Bug 813924 – sys-cluster/slurm-20.11.0.1-r101 fails to build against sci-libs/hdf5-1.12.1

• Product: Gentoo Linux
• Status: RESOLVED FIXED

[Description Denis Lisov 2021-09-19 20:25:13 UTC]

Build fails with the following problems:

 * Package:    sys-cluster/slurm-20.11.0.1-r101
 * Repository: gentoo
 * Maintainer: [e-mail] [e-mail]
 * USE:        X abi_x86_64 amd64 elibc_glibc hdf5 kernel_linux lua_single_target_lua5-1 munge pam userland_GNU
 * FEATURES:   compressdebug network-sandbox preserve-libs sandbox splitdebug userpriv usersandbox
[...]
checking for h5cc... /usr/sbin/h5cc
checking for HDF5 type... serial
checking for HDF5 libraries... ^[[01m^[[Kx86_64-pc-linux-gnu-gcc:^[[m^[[K ^[[01;31m^[[Kerror: ^[[m^[[Kunrecognized command-line option '^[[01m^[[K-show^[[m^[[K'
^[[01m^[[Kx86_64-pc-linux-gnu-gcc:^[[m^[[K ^[[01;31m^[[Kerror: ^[[m^[[Kunrecognized command-line option '^[[01m^[[K-show^[[m^[[K'
^[[01m^[[Kx86_64-pc-linux-gnu-gcc:^[[m^[[K ^[[01;31m^[[Kerror: ^[[m^[[Kunrecognized command-line option '^[[01m^[[K-showconfig^[[m^[[K'; did you mean '^[[01m^[[K-mpconfig^[[m^[[K'?
^[[01m^[[Kx86_64-pc-linux-gnu-gcc:^[[m^[[K ^[[01;31m^[[Kerror: ^[[m^[[Kunrecognized command-line option '^[[01m^[[K-showconfig^[[m^[[K'; did you mean '^[[01m^[[K-mpconfig^[[m^[[K'?
^[[01m^[[Kx86_64-pc-linux-gnu-gcc:^[[m^[[K ^[[01;31m^[[Kerror: ^[[m^[[Kunrecognized command-line option '^[[01m^[[K-showconfig^[[m^[[K'; did you mean '^[[01m^[[K-mpconfig^[[m^[[K'?
yes (version )
checking for hdf5.h... no
checking for H5Fcreate in -lhdf5... no
configure: WARNING: Unable to compile HDF5 test program
checking for main in -lhdf5_hl... no
checking for matching HDF5 Fortran wrapper... /usr/sbin/h5fc
Package hdf5-1.12.1 was not found in the pkg-config search path.
Perhaps you should add the directory containing `hdf5-1.12.1.pc'
to the PKG_CONFIG_PATH environment variable
Package 'hdf5-1.12.1', required by 'hdf5_fortran', not found
^[[01m^[[Kx86_64-pc-linux-gnu-gfortran:^[[m^[[K ^[[01;31m^[[Kerror: ^[[m^[[Kunrecognized command-line option '^[[01m^[[K-show^[[m^[[K'
^[[01m^[[Kx86_64-pc-linux-gnu-gfortran:^[[m^[[K ^[[01;31m^[[Kfatal error: ^[[m^[[Kno input files
compilation terminated.
[...]
>>> Compiling source in /tmp/portage/sys-cluster/slurm-20.11.0.1-r101/work/slurm-slurm-20-11-0-1 ...
make --jobs=9 --load-average=12
Makefile:295: *** missing separator.  Stop.

Building without the hdf5 USE flag succeeds.

Reproducible: Always

[Comment 1 Denis Lisov 2021-09-19 20:26:21 UTC]

Created attachment 740154 [details]
build log

[Comment 2 Denis Lisov 2021-09-19 20:26:38 UTC]

Created attachment 740157 [details]
emerge --info

[Comment 3 Larry the Git Cow 2021-10-12 07:06:13 UTC]

The bug has been referenced in the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=b372f20dd03c96d59ee2ef978d76ef174a026ad7

commit b372f20dd03c96d59ee2ef978d76ef174a026ad7
Author:     Sam James <[e-mail]>
AuthorDate: 2021-10-12 07:05:57 +0000
Commit:     Sam James <[e-mail]>
CommitDate: 2021-10-12 07:05:57 +0000

    sys-cluster/slurm: add < dep on hdf5lib for now
    
    Bug: https://bugs.gentoo.org/813924
    Signed-off-by: Sam James <[e-mail]>

 .../slurm/{slurm-20.11.0.1-r101.ebuild => slurm-20.11.0.1-r102.ebuild} | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

[Comment 4 Timo Rothenpieler 2022-06-22 13:48:21 UTC]

This should be fixed now.
Latest hdf5 ebuild has been switched back to autotools (from cmake) by Sam.

For some reason, when building hdf5 with cmake, it installs a massively gimped version of h5cc, that breaks slurms configure setup.

[Comment 5 Larry the Git Cow 2022-06-26 07:02:57 UTC]

The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=aa5804fc23f73e7208b06102845271edf0e8f2cc

commit aa5804fc23f73e7208b06102845271edf0e8f2cc
Author:     Sam James <[e-mail]>
AuthorDate: 2022-06-26 06:55:16 +0000
Commit:     Sam James <[e-mail]>
CommitDate: 2022-06-26 07:02:33 +0000

    sys-cluster/slurm: unpin hdf5 dep; fix MissingUseDepDefault
    
    We've ported back to autotools in hdf5 for now.
    
    Bug: https://github.com/HDFGroup/hdf5/issues/1814
    Closes: https://bugs.gentoo.org/813924
    Signed-off-by: Sam James <[e-mail]>

 sys-cluster/slurm/slurm-20.11.0.1-r105.ebuild | 275 ++++++++++++++++++++++++++
 1 file changed, 275 insertions(+)