Re: OpenBlas Pthread issue with R
Hi Seb,
On 1 May 2020 at 14:18, Sébastien Villemot wrote:
| Le vendredi 01 mai 2020 à 07:05 -0500, Dirk Eddelbuettel a écrit :
| > On 1 May 2020 at 05:16, Mo Zhou wrote:
| > > On Thu, Apr 30, 2020 at 11:26:23PM -0500, Dirk Eddelbuettel wrote:
| > > > Switching to libopenblas0-openmp works but one needs to uninstall
| > > > libopenblas0-pthread (or else fiddle with the alternatives priority).
| > >
| > > Does that mean the update-alternatives mechanism is malfunctioning?
| >
| > I do not know.
| >
| > It could just be the default ranking is wrong. I did not check, and was
| > interested in fiddling manually (as I find it always bites me years later...)
| >
| > Given that openblas-pthread renders R _unuseable_ and that Seb said it was a
| > known issue, maybe we should ensure it ranks lower than it currently does?
|
| I did not say that it is a known issue. I said that we had a similar
| issue in the past, but that it was solved.
|
| Also, I tried to reproduce the problem on an unstable system with
| OpenBLAS/pthreads selected as the alternative, but I couldn’t. The
| computation goes fine for me. So I guess the problem manifests only on
| specific systems or CPUs.
|
| I suggest that you open a bug report, providing as many details as
| possible on the system where it manifests (in particular, the precise
| CPU model).
|
| Also, I don’t think we should change the alternatives priorities. The
| OpenMP flavour of OpenBLAS has its own problems (in particular, because
| it is compiled with GNU OpenMP, it is incompatible with applications
| compiled against Intel’s OpenMP, and we cannot do anything about that).
| So we should rather fix the bug that you encountered.
For what it is worth, on my (personal) workstation I re-encountered the bug
yesterday, chiefly because "it is still there" and the default ordering does
not help me -- quite the contrary, it "causes it".
All I did was to go from Ubuntu 19.10 to 20.04; I have a i7-8700k cpu and the
simple test of `example(solve)` reliably hangs R. Rememy:
sudo apt install libopenblas-openmp-dev
sudo apt remove libopenblas0-pthread
After that things are fine again. It's a tricky issue for newb. It would be
really good if we could squash / circumvent it.
I would be happy to test newer/different version if you have them. I could
drop any new Debian sources onto my PPA to test them on this box.
Dirk
--
http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org
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