Dear All,
I am trying to install deal.ii-9.0.1 using spack v.15 on our HPC cluster
(Centos 7 OS). The installation works fine. Most of my code compiles
without any issues, but when compiling targets using Boost serilization
functionalities, I get the following linking errors:
iwtm020h@emmy1:/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build$ make
VERBOSE=1
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake
-S/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac
-B/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build --check-build-system
CMakeFiles/Makefile.cmake 0
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake
-E cmake_progress_start
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/CMakeFiles
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/CMakeFiles/progress.marks
make -f CMakeFiles/Makefile2 all
make[1]: Entering directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
make -f CMakeFiles/mncfrac.dir/build.make CMakeFiles/mncfrac.dir/depend
make[2]: Entering directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
cd /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build &&
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake
-E cmake_depends "Unix Makefiles"
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/CMakeFiles/mncfrac.dir/DependInfo.cmake
--color=
make[2]: Leaving directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
make -f CMakeFiles/mncfrac.dir/build.make CMakeFiles/mncfrac.dir/build
make[2]: Entering directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
make[2]: Nothing to be done for `CMakeFiles/mncfrac.dir/build'.
make[2]: Leaving directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
[ 54%] Built target mncfrac
make -f CMakeFiles/mncfracture.dir/build.make
CMakeFiles/mncfracture.dir/depend
make[2]: Entering directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
cd /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build &&
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake
-E cmake_depends "Unix Makefiles"
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/CMakeFiles/mncfracture.dir/DependInfo.cmake
--color=
make[2]: Leaving directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
make -f CMakeFiles/mncfracture.dir/build.make
CMakeFiles/mncfracture.dir/build
make[2]: Entering directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
make[2]: Nothing to be done for `CMakeFiles/mncfracture.dir/build'.
make[2]: Leaving directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
[ 63%] Built target mncfracture
make -f variants/CMakeFiles/cookmembranedistributed.dir/build.make
variants/CMakeFiles/cookmembranedistributed.dir/depend
make[2]: Entering directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
cd /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build &&
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake
-E cmake_depends "Unix Makefiles"
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/variants
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/variants
/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/variants/CMakeFiles/cookmembranedistributed.dir/DependInfo.cmake
--color=
make[2]: Leaving directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
make -f variants/CMakeFiles/cookmembranedistributed.dir/build.make
variants/CMakeFiles/cookmembranedistributed.dir/build
make[2]: Entering directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
[ 68%] Linking CXX executable cookmembranedistributed
cd /home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build/variants &&
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/cmake-3.17.3-yp7x4tfykdwkolbguxb2nbd46ktt5e6h/bin/cmake
-E cmake_link_script CMakeFiles/cookmembranedistributed.dir/link.txt
--verbose=1
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/openmpi-3.1.6-6d7xi6tah53fltt3wtens3wt6zoaysr7/bin/mpic++
-rdynamic -rdynamic -fuse-ld=gold -ggdb
CMakeFiles/cookmembranedistributed.dir/cook_membrane_distributed/CookMembraneDistributed.cc.o
CMakeFiles/cookmembranedistributed.dir/cook_membrane_distributed/CookMembraneDistributedMain.cc.o
-o cookmembranedistributed
-Wl,-rpath,/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/dealii-9.0.1-dealii-901-dev-mzkyyfiqp2zxw4ip4cuyx7ok6ym57bp7/lib/libdeal_II.g.so.9.0.1
../libmncfrac.so
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/dealii-9.0.1-dealii-901-dev-mzkyyfiqp2zxw4ip4cuyx7ok6ym57bp7/lib/libdeal_II.g.so.9.0.1
-ltbb_debug -lboost_iostreams-mt -lboost_serialization-mt -lboost_system-mt
-lboost_thread-mt -lboost_regex-mt -lboost_chrono-mt -lboost_date_time-mt
-lboost_atomic-mt -lmuelu-adapters -lmuelu-interface -lmuelu -lifpack2
-lanasazitpetra -lModeLaplace -lanasaziepetra -lanasazi -lmapvarlib
-lsuplib -lsuplib_c -lsuplib_cpp -lsupes -laprepro_lib -lio_info_lib
-lIonit -lIotr -lIohb -lIogs -lIogn -lIovs -lIoexo_fac -lIopx -lIofx -lIoex
-lIoss -lnemesis -lexoIIv2for32 -lexodus_for -lexodus -lamesos2
-lbelosxpetra -lbelostpetra -lbelosepetra -lbelos -lml -lifpack -lzoltan2
-lamesos -lgaleri-xpetra -lgaleri-epetra -laztecoo -lxpetra-sup -lxpetra
-ltrilinosss -ltpetraext -ltpetrainout -ltpetra -lkokkostsqr
-ltpetraclassiclinalg -ltpetraclassicnodeapi -ltpetraclassic -lepetraext
-ltriutils -lzoltan -lepetra -lsacado -lkokkoskernels -lteuchoskokkoscomm
-lteuchoskokkoscompat -lteuchosremainder -lteuchosnumerics -lteuchoscomm
-lteuchosparameterlist -lteuchosparser -lteuchoscore -lkokkosalgorithms
