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Bug 863089 - sci-libs/hdf5-1.12.2-r4: build fails with USE="unsupported mpi cxx" `../../test/.libs/libh5test.a(h5test.o): undefined reference to symbol 'ompi_mpi_comm_world`
Summary: sci-libs/hdf5-1.12.2-r4: build fails with USE="unsupported mpi cxx" `../../te...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
: 904414 (view as bug list)
Depends on:
Blocks:
 
Reported: 2022-08-02 15:03 UTC by Fat-Zer
Modified: 2023-04-18 08:25 UTC (History)
4 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
build.log.xz (build.log.xz,44.82 KB, application/x-xz)
2022-08-02 15:05 UTC, Fat-Zer
Details
emerge --info '=sci-libs/hdf5-1.12.2-r4::gentoo' (file_863089.txt,9.35 KB, text/plain)
2022-08-02 15:07 UTC, Fat-Zer
Details

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Description Fat-Zer 2022-08-02 15:03:18 UTC
subj; it's a regression comparing to `sci-libs/hdf5-1.12.2-r2`.

Reproducible: Always
Comment 1 Fat-Zer 2022-08-02 15:05:54 UTC
Created attachment 797020 [details]
build.log.xz

$ emerge -pqv '=sci-libs/hdf5-1.12.2-r4::gentoo'

[ebuild     U ] sci-libs/hdf5-1.12.2-r4 [1.12.2-r2] USE="cxx fortran hl mpi szip unsupported zlib -debug -examples -threads (-doc%) (-test%)"
Comment 2 Fat-Zer 2022-08-02 15:07:43 UTC
Created attachment 797029 [details]
emerge --info '=sci-libs/hdf5-1.12.2-r4::gentoo'
Comment 3 Fat-Zer 2022-08-02 15:55:35 UTC
It looks like this regression is caused by reverting back to autotools. I'm wondering if bug #665378 was the only reason for this decision?

The commit also references `h5cc -show` issue[1], but it seems that gentoo's sci-libs/hdf5-1.12.2-r2 was unaffected by it (at least I can't reproduce it)...

[1]: https://github.com/HDFGroup/hdf5/issues/1814
Comment 4 Sam James archtester Gentoo Infrastructure gentoo-dev Security 2022-08-04 02:17:17 UTC
(In reply to Fat-Zer from comment #3)
> It looks like this regression is caused by reverting back to autotools. I'm
> wondering if bug #665378 was the only reason for this decision?
> 
> The commit also references `h5cc -show` issue[1], but it seems that gentoo's
> sci-libs/hdf5-1.12.2-r2 was unaffected by it (at least I can't reproduce
> it)...
> 
> [1]: https://github.com/HDFGroup/hdf5/issues/1814

It broke various packages (see bug 820158 too).
Comment 5 Leonid Kopylov 2022-09-27 12:28:24 UTC
i got "undefined reference to symbol 'MPI_Info_get'"
Comment 6 dave knippers 2023-03-15 19:16:38 UTC
I'm seeing this ompi_mpi_comm_world error as well. Are there any suggestions for a fix?
Comment 7 Sam James archtester Gentoo Infrastructure gentoo-dev Security 2023-04-18 07:52:01 UTC
*** Bug 904414 has been marked as a duplicate of this bug. ***
Comment 8 Larry the Git Cow gentoo-dev 2023-04-18 08:25:07 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=52ff075678f80c88a0e8f40dd8f31c843f2399f0

commit 52ff075678f80c88a0e8f40dd8f31c843f2399f0
Author:     Sam James <sam@gentoo.org>
AuthorDate: 2023-04-18 08:06:27 +0000
Commit:     Sam James <sam@gentoo.org>
CommitDate: 2023-04-18 08:06:27 +0000

    sci-libs/hdf5: add 1.14.0
    
    Closes: https://bugs.gentoo.org/863089
    Signed-off-by: Sam James <sam@gentoo.org>

 sci-libs/hdf5/Manifest           |   1 +
 sci-libs/hdf5/hdf5-1.14.0.ebuild | 119 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 120 insertions(+)