H5Fopen check false negative #4347
Description
This is a fun corner case. We are trying to build libmesh on Argonne's AURORA. It configures and builds fine, until we try to load an exodus file it reports:
EXODUS: Error: Attempting to open the netcdf-4 file:
'/lus/flare/projects/ai4ns-composites/scratch/tmplfdetu5k/mesh.exo'
with a netcdf library that does not support netcdf-4
and indeed, the nc-config in libmesh bin suggests netcdf-4 is disabled.
We then looked into the config.log. The issue is kinda convoluted, but the relevant bits of the log is
configure:61236: checking for hdf5.h
configure:61236: mpicc -c -Werror=recommended-option -I/flare/ai4ns-composites/packages/moose/scripts/../petsc/include -I/flare/ai4ns-composites/packages/moose/scripts/../petsc/arch-moose/include -I/flare/ai4ns-composites/packages/moose/petsc/arch-moose/include -I/flare/ai4ns-composites/packages/moose/petsc/include -I/flare/ai4ns-composites/packages/moose/petsc/arch-moose/include -I/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/oneapi-2025.2.0/hdf5-1.14.6-zkruqq7/include conftest.c >&5
configure:61236: $? = 0
configure:61236: result: yes
configure:61249: checking for HDF5 version >= 1.8.0
configure:61304: mpicc -c -Werror=recommended-option -I/flare/ai4ns-composites/packages/moose/scripts/../petsc/include -I/flare/ai4ns-composites/packages/moose/scripts/../petsc/arch-moose/include -I/flare/ai4ns-composites/packages/moose/petsc/arch-moose/include -I/flare/ai4ns-composites/packages/moose/petsc/include -I/flare/ai4ns-composites/packages/moose/petsc/arch-moose/include -I/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/oneapi-2025.2.0/hdf5-1.14.6-zkruqq7/include conftest.c >&5
configure:61304: $? = 0
configure:61335: result: yes
configure:61340: checking for H5Fopen in -lhdf5
configure:61369: mpicc -o conftest -Werror=recommended-option -I/flare/ai4ns-composites/packages/moose/scripts/../petsc/include -I/flare/ai4ns-composites/packages/moose/scripts/../petsc/arch-moose/include -I/flare/ai4ns-composites/packages/moose/petsc/arch-moose/include -I/flare/ai4ns-composites/packages/moose/petsc/include -I/flare/ai4ns-composites/packages/moose/petsc/arch-moose/include -I/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/oneapi-2025.2.0/hdf5-1.14.6-zkruqq7/include -L/lib -lhdf5 -Wl,-rpath,/lib -Wl,-rpath,/flare/ai4ns-composites/packages/moose/petsc/arch-moose/lib -L/flare/ai4ns-composites/packages/moose/petsc/arch-moose/lib -Wl,-rpath,/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/oneapi-2025.2.0/hdf5-1.14.6-zkruqq7/lib -L/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/oneapi-2025.2.0/hdf5-1.14.6-zkruqq7/lib -Wl,-rpath,/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/oneapi-2025.2.0/mpich-develop-git.6037a7a-cym6jg6/lib -L/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/oneapi-2025.2.0/mpich-develop-git.6037a7a-cym6jg6/lib -Wl,-rpath,/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/hwloc-2.12.1-ioadcqu/lib -L/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/hwloc-2.12.1-ioadcqu/lib -Wl,-rpath,/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/libxml2-2.13.5-dhzcbk4/lib -L/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/libxml2-2.13.5-dhzcbk4/lib -Wl,-rpath,/opt/aurora/25.190.0/support/libraries/khronos/default/lib64 -L/opt/aurora/25.190.0/support/libraries/khronos/default/lib64 -Wl,-rpath,/opt/aurora/25.190.0/oneapi/ishmem/latest/lib -L/opt/aurora/25.190.0/oneapi/ishmem/latest/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/pti/latest/lib -L/opt/aurora/25.190.0/oneapi/pti/latest/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/tcm/latest/lib -L/opt/aurora/25.190.0/oneapi/tcm/latest/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/umf/latest/lib -L/opt/aurora/25.190.0/oneapi/umf/latest/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/ipp/latest/lib -L/opt/aurora/25.190.0/oneapi/ipp/latest/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/ippcp/latest/lib -L/opt/aurora/25.190.0/oneapi/ippcp/latest/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/ccl/latest/lib -L/opt/aurora/25.190.0/oneapi/ccl/latest/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/dal/latest/lib -L/opt/aurora/25.190.0/oneapi/dal/latest/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/dnnl/latest/lib -L/opt/aurora/25.190.0/oneapi/dnnl/latest/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/tbb/latest/lib/intel64/gcc4.8 -L/opt/aurora/25.190.0/oneapi/tbb/latest/lib/intel64/gcc4.8 -Wl,-rpath,/opt/aurora/25.190.0/oneapi/mkl/latest/lib -L/opt/aurora/25.190.0/oneapi/mkl/latest/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/compiler/latest/lib -L/opt/aurora/25.190.0/oneapi/compiler/latest/lib -Wl,-rpath,/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/gcc-13.3.0-4enwbrb/lib64 -L/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/gcc-13.3.0-4enwbrb/lib64 -Wl,-rpath,/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/gcc-13.3.0-4enwbrb/lib -L/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/gcc-13.3.0-4enwbrb/lib -Wl,-rpath,/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/mpc-1.3.1-rdrlvsl/lib -L/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/mpc-1.3.1-rdrlvsl/lib -Wl,-rpath,/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/mpfr-4.2.1-gkcdl5w/lib -L/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/mpfr-4.2.1-gkcdl5w/lib -Wl,-rpath,/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/gmp-6.3.0-mtokfaw/lib -L/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/gmp-6.3.0-mtokfaw/lib -Wl,-rpath,/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/gcc-runtime-13.3.0-ghotoln/lib -L/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/gcc-runtime-13.3.0-ghotoln/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/compiler/2025.2/lib -L/opt/aurora/25.190.0/oneapi/compiler/2025.2/lib -Wl,-rpath,/opt/aurora/25.190.0/oneapi/compiler/2025.2/lib/clang/21/lib/x86_64-unknown-linux-gnu -L/opt/aurora/25.190.0/oneapi/compiler/2025.2/lib/clang/21/lib/x86_64-unknown-linux-gnu -Wl,-rpath,/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/gcc-13.3.0-4enwbrb/lib/gcc/x86_64-pc-linux-gnu/13.3.0 -L/opt/aurora/25.190.0/spack/unified/0.10.1/install/linux-sles15-x86_64/gcc-13.3.0/gcc-13.3.0-4enwbrb/lib/gcc/x86_64-pc-linux-gnu/13.3.0 -lpetsc -lHYPRE -ldmumps -lmumps_common -lpord -lpthread -lscalapack -lsuperlu_dist -lkokkoskernels -lkokkoscontainers -lkokkoscore -lkokkossimd -lflapack -lfblas -lptesmumps -lptscotchparmetisv3 -lptscotch -lptscotcherr -lesmumps -lscotch -lscotcherr -lpthread -lhdf5_hl -lhdf5 -lparmetis -lmetis -lceed -lX11 -lmpifort -lmpi -lifport -lifcoremt_pic -limf -lsvml -lm -lipgo -lirc -lpthread -lgcc_s -lirc_s -ldl -lstdc++ conftest.c -lhdf5 >&5
/usr/bin/ld: /tmp/icx-c2a07f433e/conftest-53cb38.o: in function `main':
conftest.c:(.text+0x0): multiple definition of `main'; /opt/aurora/25.190.0/oneapi/compiler/latest/lib/libifcoremt_pic.a(for_main.o):for_main.c:(.text+0x0): first defined here
/usr/bin/ld: /opt/aurora/25.190.0/oneapi/compiler/latest/lib/libifcoremt_pic.a(for_main.o): in function `main':
for_main.c:(.text+0x28): undefined reference to `MAIN__'
icx: error: linker command failed with exit code 1 (use -v to see invocation)
and ultimately
configure:61412: optional HDF5 library not found, or does not meet version requirements
configure:61445: result: <<< HDF5 support not found or disabled >>>
and since hdf5 is disabled, netcdf-4 is disabled.
Here's my understanding of the error: our AURORA HPC uses intel's compiler. Intel's fortran compiler injects its own main (a stub that calls MAIN__), assuming our true entry point is a Fortran program (though apparently the conftest isn't).
Can we somehow patch the configure.ac so that the HDF5 test does not link PETSc libs or Fortran libs?