[Yt-dev] Nautilus: ParallelHaloProfiler I/O issue

[Geoffrey So]

Hi Stephen, Pragneshkumar

Let me know if I should move this discussion off the yt-dev list.

The box size is only 80 Mpc or 56 Mpc/h, so load balancing probably help
with peak memory more than hinder, but could still try turning it off.

Would decreasing the amount of cores alleviate some of the symptoms? Or
would that just increase the computation time too much?  I haven't done any
scaling tests on the parallelHF.

Incidentally, I've killed the job after seeing the following error, looks
like mpi was having some buffer trouble, which could be caused by the heavy
IO?:
.
.
.

MPI WARNING: Could not allocate an internal buffer in the last 30 seconds
on rank 503.  Try increasing MPI_BUFS_PER_PROC and/or MPI_BUFS_PER_HOST.
MPI WARNING: Could not allocate an internal buffer in the last 30 seconds
on rank 505.  Try increasing MPI_BUFS_PER_PROC and/or MPI_BUFS_PER_HOST.
MPI WARNING: Could not allocate an internal buffer in the last 30 seconds
on rank 509.  Try increasing MPI_BUFS_PER_PROC and/or MPI_BUFS_PER_HOST.
MPI WARNING: Could not allocate an internal buffer in the last 30 seconds
on rank 511.  Try increasing MPI_BUFS_PER_PROC and/or MPI_BUFS_PER_HOST.
Traceback (most recent call last):
  File "ParallelHaloProfiler.py", line 17, in <module>
    rearrange=True, safety=1.5, premerge=True)
  File
"/nics/b/home/gsiisg/NautilusYT/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py",
line 1861, in __init__
    root_points = self._subsample_points()
  File
"/nics/b/home/gsiisg/NautilusYT/src/yt-hg/yt/analysis_modules/halo_finding/halo_objects.py",
line 1991, in _subsample_points
    root_points = self._mpi_concatenate_array_on_root_double(my_points[0])
  File
"/nics/b/home/gsiisg/NautilusYT/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 187, in passage
    return func(self, data)
  File
"/nics/b/home/gsiisg/NautilusYT/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py",
line 794, in _mpi_concatenate_array_on_root_double
    data = na.concatenate((data, new_data))
ValueError: negative dimensions are not allowed

Can I get a refund of the SU on that job?

From
G.S.

On Fri, Sep 23, 2011 at 10:51 AM, Stephen Skory <s at skory.us> wrote:

> Geoffrey,
>
> > (1) How much data are read/written by program ?
> > - After all the particles (3200^3 of them) are read in they are linked
> with
> > a fortran KDtree if they satisfy some conditions.
> >
> > (2) How many parallel readers/writers are used by program ?
> > - It is reading using 512 cores from my submission script.  The amount of
> > write to disk depends on the distribution of the particle haloes across
> > processors, if they exist across processors then there will be more files
> > written out by write_particle_lists.
> > (3) Do you use MPI_IO ? or something else ?
> > - Yes, the program uses mpi4py-1.2.2 installed in my home directory
> > The details of the code can be found at:
> >
> http://yt-project.org/doc/analysis_modules/running_halofinder.html#halo-finding
> > under the section "Parallel HOP"
>
> The main thing you got wrong is that we do not use MPI_IO. The IO is
> done primarily through a custom HDF5 reader written in C, and each
> thread does its own reading.
>
> The issue that Pragnesh is probably seeing, and what Geoffrey alludes
> to, is how load balancing is done. Because of the details of how Enzo
> stores its data, it is difficult to know where to send the data for
> load balancing it without reading it all in, first. Out of
> convenience, once the layout is established, the data is read in again
> (instead of distributed via communication), this time by the tasks
> that have been assigned the data. Furthermore, the data as assigned
> may come from several files, meaning that each task will be
> opening/closing multiple files multiple times.
>
> If all these IO calls are causing a problem, I could see about putting
> in some kind of IO wait (configurable by the user) that basically
> slows down the reading part of the process.
>
> p.s. Geoffrey - what is the cosmological size of your box? If it's
> above about 300 Mpc/h, load balancing is probably not necessary, which
> should roughly half the IO required.
>
> --
> Stephen Skory
> s at skory.us
> http://stephenskory.com/
> 510.621.3687 (google voice)
> _______________________________________________
> Yt-dev mailing list
> Yt-dev at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-dev-spacepope.org
>
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