux-gnu/libz.so.1: error adding symbols: DSO missing from command line If I manually add -lz to the last link part, then the compilation will finish with no error. But I cannot find the nwchem executable. the linux version is 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt11-1+deb8u3 (2015-08-04) x86_64 GNU/Linux

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11:35:00 AM PDT - Fri, Oct 9th 2015
Quote:Jtravers Oct 9th 3:06 pm Dear Developers I am compiling nwchem-6.6. In the last linking step, it stopped with an error message like "//lib/x86_64-linux-gnu/libz.so.1: error adding symbols: DSO missing from command line". it seems the linkage requires -lz. I think I need to modify LDFLAGS by adding this missing library, could you please point out the easiest way to do it? Or is there any other means? Thanks! best wishes john

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12:31:08 PM PDT - Fri, Oct 9th 2015

Could you please try the following


unset PYTHONCONFIGDIR
export USE_PYTHONCONFIG=y

This is going to work only if your Python installation (under the /usr tree, I presume) has python-config.
If python-config is not present, you will need to install python-dev by typing on your debian box


sudo apt-get install python-dev

You would need to that location of python-config listed in your PATH
Please let me know if this solution works for you.

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2:40:43 PM PDT - Fri, Oct 9th 2015
Quote:Edoapra Oct 9th 7:31 pm Could you please try the following unset PYTHONCONFIGDIR export USE_PYTHONCONFIG=y This is going to work only if your Python installation (under the `/usr` tree, I presume) has `python-config`. If python-config is not present, you will need to install `python-dev` by typing on your debian box sudo apt-get install python-dev You would need to that location of `python-config` listed in your `PATH` Please let me know if this solution works for you. It did not work and python-config was installed at /usr/bin

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3:44:36 PM PDT - Fri, Oct 9th 2015
Could please post 1) full output of the command (sorry for asking again, but I would like to know when happens in your case when `USE_PYTHONCONFIG=y` is defined) cd $NWCHEM_TOP/src make link (or make FC=... link) 2) output of the command `python-config --libs` PS The recipe I gave you works for me on Debian ... I would like to understand what is causing your failure.

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11:07:42 AM PDT - Sat, Oct 10th 2015
Quote:Edoapra Oct 9th 10:44 pm Could please post 1) full output of the command (sorry for asking again, but I would like to know when happens in your case when `USE_PYTHONCONFIG=y` is defined) cd $NWCHEM_TOP/src make link (or make FC=... link) 2) output of the command `python-config --libs` PS The recipe I gave you works for me on Debian ... I would like to understand what is causing your failure. Now It worked with your recipe. (sorry, i had a typo in exporting some of the env variables. Thanks!

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