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h5fc broken (or changed) in the hdf5_1_14-9f7b987 snapshot #4308

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jefflee-icesat2 opened this issue Apr 2, 2024 · 3 comments
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h5fc broken (or changed) in the hdf5_1_14-9f7b987 snapshot #4308

jefflee-icesat2 opened this issue Apr 2, 2024 · 3 comments
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Component - Fortran Fortran wrappers Component - Tools Command-line tools like h5dump, includes high-level tools Priority - 0. Blocker ⛔ This MUST be merged for the release to happen Type - Bug Please report security issues to [email protected] instead of creating an issue on GitHub
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@jefflee-icesat2
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jefflee-icesat2 commented Apr 2, 2024

Describe the bug
h5fc repeats the source and object filenames in the wrong place in the argument list, resulting in attempting to use the output object as the input file.

gfortran: fatal error: input file 'const_glob_mod.o' is the same as output file

Expected behavior
Normal compilation

Platform (please complete the following information)

  • HDF5 version: hdf5_1_14-9f7b987
  • OS and version: MacOS Sonoma 14.3.1
  • Compiler and version: gfortran; gcc version 13.2.0
  • Build system (e.g. CMake, Autotools) and version: ./configure
  • Any configure options you specified: /configure --prefix="${BASEDIR}" --enable-fortran "${EXT_ZLIB}"
  • MPI library and version (parallel HDF5): N/A

Additional context

using the -show argument (to see the compile command) with h5fc in 1.10.8:

../../../base_libs/bin/h5fc -show -J../../modules -fPIC -cpp -DHDF5_1_10 -O2 -g -Wall -Wno-surprising -fcheck=all -fimplicit-none -fbacktrace -ffpe-trap=zero,overflow,invalid -I. -I../../modules -I../../../common_libs/modules -I../../../base_libs/include -c const_glob_mod.f90 -o const_glob_mod.o

yields:

gfortran -I/Users/jelee1/Development/asas_hotfix/base_libs/include -J../../modules -fPIC -cpp -DHDF5_1_10 -O2 -g -Wall -Wno-surprising -fcheck=all -fimplicit-none -fbacktrace -ffpe-trap=zero,overflow,invalid -I. -I../../modules -I../../../common_libs/modules -I../../../base_libs/include -c const_glob_mod.f90 -o const_glob_mod.o

using the -show argument (to see the compile command) with h5fc in 1_14-9f7b987

../../../base_libs/bin/h5fc -show -J../../modules -fPIC -cpp -DHDF5_1_10 -O2 -g -Wall -Wno-surprising -fcheck=all -fimplicit-none -fbacktrace -ffpe-trap=zero,overflow,invalid -I. -I../../modules -I../../../common_libs/modules -I../../../base_libs/include -c const_glob_mod.f90 -o const_glob_mod.o

gfortran -I/Users/jelee1/Development/asas/base_libs/include -J../../modules -fPIC -cpp -DHDF5_1_10 -O2 -g -Wall -Wno-surprising -fcheck=all -fimplicit-none -fbacktrace -ffpe-trap=zero,overflow,invalid -I. -I../../modules -I../../../common_libs/modules -I../../../base_libs/include const_glob_mod.f90 const_glob_mod.o -J../../modules -fPIC -cpp -DHDF5_1_10 -O2 -g -Wall -Wno-surprising -fcheck=all -fimplicit-none -fbacktrace -ffpe-trap=zero,overflow,invalid -I. -I../../modules -I../../../common_libs/modules -I../../../base_libs/include -c const_glob_mod.f90 -o const_glob_mod.o:

Notice the object and source filenames are repeated in the middle of the options strings.

@derobins derobins added this to the 1.14.4 milestone Apr 2, 2024
@derobins derobins added Priority - 0. Blocker ⛔ This MUST be merged for the release to happen Component - Tools Command-line tools like h5dump, includes high-level tools Component - Fortran Fortran wrappers Type - Bug Please report security issues to [email protected] instead of creating an issue on GitHub labels Apr 2, 2024
@brtnfld
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brtnfld commented Apr 4, 2024

I could not reproduce the error. Can you provide your CC,FC and flags settings and the configure line you used to build the library?

@jefflee-icesat2
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So, I can temporarily 'fix' this by using the h5fc script from an older library version (1.10.8)

My compile line looks like this:

../../../base_libs/bin/h5fc -J../../modules -fPIC -cpp -DHDF5_1_10 -O2 -g -Wall -Wno-surprising -fcheck=all -fimplicit-none -fbacktrace -ffpe-trap=zero,overflow,invalid -I. -I../../modules -I../../../common_libs/modules -I../../../base_libs/include -c const_glob_mod.f90 -o const_glob_mod.o

I compile the library like this (due to #4310)

configure --prefix="${BASEDIR}" --enable-fortran "${EXT_ZLIB} --disable-nonstandard-feature-float16

My entire config log is within #4310

@brtnfld
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brtnfld commented Apr 10, 2024

This issue has been resolved and will be included in the upcoming release. Thank you for bringing this to our attention.

@brtnfld brtnfld closed this as completed Apr 10, 2024
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Component - Fortran Fortran wrappers Component - Tools Command-line tools like h5dump, includes high-level tools Priority - 0. Blocker ⛔ This MUST be merged for the release to happen Type - Bug Please report security issues to [email protected] instead of creating an issue on GitHub
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