[SRU] openblas: -Wl,-Bsymbolic-functions should be stripped from LDFLAGS

I would like someone to investigate this further: if this is a real issue and how users can be affected. Since this looks like a regression in openblas. I built the same package that Graham prepared on a PPA with only Updates enabled and it built fine - so it's proof that the openblas in -proposed does something really fishy.

On one hand it feels like something we might hint, but first I'd like to know if this is something we only see on builders/Ubuntu-ADT and why that is happening. Julian is investigating this further.

I have reproduced the issue on the infrastructure. This seems to be related to pthread support in openblas, as if I swap it out for openblas' openmp variant, it works.

Now there have been no changes in openblas aside from restructuring the packaging, so the real cause must surely lie elsewhere - maybe it picked up a newer pthread symbol version from libc, or an inline function from liblapack?

It does not hang - it seems to be stuck in an infinite loops - all 4 processes run at 400% CPU usage, and seem busy locking and unlocking a mutex.

I also rebuilt openblas on the autopkgtest host (w/o proposed) and tested with that, but the failure is the same.

I don't think it's worthwhile exploring this further - users can switch to the openmp variant of openblas if they encounter issues in the pthread one, and who uses this on armhf anyway?

Ok, in lieu of Julian's and Graham's investigations, I will be hinting this failure - but let's maybe forward this upstream (possibly to openblas, maybe hypre to let them know it's broken).

Confirming that rebuilding openblas 0.3.8+ds-1 in Focal with

    export DEB_LDFLAGS_MAINT_STRIP="-Wl,-Bsymbolic-functions"

makes hypre autopkgtest pass on armhf.

Status changed to 'Confirmed' because the bug affects multiple users.

This bug was fixed in the package openblas - 0.3.9+ds-1ubuntu1

---------------
openblas (0.3.9+ds-1ubuntu1) groovy; urgency=medium

  * Strip -Wl,-Bsymbolic-functions from LDFLAGS (LP: #1860601)
    also see #961725 and #722252

 -- Graham Inggs <email address hidden> Sun, 31 May 2020 06:00:25 +0000

Thank you for working on this. Accepting into Focal, but please could you update "Regression Potential" with a discussion of how regressions are most likely to manifest, or may manifest even if it is unlikely, as a result of this change? See https://wiki.ubuntu.com/StableReleaseUpdates#Procedure - this is useful for making sure that appropriate testing is performed during SRU verification.

Hello Graham, or anyone else affected,

Accepted openblas into focal-proposed. The package will build now and be available at https://launchpad.net/ubuntu/+source/openblas/0.3.8+ds-1ubuntu0.20.04.1 in a few hours, and then in the -proposed repository.

Please help us by testing this new package. See https://wiki.ubuntu.com/Testing/EnableProposed for documentation on how to enable and use -proposed. Your feedback will aid us getting this update out to other Ubuntu users.

If this package fixes the bug for you, please add a comment to this bug, mentioning the version of the package you tested, what testing has been performed on the package and change the tag from verification-needed-focal to verification-done-focal. If it does not fix the bug for you, please add a comment stating that, and change the tag to verification-failed-focal. In either case, without details of your testing we will not be able to proceed.

Further information regarding the verification process can be found at https://wiki.ubuntu.com/QATeam/PerformingSRUVerification . Thank you in advance for helping!

N.B. The updated package will be released to -updates after the bug(s) fixed by this package have been verified and the package has been in -proposed for a minimum of 7 days.

All autopkgtests for the newly accepted openblas (0.3.8+ds-1ubuntu0.20.04.1) for focal have finished running.
The following regressions have been reported in tests triggered by the package:

gemma/0.98.1+dfsg-1 (arm64)
r-bioc-deseq2/unknown (armhf)
python-ltfatpy/unknown (armhf)

Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding autopkgtest regressions [1].

https://people.canonical.com/~ubuntu-archive/proposed-migration/focal/update_excuses.html#openblas

[1] https://wiki.ubuntu.com/StableReleaseUpdates#Autopkgtest_Regressions

Thank you!

The autopkgtests listed below all passed when retried.

gemma/0.98.1+dfsg-1 (arm64)
r-bioc-deseq2/unknown (armhf)
python-ltfatpy/unknown (armhf)

Installed in two stages (first OpenMP, then Pthread) verifying that

   Rscript -e 'example(solve)' # known example to 'hang' under openblas-pthread

now works again. Thanks for the fix!

edd@rob:~$ dpkg -l | grep openblas | cut -c -70
ii libopenblas-dev:amd64 0.3.8+ds-1ubuntu0.20.04
ii libopenblas-openmp-dev:amd64 0.3.8+ds-1ubuntu0.20.04
ii libopenblas-pthread-dev:amd64 0.3.8+ds-1ubuntu0.20.04
ii libopenblas0:amd64 0.3.8+ds-1ubuntu0.20.04
ii libopenblas0-openmp:amd64 0.3.8+ds-1ubuntu0.20.04
ii libopenblas0-pthread:amd64 0.3.8+ds-1ubuntu0.20.04
edd@rob:~$

Hello Dirk! Thank you for the verification. At first I was worried about the version numbers you have posted in your verification comment, as the -proposed version is 0.3.8+ds-1ubuntu0.20.04.1 instead of 0.3.8+ds-1ubuntu0.20.04 (as per your dpkg -l snippet). But then I noticed that you have used `cut -c -70`, and in this case it indeed cuts the last ".1" from the output.

Phew! So, with this in mind, I accept the verification. But next time please make sure that the full version number is recorded!

This bug was fixed in the package openblas - 0.3.8+ds-1ubuntu0.20.04.1

---------------
openblas (0.3.8+ds-1ubuntu0.20.04.1) focal; urgency=medium

  * Strip -Wl,-Bsymbolic-functions from LDFLAGS (LP: #1860601)
    also see #961725 and #722252

 -- Graham Inggs <email address hidden> Tue, 02 Jun 2020 10:55:55 +0000

The verification of the Stable Release Update for openblas has completed successfully and the package is now being released to -updates. Subsequently, the Ubuntu Stable Release Updates Team is being unsubscribed and will not receive messages about this bug report. In the event that you encounter a regression using the package from -updates please report a new bug using ubuntu-bug and tag the bug report regression-update so we can easily find any regressions.