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] -------------------------------------------------
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