[yt-users] parallel yt on ranger
Christine Simpson
csimpson at astro.columbia.edu
Thu Apr 7 19:40:54 PDT 2011
Thanks Matt. I was able to install mpi4py with this and now it works.
Christine
On Thu, 2011-04-07 at 19:47 -0400, Matthew Turk wrote:
> Hi Christine,
>
> Unfortunately, no, you have to install mpi4py yourself. You may be
> able to do this using:
>
> pip install mpi4py
>
> I've been looking at ways of including this in the installer script,
> but I've been a bit stymied by the myriad of mpi wrappers and names.
> I'm optimistic I have *some* kind of solution, but I haven't had a
> chance to test it in detail. For now it's a bit DIY.
>
> -Matt
>
> On Thu, Apr 7, 2011 at 7:45 PM, Christine Simpson
> <csimpson at astro.columbia.edu> wrote:
> > 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
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
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> >>
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