The symbols are close, but not identical. Is there is discrepancy in the Fortran compiler used to compile your application and HDF5? It must be from the same vendor, no Fortran compiler share the same naming convention than the others.
Cheers, Matthieu 2016-04-04 10:39 GMT+01:00 Martin Diehl <[email protected]>: > Dear Mark, > > thanks for the hint. > Unfortunately, that does not solve the issues (and I'm a little bit > reluctant to use the wrapper, because with MPI wrappers and PETSc > wrappers, I would in the end have a wrapper to a wrapper to a wrapper to > the compiler). > Fortunately, I found the answer in the Intel forum. It's related to the > compiler options: > > https://software.intel.com/en-us/forums/intel-fortran-compiler-for-linux-and-mac-os-x/topic/621720 > > best regards, > Martin > > > On Fri, 2016-03-18 at 12:16 +0100, Martin Diehl wrote: > > Dear HDF5 users and Developers, > > > > I'm currently struggling to compile an fortran application that contains > > HDF5 functions with the Intel compiler suite 2016 on Ubuntu 14.04 > > > > What I did > > 1) Install MPICH using the Intel compilers > > 2) Install HDF5 using the Intel compilers with MPICH > > 3) Install PETSc using the MPICH compilers and telling PETSc where HDF5 > > is located > > 4) Trying to compile my application with the PETSc makefile. That > > Fails :( > > > > Doing the same with the current GNU compilers works fine. > > Using openMPI instead of MPICH does not solve the problem, I also tried > > it on different Linux flavors. > > > > The (shortened) linker command looks like > > > > mpif90 -Wl,-rpath,/opt//petsc-3.6.3/Intel-16.0-MPICH-3.2/lib > > -Wl,-rpath,/opt//hdf5-1.8.16/Intel/16.0/MPICH/3.2/lib > > -Wl,-rpath,/opt//szip-2.1/Intel/16.0/lib -lz > > -L/opt//petsc-3.6.3/Intel-16.0-MPICH-3.2/lib > > -L/opt//hdf5-1.8.16/Intel/16.0/MPICH/3.2/lib > > -L/opt//szip-2.1/Intel/16.0/lib -fPIC -O3 -xHost -no-prec-div > > -openmp -openmp-report0 -parallel -shared-intel -O2 -stand f08 > > -standard-semantics -O2 -o DAMASK_spectral.exe DAMASK_spectral.o \ > > prec.o DAMASK_interface.o IO.o HDF5_Utilities.o > > -L/opt//petsc-3.6.3/Intel-16.0-MPICH-3.2/lib -lpetsc > > -Wl,-rpath,/opt/petsc-3.6.3/Intel-16.0-MPICH-3.2/lib > > -L/opt/petsc-3.6.3/Intel-16.0-MPICH-3.2/lib -lsuperlu_4.3 > > -lsuperlu_dist_4.1 -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common > > -lpord -lscalapack -lHYPRE > > -Wl,-rpath,/opt/fftw-3.3.4/Intel/16.0/MPICH/3.2/lib > > -L/opt/fftw-3.3.4/Intel/16.0/MPICH/3.2/lib > > -Wl,-rpath,/opt/hdf5-1.8.16/Intel/16.0/MPICH/3.2/lib > > -L/opt/hdf5-1.8.16/Intel/16.0/MPICH/3.2/lib > > -Wl,-rpath,/opt/szip-2.1/Intel/16.0/lib -L/opt/szip-2.1/Intel/16.0/lib > > -Wl,-rpath,/opt/mpich-3.2/Intel/16.0/lib -L/opt/mpich-3.2/Intel/16.0/lib > > -Wl,-rpath,/opt/intel/compilers_and_libraries_2016/linux/mkl/lib/intel64 > > -L/opt/intel/compilers_and_libraries_2016/linux/mkl/lib/intel64 > > -Wl,-rpath,/opt/intel/compilers_and_libraries_2016/linux/lib/intel64 > > -L/opt/intel/compilers_and_libraries_2016/linux/lib/intel64 > > > -Wl,-rpath,/opt/intel/compilers_and_libraries_2016.0.109/linux/compiler/lib/intel64_lin > -L/opt/intel/compilers_and_libraries_2016.0.109/linux/compiler/lib/intel64_lin > -Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/5 > -L/usr/lib/gcc/x86_64-linux-gnu/5 -Wl,-rpath,/usr/lib/x86_64-linux-gnu > -L/usr/lib/x86_64-linux-gnu -Wl,-rpath,/lib/x86_64-linux-gnu > -L/lib/x86_64-linux-gnu -lmpicxx -lumfpack -lklu -lcholmod -lbtf -lccolamd > -lcolamd -lcamd -lamd -lsuitesparseconfig -lml -lmpicxx -llapack -lblas > -lparmetis -lmetis -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 > -lfftw3_mpi -lfftw3 -lpthread -lhwloc -lchaco -lmpifort -lifport > -lifcore_pic -lm -lpthread -lm -lmpicxx -lz > -Wl,-rpath,/opt/petsc-3.6.3/Intel-16.0-MPICH-3.2/lib > -L/opt/petsc-3.6.3/Intel-16.0-MPICH-3.2/lib > -Wl,-rpath,/opt/fftw-3.3.4/Intel/16.0/MPICH/3.2/lib > -L/opt/fftw-3.3.4/Intel/16.0/MPICH/3.2/lib > -Wl,-rpath,/opt/hdf5-1.8.16/Intel/16.0/MPICH/3.2/lib > -L/opt/hdf5-1.8.16/Intel/16.0/MPICH/3.2/lib > -Wl,-rpath,/opt/szip-2.1/Intel/16.0/lib -L/opt/szip-2.1/Intel/16.0/lib -ldl > -Wl,-rpath,/opt/mpich-3.2/Intel/16.0/lib -L/opt/mpich-3.2/Intel/16.0/lib > -lmpi -Wl,-rpath,/opt/petsc-3.6.3/Intel-16.0-MPICH-3.2/lib > -L/opt/petsc-3.6.3/Intel-16.0-MPICH-3.2/lib > -Wl,-rpath,/opt/fftw-3.3.4/Intel/16.0/MPICH/3.2/lib > -L/opt/fftw-3.3.4/Intel/16.0/MPICH/3.2/lib > -Wl,-rpath,/opt/hdf5-1.8.16/Intel/16.0/MPICH/3.2/lib > > > > So I'm linking in the correct order against the 4 libraries from HDF5 > > and have the path given with -L and even as -Wl,rpath. > > > > However, I get a bunch of these messages: > > > > /nethome/storage/raid4/m.diehl/DAMASK/code/HDF5_Utilities.f90:58: > > undefined reference to `h5lib_MP_h5open_f_' > > > > even though the verbose compiler command > > -Wl,--verbose > > tells that it finds the libraries: > > > > attempt to > > open /opt//hdf5-1.8.16/Intel/16.0/MPICH/3.2/lib/libhdf5hl_fortran.so > > succeeded > > -lhdf5hl_fortran > > (/opt//hdf5-1.8.16/Intel/16.0/MPICH/3.2/lib/libhdf5hl_fortran.so) > > > > > > > > readelf readelf -Ws > /opt/hdf5-1.8.16/Intel/16.0/MPICH/3.2/lib/libhdf5_fortran.so > > 916: 0000000000024600 80 FUNC GLOBAL DEFAULT 12 > h5t_mp_h5topen_f_ > > 969: 0000000000024600 80 FUNC GLOBAL DEFAULT 12 > h5t_mp_h5topen_f_ > > > > tells that the symbols are in these files (as expected). > > > > I would appreciate any help. Please find attached the complete log files. > > > > best regards > > Martin > > > > > > > > > > -- > ------------------------------------------------- > Max-Planck-Institut für Eisenforschung GmbH > Max-Planck-Straße 1 > D-40237 Düsseldorf > > Handelsregister B 2533 > Amtsgericht Düsseldorf > > Geschäftsführung > Prof. Dr. Gerhard Dehm > Prof. Dr. Jörg Neugebauer > Prof. Dr. Dierk Raabe > Dr. Kai de Weldige > > Ust.-Id.-Nr.: DE 11 93 58 514 > Steuernummer: 105 5891 1000 > > > Please consider that invitations and e-mails of our institute are only > valid if they end with …@mpie.de. > If you are not sure of the validity please contact [email protected] > > Bitte beachten Sie, dass Einladungen zu Veranstaltungen und E-Mails aus > unserem Haus nur mit der Endung …@mpie.de gültig sind. > In Zweifelsfällen wenden Sie sich bitte an [email protected] > ------------------------------------------------- > > _______________________________________________ > Hdf-forum is for HDF software users discussion. > [email protected] > http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org > Twitter: https://twitter.com/hdf5 > -- Information System Engineer, Ph.D. Blog: http://matt.eifelle.com LinkedIn: http://www.linkedin.com/in/matthieubrucher
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