DOLFIN

dolfin.pc Libs are parsed wrong whit a --start-group argument

Bug #966100 reported by Jens
6
This bug affects 1 person
Affects Status Importance Assigned to Milestone
DOLFIN
Fix Released
Low
Johannes Ring
DOLFIN 1.0.1

Bug Description

When there's a --start-group argument in the DOLFIN_TARGET_LINK_LIBRARIES the creation of the PKG_LINKFLAGS goes wrong in dolfin/CMakeLists.txt

especially the regex used here seems to be flawed:

# Convert libraries to -L<libdir> -l<lib> form
foreach(_lib ${DOLFIN_TARGET_LINK_LIBRARIES})
  string(REGEX REPLACE "(.?:?/[^ ]*)/lib([^ ]*)\\.(a|so|dylib|dll)" "-L\\1 -l\\2"
    _linkflags
    "${_lib}"
    )

  # Only add libraries that matches the form -L<libdir> -l<lib>
  if ("${_linkflags}" MATCHES "-L.+ -l.+")
    set(PKG_LINKFLAGS "${PKG_LINKFLAGS} ${_linkflags}")
  endif()
endforeach()

I printed out DOLFIN_TARGET_LINK_LIBRARIES and PKG_LINKFLAGS just after this piece of code was run and got these results:
Note the "-L " : the space is after the -L instead of before it, making things fail when trying to use these flags when compiling with instant.

 DOLFIN_TARGET_LINK_LIBRARIES:
  /usr/lib64/libxml2.so;/tmp/software/Armadillo/2.4.4-ictce-4.0.6/lib/libarmadillo.so;optimized;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_filesystem.so;debug;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_filesystem.so;optimized;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_program_options.so;debug;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_program_options.so;optimized;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_system.so;debug;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_system.so;optimized;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_thread.so;debug;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_thread.so;optimized;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_iostreams.so;debug;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_iostreams.so;optimized;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_math_tr1.so;debug;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_math_tr1.so;optimized;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_mpi.so;debug;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_mpi.so;optimized;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_serialization.so;debug;/tmp/software/Boost/1.49.0-ictce-4.0.6/lib/libboost_serialization.so;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/UMFPACK/lib/libumfpack.a;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/UMFPACK/lib/libamd.a;-Wl,--start-group
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_intel_lp64.a
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_sequential.a
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_core.a
  -Wl,--end-group;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CHOLMOD/lib/libcholmod.a;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/UMFPACK/lib/libamd.a;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CAMD/lib/libcamd.a;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/COLAMD/lib/libcolamd.a;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CCOLAMD/lib/libccolamd.a;-Wl,--start-group
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_intel_lp64.a
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_sequential.a
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_core.a
  -Wl,--end-group;/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib/libparmetis.a;/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib/libmetis.a;-Wl,--start-group
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_intel_lp64.a
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_sequential.a
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_core.a
  -Wl,--end-group;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CHOLMOD/lib/libcholmod.a;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/UMFPACK/lib/libamd.a;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CAMD/lib/libcamd.a;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/COLAMD/lib/libcolamd.a;/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CCOLAMD/lib/libccolamd.a;-Wl,--start-group
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_intel_lp64.a
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_sequential.a
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_core.a
  -Wl,--end-group;/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib/libparmetis.a;/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib/libmetis.a;-Wl,--start-group
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_intel_lp64.a
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_sequential.a
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_core.a
  -Wl,--end-group;/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib/libparmetis.a;/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib/libmetis.a;/usr/lib64/libz.so;/apps/gent/gengar/harpertown/software/impi/4.0.2.003/lib64/libmpi.so

