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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
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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
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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.
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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.
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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
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Hey guys,
Do you have any updates on this?
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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.

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