| 2:39:27 PM PDT - Mon, Apr 17th 2017 |
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Problem linking python
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I'm having problems linking python into NWChem. I'm following the instructions for setting the environment variables. Here's a script for compiling:
- !/bin/bash
export USE_MPI="y"
- export USE_PYTHONCONFIG="Y"
export PYTHONVERSION="2.7"
export PYTHONHOME="/scr_haswell/swsides/opt/contrib-qmcpack/Python-2.7.13-sersh"
export PYTHONLIBTYPE="so"
export PYTHONCONFIGDIR="config/../.."
export BLASOPT="-llapack -lblas"
export BLAS_SIZE="8"
export USE_ARUR="n"
export NWCHEM_TOP="/scr_haswell/swsides/directpkgs/nwchem-6.6"
export NWCHEM_TARGET="LINUX64"
echo ""
echo "-------------------------------------------------------------"
echo "Setup environment settings"
echo ""
echo "NWCHEM_TOP =$NWCHEM_TOP"
echo "NWCHEM_TARGET=$NWCHEM_TARGET"
echo "-------------------------------------------------------------"
echo ""
echo "Running make nwchem_config..."
echo ""
make nwchem_config NWCHEM_MODULES="all python" > test-config.log
sleep 2
echo ""
echo "Running make"
echo ""
make -j 8
========================================================================
The error is:
make nwchem.o stubs.o
make[1]: Entering directory `/scr_haswell/swsides/directpkgs/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/scr_haswell/swsides/directpkgs/nwchem-6.6/src/include -I/scr_haswell/swsides/directpkgs/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="'/scr_haswell/swsides/directpkgs/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/scr_haswell/swsides/directpkgs/nwchem-6.6/src/include -I/scr_haswell/swsides/directpkgs/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="'/scr_haswell/swsides/directpkgs/nwchem-6.6'" -DNWCHEM_BRANCH="'6.6'" -c -o stubs.o stubs.F
make[1]: Leaving directory `/scr_haswell/swsides/directpkgs/nwchem-6.6/src'
gfortran -Wl,--export-dynamic -L/scr_haswell/swsides/directpkgs/nwchem-6.6/lib/LINUX64 -L/scr_haswell/swsides/directpkgs/nwchem-6.6/src/tools/install/lib -o /scr_haswell/swsides/directpkgs/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 -lnwpython -ldrdy -lvscf -lqmmm -lqmd -letrans -lpspw -ltce -lbq -lmm -lcons -lperfm -ldntmc -lccca -lnwcutil -lga -larmci -lpeigs -lperfm -lcons -lbq -lnwcutil /scr_haswell/swsides/opt/contrib-qmcpack/Python-2.7.13-sersh/lib/python2.7/config/../../libpython2.7.so -llapack -lblas -lnwclapack -lnwcblas -L/scr_haswell/swsides/opt/contrib-qmcpack/mpich-3.1.4-shared/lib -lmpifort -lmpi -lrt -lm -lpthread -lnwcutil -lpython2.7 -lpthread -ldl -lutil -lm
/usr/bin/ld: cannot find -lpython2.7
collect2: error: ld returned 1 exit status
make: *** [all] Error 1
I can adjust the
/scr_haswell/swsides/opt/contrib-qmcpack/Python-2.7.13-sersh/lib/python2.7/config/../../libpython2.7.so
line to
-L /scr_haswell/swsides/opt/contrib-qmcpack/Python-2.7.13-sersh/lib (where the shared lib actually is)
and this will work. But the entire logic of the make files is broken. Is there a fix or a patch? I've got an automatic build system that need to use the in-place
build system of the application and I can't edit make files by hand.
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