Hi Dirk
On Thu, 4 Jun 2020 at 14:15, Dirk Eddelbuettel wrote:
> Good to know, thanks for the update!
You are welcome!
On Wed, 3 Jun 2020 at 18:36, Dirk Eddelbuettel wrote:
> According to an Intel report back from 2011, -Bsymbolic-functions "is
> a dangerous option which can often result in
Hi Graham,
On 4 June 2020 at 10:50, Graham Inggs wrote:
| On Wed, 3 Jun 2020 at 18:36, Dirk Eddelbuettel 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 re
Hi Dirk
On Wed, 3 Jun 2020 at 18:36, Dirk Eddelbuettel 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://launchpa
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:/
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.eddel
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 wit
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,
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
Hmm, my last reply to this bug seems to have gone astray.
> 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.
Rebuilt without change: hang with libopenblas0-pthread
Rebuilt with USE_TLS=0: hang
Rebuilt with USE_SIMPLE_THREADED_LEVEL3=1: hang
Rebui
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 wrote:
> Just one quest
> 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.
Rebuilt without change: hang with libopenblas0-pthread
Rebuilt with USE_TLS=0: hang
Rebuilt with USE_SIMPLE_THREADED_LEVEL3=1: hang
Reb
Le samedi 30 mai 2020 à 01:19 +, 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.
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 wor
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.
Le vendredi 29 mai 2020 à 14:55 +0200, Sébastien Villemot a écrit :
> Since Ubuntu did not modify the Debian source package, it means that
> it’s the way of generating the openblas binary within Ubuntu that
> causes the bug.
>
> Compilation flags (as given by dpkg-buildflags) are currently the sa
Le vendredi 29 mai 2020 à 01:13 +, Mo Zhou a écrit :
> Clarification: possibly a Ubuntu bug
> The way to reproduce with nspawn/chroot + ubuntu focal (20.04)
> if you don't have docker
>
> 1. mkdir Focal
> 2. debootstrap focal Focal/
> 3. systemd-nspawn -D Focal
> 4. apt update -y; apt upgrad
On 29 May 2020 at 01:13, Mo Zhou wrote:
| Control: severity -1 important
| Control: tags -1 +moreinfo
| Clarification: possibly a Ubuntu bug
You may be right! I just double checked the earliest report (on the
r-sig-debian list) and it too was on Ubuntu 20.04!
| Hello guys,
|
| The way to repr
Control: severity -1 important
Control: tags -1 +moreinfo
Clarification: possibly a Ubuntu bug
Hello guys,
The way to reproduce with docker + ubuntu devel (20.10)
1. docker image pull ubuntu:devel
2. docker run -ti ubuntu:devel
3. apt update -y ; apt upgrade -y
4. apt install -y r-base-core
5. R
On 28 May 2020 at 16:55, Sébastien Villemot wrote:
| Hi Dirk,
|
| Le jeudi 28 mai 2020 à 07:07 -0500, Dirk Eddelbuettel a écrit :
| > Package: libopenblas-dev
| > Version: 0.3.8+ds-1
| > Severity: serious
|
| > In short, when libopenblas-dev is installed (as e.g. from r-base-dev as a
| > depend
Hi Dirk,
Le jeudi 28 mai 2020 à 07:07 -0500, Dirk Eddelbuettel a écrit :
> Package: libopenblas-dev
> Version: 0.3.8+ds-1
> Severity: serious
> In short, when libopenblas-dev is installed (as e.g. from r-base-dev as a
> dependency from libblas-dev, liblapack-dev) then
>
> libopenblas0-pthrea
Package: libopenblas-dev
Version: 0.3.8+ds-1
Severity: serious
This is a somewhat 'late' bug report followed several on and off discussion
threads on debian-science and/or debian-r (and started on the r-sig-debian
list from the R Project).
In short, when libopenblas-dev is installed (as e.g. fr
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