Failure of HDF5 compilation with new MPI libraries

[Sergei_Kliavinek]

Dear developers, 

I'm trying to compile HDF5 package inside of the container, based on the intel/oneapi-hpckit:2025.0.0-0-devel-ubuntu22.04

I'm using the following procedure:

RUN wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.0/src/hdf5-1.14.0.tar.gz && \
    tar -xzf hdf5-1.14.0.tar.gz && \
    cd hdf5-1.14.0 && \
    export PATH=$PATH:/opt/intel/oneapi/mpi/2021.14/bin:/opt/intel/oneapi/compiler/2025.0/bin && \
    export LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/2025.0/lib:/opt/intel/oneapi/mpi/2021.14/lib:$LD_LIBRARY_PATH && \
    export LIBRARY_PATH=/opt/intel/oneapi/compiler/2025.0/lib:/opt/intel/oneapi/mpi/2021.14/lib:$LIBRARY_PATH && \
    export LDFLAGS="-L/opt/intel/oneapi/compiler/2025.0/lib -Wl,--no-as-needed -Wl,-rpath,/opt/intel/oneapi/compiler/2025.0/lib -lifcoremt -lifport -limf -lsvml -lpthread -ldl" && \
    export FCLDFLAGS="$LDFLAGS" && \
    ./configure --enable-fortran --enable-parallel \
        CXX=mpiicpx CC=mpiicx FC=mpiifx \
        FCLDFLAGS="$FCLDFLAGS" LDFLAGS="$LDFLAGS" && \
    make -j 8 && \
    make install && \
    rm ../hdf5-1.14.0.tar.gz

So I'm directly define all the paths to the libraries. However, I receive en error:

66.52 checking for Fortran libraries of mpiifx...  -L/opt/intel/oneapi/compiler/2025.0/lib -lifcoremt -lifport -limf -lsvml -lpthread -ldl -loopopt=1 -L/opt/intel/oneapi/mpi/2021.14/lib -L/opt/intel/oneapi/tcm/1.2/lib -L/opt/intel/oneapi/umf/0.9/lib -L/opt/intel/oneapi/tbb/2022.0/env/../lib/intel64/gcc4.8 -L/opt/intel/oneapi/pti/0.10/lib -L/opt/intel/oneapi/mkl/2025.0/lib -L/opt/intel/oneapi/ippcp/2025.0/lib/ -L/opt/intel/oneapi/ipp/2022.0/lib -L/opt/intel/oneapi/dnnl/2025.0/lib -L/opt/intel/oneapi/dal/2025.0/lib -L/opt/intel/oneapi/ccl/2021.14/lib/ -L/opt/intel/oneapi/compiler/2025.0/lib/clang/19/lib/x86_64-unknown-linux-gnu -L/opt/intel/oneapi/compiler/2025.0/lib/../lib/ -L/opt/intel/oneapi/mpi/2021.14/lib/../lib/ -L/opt/intel/oneapi/tcm/1.2/lib/../lib/ -L/opt/intel/oneapi/umf/0.9/lib/../lib/ -L/opt/intel/oneapi/tbb/2022.0/env/../lib/intel64/gcc4.8/../lib/ -L/opt/intel/oneapi/pti/0.10/lib/../lib/ -L/opt/intel/oneapi/mkl/2025.0/lib/../lib/ -L/opt/intel/oneapi/ippcp/2025.0/lib/../lib/ -L/opt/intel/oneapi/ipp/2022.0/lib/../lib/ -L/opt/intel/oneapi/dnnl/2025.0/lib/../lib/ -L/opt/intel/oneapi/dal/2025.0/lib/../lib/ -L/opt/intel/oneapi/ccl/2021.14/lib/../lib/ -L/usr/lib/gcc/x86_64-linux-gnu/11/ -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../x86_64-linux-gnu/ -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib64 -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../../lib/ -L/lib/x86_64-linux-gnu/ -L/lib/../lib64 -L/lib/../lib/ -L/usr/lib/x86_64-linux-gnu/ -L/usr/lib/../lib64 -L/usr/lib/../lib/ -L/opt/intel/oneapi/compiler/2025.0/lib/ -L/opt/intel/oneapi/mpi/2021.14/lib/ -L/opt/intel/oneapi/tcm/1.2/lib/ -L/opt/intel/oneapi/umf/0.9/lib/ -L/opt/intel/oneapi/tbb/2022.0/env/../lib/intel64/gcc4.8/ -L/opt/intel/oneapi/pti/0.10/lib/ -L/opt/intel/oneapi/mkl/2025.0/lib/ -L/opt/intel/oneapi/ipp/2022.0/lib/ -L/opt/intel/oneapi/dnnl/2025.0/lib/ -L/opt/intel/oneapi/dal/2025.0/lib/ -L/usr/lib/gcc/x86_64-linux-gnu/11/../../../ -L/lib64 -L/lib/ -L/usr/lib64 -L/usr/lib -lm -lipgo -lirc -lirc_s
67.80 checking for dummy main to link with Fortran libraries... unknown
79.55 configure: error: in `/opt/hdf5-1.14.0':
79.55 configure: error: linking to Fortran libraries from C fails

 What could be the reason for this issue?

Best, 
Sergei

[TobiasK]

Please do not set any LD_LIBRARY_PATH etc environment variables yourself, please use the script provided:

source /opt/intel/oneapi/setvars.sh

 Also please provide the config.log output

[Sergei_Kliavinek]

Hey, sure, here is the updated command:

SHELL ["/bin/bash", "-c"]

WORKDIR /opt

RUN wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.14/hdf5-1.14.0/src/hdf5-1.14.0.tar.gz && \
    tar -xzf hdf5-1.14.0.tar.gz && \
    cd hdf5-1.14.0 && \
    source /opt/intel/oneapi/setvars.sh --force && \
    ./configure --enable-fortran --enable-parallel \
        CXX=mpiicpx CC=mpiicx FC=mpiifx && \
    make -j 8 && \
    make install && \
    rm ../hdf5-1.14.0.tar.gz

But the error still the same. I can't provide config.log, because I build hdf5 during the docker container construction. However, If I make compilation inside builded container on ARM, everything works fine.  So it could be some issue related multi-platform building, idk.

At least, in the file I present output of the Docker during receiving this error.   

[TobiasK]

Without the config.log I cannot help you. Maybe the configure version is too old. How is ARM involved here? Intel MPI / compilers do not support ARM at all.

[Sergei_Kliavinek]

Hey, 

About the ARM - Docker Engine is able to wrap the container properly in order to run for the usage of different systems. 

On the config.log -  I've tried different HDF5 versions, the most new as well, but the error is the same. Btw, in case of intel/oneapi-hpckit:2023.0.0-devel-ubuntu22.04 everything worked great

[Sergei_Kliavinek]

Hey guys,

Do you have any updates on this? 

[TobiasK]

@Sergei_Kliavinek sorry we cannot provide any update since you still not provided any config.log

[Sergei_Kliavinek]

Hey,
So you have no way to reproduce the error? As I said, the error occurs when building the container in parallel, so there is simply no way to get the config.log.