[yt-users] Problem with Rockstar + time series in yt 3.2-dev

Matthew Turk matthewturk at gmail.com
Wed Jun 3 06:06:13 PDT 2015


Hi Brian,

If I had to guess, I'd say that it's not related to MPI, since you're
excluding the infiniband.  I think it's more likely there's an issue
with yt freeing or not freeing one or more of the Rockstar global data
structures, and MPI is the one that catches it or throws the segfault
somehow.  Can you try to get a core dump, check the most recent stack
frame in all threads that lives inside Python space, and see if you
can get a coarse estimate of where it's happening?

-Matt

On Tue, Jun 2, 2015 at 9:31 PM, Brian O'Shea <bwoshea at gmail.com> wrote:
> Hi folks,
>
> I'm having some problems creating a time series of halo catalogs with
> Rockstar on a small cosmology run, using the tip of yt 3.2-dev (changeset
> a2b03516ed2c) with mpi4py v1.3.1 (and OpenMPI v1.4.3) installed on a local
> Linux cluster.
>
> I'm pretty confident that it has something specifically to do with a time
> series. When I use this script to call rockstar on a single dataset:
>
>     http://paste.yt-project.org/show/5586/
>
> with this command line:
>
>     mpirun -np 8 --mca btl ^openib python new_rockstar_ts.py --parallel
>
> everything works just fine, and does so for every RDNNNN dataset.  However,
> when I uncomment lines 40-44 and comment out lines 47-53 in the same script
> (i.e., like this: http://paste.yt-project.org/show/5587/) so that the code
> now uses a time series of all of the RDNNNN datasets rather than a single
> dataset, and use the same command line, I immediately get a seg fault that
> appears to be related to the mpi4py package:
>
> http://paste.yt-project.org/show/5588/
>
> The datasets that I'm using for the time series can be found here:
>
> http://galactica.pa.msu.edu/~bwoshea/data/datasets/rockstar_timeseries.tar.gz
>
> (total size ~300 MB).
>
> Does anybody have any idea what's going on?
>
> Thanks!
>
> --Brian
>
>
>
>
>
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