On Thu, 27 Mar 2014 20:51:37 +0000 Chris Richardson <[email protected]> wrote:
> > 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... Ok, I will try rewriting it without temporary. Jan > > 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 > > _______________________________________________ fenics mailing list > > [email protected] <mailto:[email protected]> > > http://fenicsproject.org/mailman/listinfo/fenics > > > > > > > > _______________________________________________ > > fenics mailing list > > [email protected] <mailto:[email protected]> > > http://fenicsproject.org/mailman/listinfo/fenics > > > > > > > > > > _______________________________________________ > > fenics mailing list > > [email protected] > > http://fenicsproject.org/mailman/listinfo/fenics > _______________________________________________ fenics mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics
