Polished patched is for a while ready at https://bitbucket.org/fenics-project/instant/pull-request/2 Make sure to read README file, then try.
On two clusters here it looks that patch (with os.system version) saves the day. Looking forward for feedback. Jan On Fri, 28 Mar 2014 10:19:57 +0100 Jan Blechta <[email protected]> wrote: > 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 _______________________________________________ fenics mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics
