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Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock

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  Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Mo Zhou <lumin@debian.org> - 2020-05-30 03:30 +0200
    Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Dirk Eddelbuettel <edd@debian.org> - 2020-05-30 04:00 +0200
    Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Sébastien Villemot <sebastien@debian.org> - 2020-05-30 09:20 +0200
      Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Graham Inggs <ginggs@debian.org> - 2020-05-30 21:40 +0200
        Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Sébastien Villemot <sebastien@debian.org> - 2020-05-30 21:50 +0200
          Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Dirk Eddelbuettel <edd@debian.org> - 2020-05-30 22:20 +0200
            Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Dirk Eddelbuettel <edd@debian.org> - 2020-06-01 13:30 +0200
              Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Dirk Eddelbuettel <edd@debian.org> - 2020-06-03 18:40 +0200
                Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Graham Inggs <ginggs@debian.org> - 2020-06-04 10:50 +0200
                  Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Dirk Eddelbuettel <edd@debian.org> - 2020-06-04 14:20 +0200
                    Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Graham Inggs <ginggs@debian.org> - 2020-06-04 14:40 +0200
        Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock Dirk Eddelbuettel <edd@debian.org> - 2020-05-30 22:20 +0200

#1011955 — Bug#961725: libopenblas-dev: On some cpus, openmp and pthread dead-lock

Control: tags -1 -moreinfo

Hi Sébastien,

Good catch! I tried to remove the mentioned LDFLAG

  DEB_LDFLAGS_MAINT_STRIP="-Wl,-Bsymbolic-functions"

and rebuilt the openblas 3.8 package.

Then deadlock issue disappeared.

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#1011956

On 30 May 2020 at 01:19, Mo Zhou wrote:
| Control: tags -1 -moreinfo
| 
| Hi Sébastien,
| 
| Good catch! I tried to remove the mentioned LDFLAG
| 
|   DEB_LDFLAGS_MAINT_STRIP="-Wl,-Bsymbolic-functions"
| 
| and rebuilt the openblas 3.8 package.
| 
| Then deadlock issue disappeared.

Wow. Nice work.

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org

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#1011966

[Multipart message — attachments visible in raw view] — view raw

Le samedi 30 mai 2020 à 01:19 +0000, Mo Zhou a écrit :
> Control: tags -1 -moreinfo
> 
> Hi Sébastien,
> 
> Good catch! I tried to remove the mentioned LDFLAG
> 
>   DEB_LDFLAGS_MAINT_STRIP="-Wl,-Bsymbolic-functions"
> 
> and rebuilt the openblas 3.8 package.
> 
> Then deadlock issue disappeared.

Just one question: did you try to rebuild it from source without
changing anything? Maybe it’s just the rebuild that fixed it, and not
the flag change.

-- 
⢀⣴⠾⠻⢶⣦⠀  Sébastien Villemot
⣾⠁⢠⠒⠀⣿⡁  Debian Developer
⢿⡄⠘⠷⠚⠋⠀  https://sebastien.villemot.name
⠈⠳⣄⠀⠀⠀⠀  https://www.debian.org

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#1012032

Hi

I was able to reproduce this in Ubuntu 20.04 on i7-2600 with the
    Rscript -e "example(solve)"
test case.  Rebuilding with
    export DEB_LDFLAGS_MAINT_STRIP="-Wl,-Bsymbolic-functions"
in debian/rules solved it for me.

On Sat, 30 May 2020 at 09:15, Sébastien Villemot <sebastien@debian.org> wrote:
> Just one question: did you try to rebuild it from source without
> changing anything? Maybe it’s just the rebuild that fixed it, and not
> the flag change.

I confirm that a no-change rebuild had no effect.

I suspect this is the same problem that was discovered in LP: #1860601
[1], but I was unable to reproduce it locally.
I'll take care of fixing this in Ubuntu Groovy and SRU for Ubuntu Focal.

Could we get this fixed in Debian?  At worst, it should be a no-op in
Debian, and should someone try rebuilding locally with -Bsymbolic-
functions they won't fall into this trap.

Regards
Graham


[1] https://pad.lv/1860601

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#1012035

[Multipart message — attachments visible in raw view] — view raw

Control: tags -1 + patch

Hi Graham,

Le samedi 30 mai 2020 à 15:09 +0200, Graham Inggs a écrit :

> I was able to reproduce this in Ubuntu 20.04 on i7-2600 with the
>     Rscript -e "example(solve)"
> test case.  Rebuilding with
>     export DEB_LDFLAGS_MAINT_STRIP="-Wl,-Bsymbolic-functions"
> in debian/rules solved it for me.
> 
> On Sat, 30 May 2020 at 09:15, Sébastien Villemot <
> sebastien@debian.org
> > wrote:
> > Just one question: did you try to rebuild it from source without
> > changing anything? Maybe it’s just the rebuild that fixed it, and not
> > the flag change.
> 
> I confirm that a no-change rebuild had no effect.

Thanks to you (and to Mo) for doing those rebuilds.

> Could we get this fixed in Debian?  At worst, it should be a no-op in
> Debian, and should someone try rebuilding locally with -Bsymbolic-
> functions they won't fall into this trap.

Sure, we’ll fix it in Debian (a similar fix is present in src:lapack,
by the way).

It could however take some time, because we are currently waiting for
NEW clearance from the most recent upload of src:openblas.

Best,

-- 
⢀⣴⠾⠻⢶⣦⠀  Sébastien Villemot
⣾⠁⢠⠒⠀⣿⡁  Debian Developer
⢿⡄⠘⠷⠚⠋⠀  https://sebastien.villemot.name
⠈⠳⣄⠀⠀⠀⠀  https://www.debian.org

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#1012039

On 30 May 2020 at 21:39, Sébastien Villemot wrote:
| Control: tags -1 + patch
| 
| Hi Graham,
| 
| Le samedi 30 mai 2020 à 15:09 +0200, Graham Inggs a écrit :
| 
| > I was able to reproduce this in Ubuntu 20.04 on i7-2600 with the
| >     Rscript -e "example(solve)"
| > test case.  Rebuilding with
| >     export DEB_LDFLAGS_MAINT_STRIP="-Wl,-Bsymbolic-functions"
| > in debian/rules solved it for me.
| > 
| > On Sat, 30 May 2020 at 09:15, Sébastien Villemot <
| > sebastien@debian.org
| > > wrote:
| > > Just one question: did you try to rebuild it from source without
| > > changing anything? Maybe it’s just the rebuild that fixed it, and not
| > > the flag change.
| > 
| > I confirm that a no-change rebuild had no effect.
| 
| Thanks to you (and to Mo) for doing those rebuilds.
| 
| > Could we get this fixed in Debian?  At worst, it should be a no-op in
| > Debian, and should someone try rebuilding locally with -Bsymbolic-
| > functions they won't fall into this trap.
| 
| Sure, we’ll fix it in Debian (a similar fix is present in src:lapack,
| by the way).
| 
| It could however take some time, because we are currently waiting for
| NEW clearance from the most recent upload of src:openblas.

Awesome too. Really good to see everybody remains on top of this.

Dirk
 
| Best,
| 
| -- 
| ⢀⣴⠾⠻⢶⣦⠀  Sébastien Villemot
| ⣾⠁⢠⠒⠀⣿⡁  Debian Developer
| ⢿⡄⠘⠷⠚⠋⠀  https://sebastien.villemot.name
| ⠈⠳⣄⠀⠀⠀⠀  https://www.debian.org
| 
| [DELETED ATTACHMENT signature.asc, application/pgp-signature]

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org

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#1012213

For completeness, Conrad Sanderson (who is the main author of Armadillo,
which is used inter alia by MLPACK) posted another good summary with links to
other projects including also a launchpad bug report:
https://bugs.launchpad.net/ubuntu/+source/openblas/+bug/1870138

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org

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#1012513

Conrad (of Armadillo fame) sent me this (and ok'ed passing it on):

  According to an Intel report back from 2011, -Bsymbolic-functions "is
  a dangerous option which can often result in some non-intuitive side
  effects".
  The report explicitly shows various problems with the option.
  https://software.intel.com/content/www/us/en/develop/articles/performance-tools-for-software-developers-bsymbolic-can-cause-dangerous-side-effects.html

  In the light of the above, it's a real wonder that Ubuntu uses the
  option at all.

  Perhaps Ubuntu developers meant well, but are not aware of the side effects ?

Graham do you think you can get it turned off for at least openblas?

Dirk

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org

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#1012582

Hi Dirk

On Wed, 3 Jun 2020 at 18:36, Dirk Eddelbuettel <edd@debian.org> wrote:
> Graham do you think you can get it turned off for at least openblas?

Already fixed in Groovy [1] and the Stable Release Update [2] for
Focal is in the queue [3] awaiting review by the SRU Team.

Regards
Graham


[1] https://launchpad.net/ubuntu/+source/openblas
[2] https://wiki.ubuntu.com/StableReleaseUpdates#Procedure
[3] https://launchpad.net/ubuntu/focal/+queue?queue_state=1

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#1012615

Hi Graham,

On 4 June 2020 at 10:50, Graham Inggs wrote:
| On Wed, 3 Jun 2020 at 18:36, Dirk Eddelbuettel <edd@debian.org> wrote:
| > Graham do you think you can get it turned off for at least openblas?
| 
| Already fixed in Groovy [1] and the Stable Release Update [2] for
| Focal is in the queue [3] awaiting review by the SRU Team.

Good to know, thanks for the update!

Dirk
 
| Regards
| Graham
| 
| 
| [1] https://launchpad.net/ubuntu/+source/openblas
| [2] https://wiki.ubuntu.com/StableReleaseUpdates#Procedure
| [3] https://launchpad.net/ubuntu/focal/+queue?queue_state=1

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org

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#1012622

Hi Dirk

On Thu, 4 Jun 2020 at 14:15, Dirk Eddelbuettel <edd@debian.org> wrote:
> Good to know, thanks for the update!

You are welcome!

On Wed, 3 Jun 2020 at 18:36, Dirk Eddelbuettel <edd@debian.org> wrote:
>   According to an Intel report back from 2011, -Bsymbolic-functions "is
>   a dangerous option which can often result in some non-intuitive side
>   effects".
>   The report explicitly shows various problems with the option.
>   https://software.intel.com/content/www/us/en/develop/articles/performance-tools-for-software-developers-bsymbolic-can-cause-dangerous-side-effects.html
>
>   In the light of the above, it's a real wonder that Ubuntu uses the
>   option at all.

By the way, note that -Bsymbolic != -Bsymbolic-functions

From dpgk's changelog, it seems Ubuntu have linking with
-Bsymbolic-functions as default since about 2008.
codesearch.debian.net only shows about 62 source packages (of the 10s
of thousands in Debian) where this needs to be overridden.
It seems overriding it in openblas only became necessary since the
restructuring in 0.3.7+ds-2, so no versions prior to Focal should be
affected.

Regards
Graham

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#1012040

On 30 May 2020 at 15:09, Graham Inggs wrote:
| Hi
| 
| I was able to reproduce this in Ubuntu 20.04 on i7-2600 with the
|     Rscript -e "example(solve)"
| test case.  Rebuilding with
|     export DEB_LDFLAGS_MAINT_STRIP="-Wl,-Bsymbolic-functions"
| in debian/rules solved it for me.
| 
| On Sat, 30 May 2020 at 09:15, Sébastien Villemot <sebastien@debian.org> wrote:
| > Just one question: did you try to rebuild it from source without
| > changing anything? Maybe it’s just the rebuild that fixed it, and not
| > the flag change.
| 
| I confirm that a no-change rebuild had no effect.
| 
| I suspect this is the same problem that was discovered in LP: #1860601
| [1], but I was unable to reproduce it locally.
| I'll take care of fixing this in Ubuntu Groovy and SRU for Ubuntu Focal.

Lovely!  I was wondering how we could possibly reach out and get to someone!

Dirk

| Could we get this fixed in Debian?  At worst, it should be a no-op in
| Debian, and should someone try rebuilding locally with -Bsymbolic-
| functions they won't fall into this trap.
| 
| Regards
| Graham
| 
| 
| [1] https://pad.lv/1860601

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org

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