topic Re: compiling HDF5P 1.10.7 --enable-fortran fails with error: C compiler cannot create executables in Intel® MPI Library

compiling HDF5P 1.10.7 --enable-fortran fails with error: C compiler cannot create executables

RobbieTheK — Mon, 29 Apr 2024 19:09:49 GMT

What options do I need to get --enable-fortran to work? Just --enable-parallel works without errors.

checking for gcc... mpiicc
checking whether the C compiler works... no
configure: error: in `/cluster/home/me/hdf5-hdf5-1_10_7':
configure: error: C compiler cannot create executables

./configure --prefix=/cluster/shared/apps/hdf5p/1.10.7 --enable-fortran --enable-parallel CC=mpiicc FC=mpiifort CXX=mpiicpc CFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" FFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" CXXFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" FFLAGS="-I$INTEL/oneapi/mpi/latest/include -L$INTEL/oneapi/mpi/latest/lib"

module loaded:

1) oneapi/tbb/2021.11  oneapi/intel_ipp_intel64/2021.10 15) oneapi/dal/2024.0.0
2) oneapi/oclfpga/2024.0.0 9) oneapi/ifort/2024.0.2 16) oneapi/compiler/2024.0.2
3) oneapi/compiler-rt/2024.0.2 10) oneapi/dpl/2022.3 17) oneapi/ccl/2021.11.2
4) oneapi/vtune/2024.0 11) oneapi/dpct/2024.0.0 18) oneapi/advisor/2024.0
5) oneapi/mpi/2021.11 12) oneapi/dnnl/3.3.0 19) oneapi/2024.0.0/2024.0.0
6) oneapi/mkl/2024.0 13) oneapi/dev-utilities/2024.0.0 20) oneapi/hpctoolkit/mpi/2021.11
7) oneapi/intel_ippcp_intel64/2021.9 14) oneapi/debugger/2024.0.0

Re: compiling HDF5P 1.10.7 --enable-fortran fails with error: C compiler cannot create executables

TobiasK — Tue, 30 Apr 2024 13:55:36 GMT

@RobbieTheK

You set:
MPICC='mpiicc -cc=icx'
MPICXX='mpiicpc -cxx=icpx'
MPIF77='mpiifort -fc=ifx'
MPIF90='mpiifort -fc=ifx'
MPIFC='mpiifort -fc=ifx'

which is not recognized by configure.

Just please use the corresponding llvm wrapper scripts

./configure --prefix=/cluster/shared/apps/hdf5p/1.10.7 --enable-fortran --enable-parallel CC=mpiicx FC=mpiifx CXX=mpiicpx CFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" FFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align" CXXFLAGS="-fPIC -O3 -xHost -ip -fno-alias -align"

+ I think I remember there was an issue with -align so I would just skip it and use -O3 -xHOST as compiler flags.

Re: compiling HDF5P 1.10.7 --enable-fortran fails with error: C compiler cannot create executables

RobbieTheK — Tue, 30 Apr 2024 15:03:22 GMT

Well that fails with:

checking if Fortran interface enabled... yes
checking whether we are using the GNU Fortran compiler... no
checking whether mpiifx accepts -g... no
checking for Fortran flag to compile .f90 files... unknown
configure: error: Fortran could not compile .f90 files

Then I export PATH to include /cluster/shared/apps/oneapi/2024.0/etc/modulefiles/, which I'm surprise does not get exported with the setvars

And then a different failure as noted in uploaded config.log:

checking if Fortran compiler version compatible with Fortran 2003 HDF... yes
checking how to get verbose linking output from mpiifx... -v
checking for Fortran libraries of mpiifx... -loopopt=1 -L/cluster/shared/apps/oneapi/hpctoolkit/mpi/2021.11/opt/mpi/libfabric/lib -L/cluster/shared/apps/oneapi/hpctoolkit/mpi/2021.11/lib -L/cluster/shared/apps/oneapi/ccl/2021.11/lib/ -L/cluster/shared/apps/oneapi/dal/2024.0/lib -L/cluster/shared/apps/oneapi/dnnl/2024.0/lib -L/cluster/shared/apps/oneapi/compiler/2024.0/lib -L/cluster/shared/apps/oneapi/ipp/2021.10/lib -L/cluster/shared/apps/oneapi/ippcp/2021.9/lib -L/cluster/shared/apps/oneapi/mkl/2024.0/lib -L/cluster/shared/apps/oneapi/mpi/2021.11/opt/mpi/libfabric/lib -L/cluster/shared/apps/oneapi/mpi/2021.11/lib -L/cluster/shared/apps/oneapi/tbb/2021.11/lib -L/usr/lib64/openmpi/lib -L/usr/lib64/openmpi/lib/paraview -L/cluster/shared/apps/oneapi/hpctoolkit/compiler/2024.0/lib -L/cluster/shared/apps/oneapi/hpctoolkit/compiler/2024.0/lib/clang/17/lib/x86_64-unknown-linux-gnu -L/usr/lib/gcc/x86_64-redhat-linux/11/ -L/usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64 -L/usr/lib/gcc/x86_64-redhat-linux/11/../../../../lib64/ -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64 -L/usr/lib/../lib64/ -L/cluster/shared/apps/oneapi/hpctoolkit/mpi/2021.11/opt/mpi/libfabric/lib/ -L/cluster/shared/apps/oneapi/hpctoolkit/mpi/2021.11/lib/ -L/cluster/shared/apps/oneapi/dal/2024.0/lib/ -L/cluster/shared/apps/oneapi/dnnl/2024.0/lib/ -L/cluster/shared/apps/oneapi/compiler/2024.0/lib/ -L/cluster/shared/apps/oneapi/ipp/2021.10/lib/ -L/cluster/shared/apps/oneapi/ippcp/2021.9/lib/ -L/cluster/shared/apps/oneapi/mkl/2024.0/lib/ -L/cluster/shared/apps/oneapi/mpi/2021.11/opt/mpi/libfabric/lib/ -L/cluster/shared/apps/oneapi/mpi/2021.11/lib/ -L/cluster/shared/apps/oneapi/tbb/2021.11/lib/ -L./ -L/usr/lib64/openmpi/lib/ -L/usr/lib64/openmpi/lib/paraview/ -L/usr/lib/gcc/x86_64-redhat-linux/11/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -lifport -lifcoremt -limf -lsvml -lm -lipgo -lirc -lpthread -lirc_s -ldl
checking for dummy main to link with Fortran libraries... unknown
configure: error: in `/cluster/home/me/hdf5-hdf5-1_10_7':
configure: error: linking to Fortran libraries from C fails
See `config.log' for more details

Re: compiling HDF5P 1.10.7 --enable-fortran fails with error: C compiler cannot create executables

RobbieTheK — Wed, 01 May 2024 18:55:03 GMT

Hat tip to this HDF5 discussion thread I had to install autotools 2.71 and re-run autogen.sh and as the user said there "Intel introduced a compiler flag starting with “-l” which is getting interpreted as a library".

Re: compiling HDF5P 1.10.7 --enable-fortran fails with error: C compiler cannot create executables

TobiasK — Thu, 02 May 2024 08:21:38 GMT

@RobbieTheK
glad you found what's going wrong.

If you had uploaded the new config.log and not the original again I would have been able to point you to our known issues:

https://www.intel.com/content/www/us/en/developer/articles/release-notes/oneapi-fortran-compiler-release-notes.html#inpage-nav-5-6