[yt-users] parallel yt on ranger

Christine Simpson csimpson at astro.columbia.edu
Thu Apr 7 16:45:33 PDT 2011


Hi Britton,

Yes, this was my understanding of ibrun, and what you suggested is the
first thing I tried.  It did not work, however, and I was led to try
something like ibrun mpirun from some old discussions on the list.

However, now looking back on the crash, there was no useful info in
the .o file but in the .e file, it looks like it actually got to the
script, but couldn't import some modules, specifically the mpi4py
module.  Does this come with the yt package?  The script runs on the
command line.  Here is the output from the .e file and the script:

Traceback (most recent call last):
  File "test_parallel_yt.py", line 1, in <module>
    from yt.mods import * 
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/mods.py",
line 44, in <module>
Traceback (most recent call last):
  File "test_parallel_yt.py", line 1, in <module>
    from yt.mods import * 
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/mods.py",
line 44, in <module>
    from yt.data_objects.api import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 34, in <module>
    from yt.data_objects.api import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 34, in <module>
Traceback (most recent call last):
  File "test_parallel_yt.py", line 1, in <module>
    from yt.mods import * 
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/mods.py",
line 44, in <module>
    from yt.data_objects.api import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 34, in <module>
Traceback (most recent call last):
  File "test_parallel_yt.py", line 1, in <module>
    from yt.mods import * 
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/mods.py",
line 44, in <module>
    from yt.data_objects.api import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 34, in <module>
    from hierarchy import \
        from hierarchy import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 40, in <module>
from hierarchy import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 40, in <module>
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 40, in <module>
    from hierarchy import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 40, in <module>
Traceback (most recent call last):
  File "test_parallel_yt.py", line 1, in <module>
    from yt.mods import * 
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/mods.py",
line 44, in <module>
Traceback (most recent call last):
  File "test_parallel_yt.py", line 1, in <module>
    from yt.mods import * 
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/mods.py",
line 44, in <module>
    from yt.data_objects.api import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 34, in <module>
    from yt.data_objects.api import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 34, in <module>
    from hierarchy import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 40, in <module>
    from yt.utilities.parallel_tools.parallel_analysis_interface import
\
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 
47, in <module>
    from yt.utilities.parallel_tools.parallel_analysis_interface import
\
    from yt.utilities.parallel_tools.parallel_analysis_interface import
\
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 
47, in <module>
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 
47, in <module>
    from yt.utilities.parallel_tools.parallel_analysis_interface import
\
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 
47, in <module>
    from hierarchy import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 40, in <module>
Traceback (most recent call last):
  File "test_parallel_yt.py", line 1, in <module>
    from yt.mods import * 
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/mods.py",
line 44, in <module>
    from yt.utilities.parallel_tools.parallel_analysis_interface import
\
    from yt.data_objects.api import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 
47, in <module>
    from yt.utilities.parallel_tools.parallel_analysis_interface import
\
Traceback (most recent call last):
  File "test_parallel_yt.py", line 1, in <module>
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 34, in <module>
    from yt.mods import * 
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/mods.py",
line 44, in <module>
   from hierarchy import \
    from yt.data_objects.api import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 
47, in <module>
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 40, in <module>
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/api.py", line 34, in <module>
    from yt.utilities.parallel_tools.parallel_analysis_interface import
\
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 
47, in <module>
    from hierarchy import \
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/data_objects/hierarchy.py", line 40, in <module>
    from yt.utilities.parallel_tools.parallel_analysis_interface import
\
  File
"/share/home/01112/tg803911/yt_4apr2011/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 
47, in <module>
    from mpi4py import MPI
    from mpi4py import MPI
    from mpi4py import MPI
ImportError    : from mpi4py import MPI
    from mpi4py import MPI
ImportErrorNo module named mpi4py: 
    No module named mpi4py    from mpi4py import MPI

from mpi4py import MPI
ImportErrorImportError: : ImportError: No module named mpi4pyNo module
named mpi4pyNo module named mpi4py


ImportError: ImportError: No module named mpi4py
No module named mpi4py
    from mpi4py import MPI
ImportError: No module named mpi4py
mpispawn.c:303 Unexpected exit status

Child exited abnormally!
Killing remote processes...DONE


script:
from yt.mods import * 
from yt.visualization.api import PlotCollection

import matplotlib.colorbar as cb

path =
"/scratch/01112/tg803911/halo88_therm_feed_1e-6_LW_RadiationShield_lmax12/DD0010/"
fn = "output_0010"
pf = load(path+fn)
pc = PlotCollection(pf)
pc.add_projection("Density",0)
pc.set_width(20,'kpc')
pc.save(fn)