-lkokkoscontainers -lkokkoscore -lgtest -lmatio -ldmumps -lmumps_common
-lpord -lumfpack -lcholmod -lccolamd -lcolamd -lcamd -lsuitesparseconfig
-lamd -lrt -ladolc -lparpack -larpack -lassimp -lgsl -lgslcblas -lmuparser
-lnetcdf_c++ -lnetcdf -lTKBO -lTKBool -lTKBRep -lTKernel -lTKFeat
-lTKFillet -lTKG2d -lTKG3d -lTKGeomAlgo -lTKGeomBase -lTKHLR -lTKIGES
-lTKMath -lTKMesh -lTKOffset -lTKPrim -lTKShHealing -lTKSTEP -lTKSTEPAttr
-lTKSTEPBase -lTKSTEP209 -lTKSTL -lTKTopAlgo -lTKXSBase -lp4est -lsc
-lscalapack -lslepc -lpetsc -lHYPRE -lsuperlu_dist -lopenblas
-lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5 -lparmetis -lmetis -lz
-lmpi_usempif08 -lmpi_usempi_ignore_tkr -lmpi_mpifh -lmpi -lgfortran -lm
-lpthread -lquadmath -ldl -lsundials_idas -lsundials_arkode
-lsundials_kinsol -lsundials_nvecserial -lsundials_nvecparallel
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/boost-1.73.0-qq6dfhn4upamtqfmtvqy5pe4obuy6wkx/include/boost/archive/binary_iarchive_impl.hpp:58:
error: undefined reference to
'boost::archive::basic_binary_iarchive<boost::archive::binary_iarchive>::load_override(boost::archive::class_name_type&)'
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/boost-1.73.0-qq6dfhn4upamtqfmtvqy5pe4obuy6wkx/include/boost/archive/detail/oserializer.hpp:93:
error: undefined reference to
'boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive,
char, std::char_traits<char> >::save(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/boost-1.73.0-qq6dfhn4upamtqfmtvqy5pe4obuy6wkx/include/boost/serialization/throw_exception.hpp:36:
error: undefined reference to
'boost::archive::archive_exception::archive_exception(boost::archive::archive_exception
const&)'
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/boost-1.73.0-qq6dfhn4upamtqfmtvqy5pe4obuy6wkx/include/boost/archive/detail/oserializer.hpp:93:
error: undefined reference to
'boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive,
char, std::char_traits<char> >::save(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/boost-1.73.0-qq6dfhn4upamtqfmtvqy5pe4obuy6wkx/include/boost/archive/detail/oserializer.hpp:93:
error: undefined reference to
'boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive,
char, std::char_traits<char> >::save(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/boost-1.73.0-qq6dfhn4upamtqfmtvqy5pe4obuy6wkx/include/boost/archive/detail/iserializer.hpp:108:
error: undefined reference to
'boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive,
char, std::char_traits<char> >::load(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&)'
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/boost-1.73.0-qq6dfhn4upamtqfmtvqy5pe4obuy6wkx/include/boost/archive/detail/iserializer.hpp:108:
error: undefined reference to
'boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive,
char, std::char_traits<char> >::load(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&)'
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/boost-1.73.0-qq6dfhn4upamtqfmtvqy5pe4obuy6wkx/include/boost/archive/detail/iserializer.hpp:108:
error: undefined reference to
'boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive,
char, std::char_traits<char> >::load(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&)'
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/boost-1.73.0-qq6dfhn4upamtqfmtvqy5pe4obuy6wkx/include/boost/archive/detail/oserializer.hpp:93:
error: undefined reference to
'boost::archive::basic_binary_oprimitive<boost::archive::binary_oarchive,
char, std::char_traits<char> >::save(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
/home/woody/iwtm/iwtm020h/spack-install/dealii901-spackv15-gcc/spack/opt/spack/linux-centos7-ivybridge/gcc-7.3.0/boost-1.73.0-qq6dfhn4upamtqfmtvqy5pe4obuy6wkx/include/boost/archive/detail/iserializer.hpp:108:
error: undefined reference to
'boost::archive::basic_binary_iprimitive<boost::archive::binary_iarchive,
char, std::char_traits<char> >::load(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&)'
collect2: error: ld returned 1 exit status
make[2]: *** [variants/cookmembranedistributed] Error 1
make[2]: Leaving directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
make[1]: *** [variants/CMakeFiles/cookmembranedistributed.dir/all] Error 2
make[1]: Leaving directory
`/home/woody/iwtm/iwtm020h/trial-code/MNC-Frac/_build'
make: *** [all] Error 2
I also tried to employ the patch from PR# 11024 as described in
https://groups.google.com/g/dealii/c/dClF4Men1iY/m/o8tHBvoCAQAJ but got the
same linking errors. Further, the infromation from 'make VERBOSE=1' does
not seem to hint towards system Boost (if I interpret things correctly).
The boost version is 1.73, which is default with spack v0.15.
Some further search revealed that a possible remedy could be to switch the
order in which the libraries are linked as discussed here for some other
Boost dependent project: https://github.com/esa/pagmo/issues/174 . But, I
could not figure out how to change the linking order. I have boost as an
explicit dependency in my CMakeLists.txt and the order in which the
FIND_PACKAGE() commands for dealii and Boost appear in the CMakeLists.txt
does not seem to change the outcome.
It is note worthy that the Boost library is found by my code, since other
parts of the code using some other boost functions work fine. Also, the
same code compiles on my local machine having Ubuntu 18.04
Could someone please help me understand where I go wrong?
Best regards,
Paras Kumar
--
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