  PKG_LINKFLAGS: -L/apps/gent/gengar/harpertown/software/impi/4.0.2.003/lib64
  -lmpi -L/usr/lib64 -lz -L/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib
  -lmetis -L/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib -lparmetis
  -Wl,--start-group-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_intel_lp64-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_sequential-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_core -Wl,--end-group -L/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib
  -lmetis -L/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib -lparmetis
  -Wl,--start-group-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_intel_lp64-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_sequential-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_core -Wl,--end-group
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CCOLAMD/lib
  -lccolamd
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/COLAMD/lib
  -lcolamd
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CAMD/lib -lcamd
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/UMFPACK/lib
  -lamd
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CHOLMOD/lib
  -lcholmod -Wl,--start-group-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_intel_lp64-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_sequential-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_core -Wl,--end-group -L/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib
  -lmetis -L/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib -lparmetis
  -Wl,--start-group-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_intel_lp64-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_sequential-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_core -Wl,--end-group
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CCOLAMD/lib
  -lccolamd
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/COLAMD/lib
  -lcolamd
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CAMD/lib -lcamd
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/UMFPACK/lib
  -lamd
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/CHOLMOD/lib
  -lcholmod -Wl,--start-group-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_intel_lp64-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_sequential-L
  /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -lmkl_core -Wl,--end-group
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/UMFPACK/lib
  -lamd
  -L/tmp/software/SuiteSparse/3.7.0-ictce-4.0.6-withparmetis/UMFPACK/lib
  -lumfpack -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib
  -lboost_serialization -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib
  -lboost_serialization -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib
  -lboost_mpi -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_mpi
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_math_tr1
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_math_tr1
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_iostreams
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_iostreams
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_thread
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_thread
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_system
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_system
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_program_options
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_program_options
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_filesystem
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib -lboost_filesystem
  -L/tmp/software/Armadillo/2.4.4-ictce-4.0.6/lib -larmadillo -L/usr/lib64
  -lxml2
  -L/apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64
  -L/apps/gent/gengar/harpertown/software/Python/2.7.2-ictce-4.0.6/lib
  -L/tmp/software/Boost/1.49.0-ictce-4.0.6/lib
  -L/tmp/software/UFC/2.0.5-ictce-4.0.6/lib -L/tmp/software/FFC/1.0.0/lib
  -L/tmp/software/FIAT/1.0.0/lib -L/tmp/software/Instant/1.0.0/lib
  -L/tmp/software/Viper/1.0.0/lib -L/tmp/software/UFL/1.0.0/lib
  -L/tmp/software/SCOTCH/5.1.12b_esmumps-ictce-4.0.6/lib
  -L/tmp/software/Armadillo/2.4.4-ictce-4.0.6/lib
  -L/tmp/software/ParMETIS/4.0.2-ictce-4.0.6/lib

Revision history for this message
Johannes Ring (johannr) wrote :

Do you know where the -Wl,--start-group flag comes from. Why is it added to DOLFIN_TARGET_LINK_LIBRARIES?

Revision history for this message
Jens (jens.timmerman) wrote :

Yes, I'm explicitly setting them.

