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
Log_compile.txt (156 KB)
Log_config.txt (2.66 KB)
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