This bug is hitting me right now on the HPC system I am using.
It would be nice to be able to get the output without having to use a
temporary file though.
/tmp is not available on this system, for example...
Chris
On 26/03/2014 09:43, Kent-Andre Mardal wrote:
On 26 March 2014 08:16, Johan Hake <[email protected]
<mailto:[email protected]>> wrote:
If none else object, I think we should just push this fix into
instant, as it has been a returning headache for quite a long time.
Sounds good. Then we may check if the patch affects stuff on our local
cluster (where
it has run smoothly for the last year or so)
Kent
Could you make a pull request for your fork? But as os.system does
not work on windows it would be nice to stick with Popen there.
Also see the commented out code in the same module.
Johan
On Tue, Mar 25, 2014 at 2:57 PM, Jan Blechta
<[email protected] <mailto:[email protected]>>
wrote:
After some digging, it seems that segfaults observed on
OFED/InfiniBand
clusters (see [1], [2], [3]) are caused by implementation of
subprocess.Popen
Check your local subprocess.py:_execute_child. Parent does not
seem to
keep hands of memory between fork() and exec() (as required
[4], [5]),
especially as it is fiddling with garbage collector.
I tried switching to os.system (posix implementation in [6])
instead of
subprocess.Popen and it seems promising. Check out [7] or enclosed
patch.
Jan
[1] https://answers.launchpad.net/dolfin/+question/219270
[2] https://answers.launchpad.net/dolfin/+question/225946
[3]
http://fenicsproject.org/pipermail/fenics/2013-June/000398.html
[4] https://www.open-mpi.org/faq/?category=openfabrics#ofa-fork
[5]
http://www.openfabrics.org/downloads/OFED/release_notes/OFED_3.12_rc1_release_notes#3.03
[6]
http://svn.python.org/projects/python/trunk/Modules/posixmodule.c
[7] https://bitbucket.org/blechta/instant/branch/blechta/ofed-fork
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