I'm running

cmake -DCMAKE_INSTALL_PREFIX=/tmp/software/DOLFIN/1.0.0-ictce-4.0.6 . -DBoost_DIR=$SOFTROOTBOOST -DBOOST_INCLUDEDIR=$SOFTROOTBOOST/include -DBoost_DEBUG=ON -DBOOST_ROOT=$SOFTROOTBOOST -DUFC_DIR=$SOFTROOTUFC -DARMADILLO_DIR:PATH=$SOFTROOTARMADILLO -DMPI_COMPILER="$MPICC" -DMPI_LIBRARY="$SOFTROOTIMPI/lib64/libmpi.so" -DMPI_INCLUDE_PATH="$SOFTROOTIMPI/include64" -DPYTHON_LIBRARY=$SOFTROOTPYTHON/lib/libpython2.7.so -DPYTHON_INCLUDE_PATH=$SOFTROOTPYTHON/include/python2.7 -DPYTHON_LIBRARIES=$SOFTROOTPYTHON/lib/libpython2.7.so -DMPI_C_COMPILER="$MPICC" -DMPI_CXX_COMPILER="$MPICXX" -DUMFPACK_DIR="$SOFTROOTSUITESPARSE/UMFPACK" -DAMD_DIR="$SOFTROOTSUITESPARSE/UMFPACK" -DCHOLMOD_DIR="$SOFTROOTSUITESPARSE/CHOLMOD" -DUFCONFIG_DIR="$SOFTROOTSUITESPARSE/UFconfig" -DCAMD_LIBRARY:PATH="$SOFTROOTSUITESPARSE/CAMD/lib/libcamd.a" -DCCOLAMD_LIBRARY:PATH="$SOFTROOTSUITESPARSE/CCOLAMD/lib/libccolamd.a" -DCOLAMD_LIBRARY:PATH="$SOFTROOTSUITESPARSE/COLAMD/lib/libcolamd.a" -DBLAS_LIBRARIES:PATH="$LIBBLAS" -DLAPACK_LIBRARIES:PATH="$LIBLAPACK" -DPARMETIS_DIR="$SOFTROOTPARMETIS" -DSCOTCH_DIR="$SOFTROOTSCOTCH" -DOpenMP_CXX_FLAGS="-openmp" -DOpenMP_C_FLAGS="-openmp"

with for example
LIBBLAS set to " -Wl,--start-group /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_intel_lp64.a /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_sequential.a /apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_core.a -Wl,--end-group"

Revision history for this message
Jens (jens.timmerman) wrote :

This is how it's recommended by Intel: http://software.intel.com/en-us/articles/intel-math-kernel-library-intel-mkl-for-linux-linking-applications-with-intel-mkl-version-100/

Revision history for this message
Jens (jens.timmerman) wrote :

When debugging this I also noticed pkg-utils doesn't like the -Wl,--start-group either.

So I changed my LIBBLAS to -Wl,--start-group,/apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_intel_lp64.a,/apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_sequential.a,/apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_core.a,--end-group

this makes pkg-utils work as expected, however, I can't get cmake to create the correct dolfin.pc yet

Revision history for this message
Jens (jens.timmerman) wrote :

Using this (proof of concept) patch I can get instant to work after building everything:

- # Only add libraries that matches the form -L<libdir> -l<lib>
- if ("${_linkflags}" MATCHES "-L.+ -l.+")
- set(PKG_LINKFLAGS "${_linkflags} ${PKG_LINKFLAGS}")
+ #also add -Wl,x,x,x,x directives
+ if ("${_lib}" MATCHES "-Wl,[^ ]*")
+ set(PKG_LINKFLAGS "${_lib} ${PKG_LINKFLAGS}")
+ else()
+ # Only add libraries that matches the form -L<libdir> -l<lib>
+ if ("${_linkflags}" MATCHES "-L.+ -l.+")
+ set(PKG_LINKFLAGS "${_linkflags} ${PKG_LINKFLAGS}")
+ endif()
   endif()
 endforeach()

Revision history for this message
Jens (jens.timmerman) wrote :
Revision history for this message
Johannes Ring (johannr) wrote :

Does it work if you try

  -DBLAS_LIBRARIES="/apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_intel_lp64.a;/apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_sequential.a;/apps/gent/gengar/harpertown/software/imkl/10.3.6.233/mkl/lib/intel64/libmkl_core.a"

?

Revision history for this message
Jens (jens.timmerman) wrote :

No, this is not possible since there are unavoidable circular references between two or more archives.

Revision history for this message
Johannes Ring (johannr) wrote :

OK.

Thanks for the patch. I have pushed a slightly modified version of it now.

Changed in dolfin:
status: New → Fix Committed
assignee: nobody → Johannes Ring (johannr)
milestone: none → 1.0.1
importance: Undecided → Low
Marie Rognes (meg-simula)
Changed in dolfin:
status: Fix Committed → Fix Released
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