I am not sure how much help it might be but I found similar issue from 2011,
http://hdf-forum.184993.n3.nabble.com/HDF5-and-undefined-reference-td2475757.html Mark From: Hdf-forum <[email protected]<mailto:[email protected]>> on behalf of Martin Diehl <[email protected]<mailto:[email protected]>> Organization: Max-Planck-Institut für Eisenforschung GmbH Reply-To: HDF Users Discussion List <[email protected]<mailto:[email protected]>> Date: Friday, March 18, 2016 4:16 AM To: "[email protected]<mailto:[email protected]>" <[email protected]<mailto:[email protected]>> Subject: [Hdf-forum] Compiling HDF5 Intel Compiler [Completed Mail] 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<mailto:…@mpie.de>. If you are not sure of the validity please contact [email protected]<mailto:[email protected]> Bitte beachten Sie, dass Einladungen zu Veranstaltungen und E-Mails aus unserem Haus nur mit der Endung …@mpie.de<mailto:…@mpie.de> gültig sind. In Zweifelsfällen wenden Sie sich bitte an [email protected]<mailto:[email protected]> -------------------------------------------------
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