Installation issue: hdf5+fortran with intel-oneapi-mpi and gcc

[nboelte]

Steps to reproduce the issue

$spack install hdf5+fortran %gcc ^intel-oneapi-mpi
...

Error message

Error message

  [ 89%] Building Fortran object fortran/src/CMakeFiles/hdf5_fortran-shared.dir/H5Pff.F90.o
  cd /tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-build-ax7sikc/fortran/src && /home/niklas/git/spack/opt/spack/linux-zen5/compiler-wrapper-1.1.0-4r3r2ym3k2ruateez53zkyddma2r2ihi/libexec/spack/gcc/gfortran -DH5_BUILT_AS_DYNAMIC_LIB -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -Dhdf5_fortran_shared_EXPORTS -I/tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-src/fortran/src -I/tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-build-ax7sikc/mod/shared -I/tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-build-ax7sikc/fortran -I/tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-build-ax7sikc/fortran/src -I/tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-src/src -I/tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-src/src/H5FDsubfiling -I/tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-build-ax7sikc/src -I/home/niklas/git/spack/opt/spack/linux-zen5/intel-oneapi-mpi-2021.18.0-jh33lacgqhyiwdrziwyu4hzi4astq3pr/mpi/2021.18/include/mpi -I/home/niklas/git/spack/opt/spack/linux-zen5/intel-oneapi-mpi-2021.18.0-jh33lacgqhyiwdrziwyu4hzi4astq3pr/mpi/2021.18/include -O3 -J../../mod/shared -fPIC -c /tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-src/fortran/src/H5Pff.F90 -o CMakeFiles/hdf5_fortran-shared.dir/H5Pff.F90.o
  cd /tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-build-ax7sikc/tools/lib && /home/niklas/git/spack/opt/spack/linux-zen5/compiler-wrapper-1.1.0-4r3r2ym3k2ruateez53zkyddma2r2ihi/libexec/spack/gcc/gcc -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -D_LARGEFILE_SOURCE -D_POSIX_C_SOURCE=200809L -I/tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-src/tools/lib -I/tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-src/src -I/tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-src/src/H5FDsubfiling -I/tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-build-ax7sikc/src -std=c99 -Wno-error=implicit-function-declaration -fstdarg-opt -fdiagnostics-urls=never -fno-diagnostics-color -fmessage-length=0 -O3 -DNDEBUG -std=gnu99 -fPIC -Wall -Wcast-qual -Wconversion -Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-include-dirs -Wshadow -Wundef -Wwrite-strings -pedantic -Wno-c++-compat -Wbad-function-cast -Wcast-align -Wformat -Wimplicit-function-declaration -Wint-to-pointer-cast -Wmissing-declarations -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-sign -Wpointer-to-int-cast -Wredundant-decls -Wstrict-prototypes -Wswitch -Wunused-but-set-variable -Wunused-variable -Wunused-function -Wunused-parameter -finline-functions -Wno-aggregate-return -Wno-inline -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings -Wlarger-than=2560 -Wlogical-op -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand -Wno-unsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wno-jump-misses-init -Wstrict-overflow=2 -Wno-suggest-attribute=const -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure -Wno-suggest-attribute=format -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -Wincompatible-pointer-types -Wint-conversion -Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wrestrict -Wattribute-alias -Wshift-overflow=2 -Wcast-function-type -Wcast-align=strict -Wno-suggest-attribute=cold -Wno-suggest-attribute=malloc -Wattribute-alias=2 -Wmissing-profile -Wc11-c2x-compat -MD -MT tools/lib/CMakeFiles/hdf5_tools-static.dir/h5trav.c.o -MF CMakeFiles/hdf5_tools-static.dir/h5trav.c.o.d -o CMakeFiles/hdf5_tools-static.dir/h5trav.c.o -c /tmp/niklas/spack-stage/spack-stage-hdf5-1.14.6-ax7sikcjv6lt5q6im73zkn5dszwgajfn/spack-src/tools/lib/h5trav.c
  f951: Fatal Error: Reading module '/home/niklas/git/spack/opt/spack/linux-zen5/intel-oneapi-mpi-2021.18.0-jh33lacgqhyiwdrziwyu4hzi4astq3pr/mpi/2021.18/include/mpi/mpi.mod' at line 1 column 2: Unexpected EOF

Information on your system

* **Spack:** 1.2.0.dev0 (https://github.com/spack/spack/commit/dd8eb875d0dc879bf0b32b63997fdb94727f88ec)
* **Builtin repo:** https://github.com/spack/spack-packages/commit/d5a3282fd7cb81e7053396ecf3196acae89920aa
* **Python:** 3.14.5
* **Platform:** linux-fedora44-zen5

Additional information

@rscohn2

spack-build-env.txt
spack-build-out.txt

General information

• I have run spack debug report and reported the version of Spack/Python/Platform
• I have run spack maintainers <name-of-the-package> and @mentioned any maintainers
• I have uploaded the build log and environment files
• I have searched the issues of this repo and believe this is not a duplicate

[nboelte]

I use this workaround on our system to replace the .mod files with the appropriate ones for the compiler. I am not sure if this is the best method to do it, since the Intel OneAPI spack classes are quite complex and i don't really understand them.

intel-oneapi-mpi/package.py

import glob

# ....

    @run_after("install")
    def fixup_mod_files(self):
        # Fixes these errors when gfortran tries to open the intel .mod files:
        # Fatal Error: Reading module <...> at line 1 column 2: Unexpected EOF
        if self.spec.satisfies("%gcc"):
            default_mod_path = self.component_prefix.include.mpi
            for mod in glob.glob(
                default_mod_path + "/gfortran/" + str(self.compiler.version.up_to(1)) + "*/*.mod"
            ):
                force_symlink(mod, join_path(default_mod_path, os.path.basename(mod)))