On Thu, 2011-04-07 at 17:24 -0400, Britton Smith wrote:
> Hi Christine,
> 
> Mpirun and ibrun are basically the same thing.  On Ranger, you just
> want to use ibrun.  You also don't need to specify the number of
> processors on Ranger.  It gets that from the "8way 16" line at the
> top.
> 
> The command in your script should be:
> 
> ibrun python2.7 test_parallel_yt.py --parallel
> 
> Britton
> 
> On Thu, Apr 7, 2011 at 5:20 PM, Christine Simpson
> <csimpson at astro.columbia.edu> wrote:
>         Hi all,
>         
>         I'm trying to run yt in parallel on ranger.  I gather from
>         previous
>         messages to this list that others have had issues in the past,
>         but I
>         haven't been able to find something that works from those
>         posts.
>         
>         I'm trying to run a test script that does a simple projection.
>         
>         First I tried this (from the yt docs):
>         
>         ibrun mpirun -np 8 python2.7 test_parallel_yt.py --parallel
>         
>         I got this output in the output file:
>         TACC: Setting memory limits for job 1896644 to unlimited KB
>         TACC: Dumping job script:
>         --------------------------------------------------------------------------------
>         #  Submit this script using the "qsub" command.
>         #  Use the "qstat" command to check the status of a job.
>         #
>         #$-l h_rt=00:05:00
>         #$-pe 8way 16
>         #$-N test_parallel_yt
>         #$-o $JOB_NAME.o$JOB_ID
>         #$-q development
>         #$-M csimpson at astro.columbia.edu
>         #$-m be
>         #$-V
>         #$-cwd
>         
>         ibrun mpirun -np 8 python2.7 test_parallel_yt.py --parallel
>         
>         
>         
>         
>         --------------------------------------------------------------------------------
>         TACC: Done.
>         TACC: Starting up job 1896644
>         TACC: Setting up parallel environment for MVAPICH ssh-based
>         mpirun.
>         TACC: Setup complete. Running job script.
>         TACC: starting parallel tasks...
>         Warning: Command line arguments for program should be given
>         after the program name.  Assuming that test_parallel_yt.py is
>         a
>         command line argument for the program.
>         Warning: Command line arguments for program should be given
>         after the program name.  Assuming that test_parallel_yt.py is
>         a
>         command line argument for the program.
>         Warning: Command line arguments for program should be given
>         after the program name.  Assuming that test_parallel_yt.py is
>         a
>         command line argument for the program.
>         Warning: Command line arguments for program should be given
>         after the program name.  Assuming that test_parallel_yt.py is
>         a
>         command line argument for the program.
>         Warning: Command line arguments for program should be given
>         after the program name.  Assuming that test_parallel_yt.py is
>         a
>         command line argument for the program.
>         Warning: Command line arguments for program should be given
>         after the program name.  Assuming that test_parallel_yt.py is
>         a
>         command line argument for the program.
>         Warning: Command line arguments for program should be given
>         after the program name.  Assuming that test_parallel_yt.py is
>         a
>         command line argument for the program.
>         Warning: Command line arguments for program should be given
>         after the program name.  Assuming that test_parallel_yt.py is
>         a
>         command line argument for the program.
>         Warning: Command line arguments for program should be given
>         after the program name.  Assuming that --parallel is a
>         command line argument for the program.
>         Missing: program name
>         Program python2.7 either does not exist, is not
>         executable, or is an erroneous argument to mpirun.
>         Warning: Command line arguments for program should be given
>         after the program name.  Assuming that --parallel is a
>         command line argument for the program.
>         TACC: MPI job exited with code: 1
>         TACC: Shutting down parallel environment.
>         TACC: Shutdown complete. Exiting.
>         TACC: Cleaning up after job: 1896644
>         TACC: Done.
>         
>         
>         I also tried this:
>         
>         ibrun mpi4py -np 8 python2.7 test_parallel_yt.py --parallel
>         
>         and got this output:
>         TACC: Setting memory limits for job 1896674 to unlimited KB
>         TACC: Dumping job script:
>         --------------------------------------------------------------------------------
>         #!/bin/sh
>         #
>         #  Submit this script using the "qsub" command.
>         #  Use the "qstat" command to check the status of a job.
>         #
>         #$-l h_rt=00:05:00
>         #$-pe 8way 16
>         #$-N test_parallel_yt
>         #$-o $JOB_NAME.o$JOB_ID
>         #$-q development
>         #$-M csimpson at astro.columbia.edu
>         #$-m be
>         #$-V
>         #$-cwd
>         
>         ibrun mpi4py -np 8 python2.7 test_parallel_yt.py --parallel
>         
>         
>         
>         
>         --------------------------------------------------------------------------------
>         TACC: Done.
>         TACC: Starting up job 1896674
>         TACC: Setting up parallel environment for MVAPICH ssh-based
>         mpirun.
>         TACC: Setup complete. Running job script.
>         TACC: starting parallel tasks...
>         TACC: MPI job exited with code: 1
>         TACC: Shutting down parallel environment.
>         TACC: Shutdown complete. Exiting.
>         TACC: Cleaning up after job: 1896674
>         TACC: Done.
>         
>         
>         Any ideas?  I guess in the first instance it is not finding
>         python, but
>         the test script I run works fine on the command line and doing
>         -V should
>         import the same environment settings, right?  I guess in the
>         second
>         instance I'm using the wrong mpi call.  I found info on that
>         call in
>         some old posts to the email list.
>         
>         Christine
>         
>         
>         
>         
>         
>         
>         
>         
>         
>         
>         _______________________________________________
>         yt-users mailing list
>         yt-users at lists.spacepope.org
>         http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> 
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