[yt-users] error on pmods import

[Nathan Goldbaum]

I helped Morgan with this off-list - he fixed the issue by replacing
yt.pmods with yt.mods.  I'm not sure what's going wrong with the parallel
import that pmods does.

For what it's worth, it's not totally clear from the docs that pmods isn't
necessary to use yt's parallelism.


On Sun, Oct 6, 2013 at 12:26 AM, Morgan MacLeod <mmacleod at ucolick.org>wrote:

> Dear YT developers,
>
> I'm having a slight yt parallelism issue on one cluster at UCSC, "Laozi".
>  I just installed a fresh version of yt-3.0 on this machine.
>
> I'm pasting the full info below, but I will note that this is similar to
> an issue reported on the list:
> http://lists.spacepope.org/pipermail/yt-users-spacepope.org/2012-October/003016.html
>
> There was no published resolution on the list to this issue at that date.
> Have others seen this behavior since? If so, how should I proceed on this
> machine? The code below is a minimal example. In general, I would like to
> implement code similar to the examples here:
> http://yt-project.org/doc/advanced/parallel_computation.html using
> parallel_objects. The simple scripts I am trying to run proceed without
> warning or error on the other machines I have access to (Mac laptop, and
> ucsc cluster "hyades"). The error message mentions that the warning may be
> disabled. Is this the recommended setting for the cluster?
>
> Thanks for your advice.
>
> Morgan
>
>
>
>
>
> If I try to run this script:
>
> from yt.config import ytcfg
> from yt.pmods import *
>
> print range(10)
>
>
>
> I get this error output (related to the pmods import):
>
> (yt-x86_64)[morgan at laozi ytpar]$ mpirun -np 1 python test.py --parallel
> --------------------------------------------------------------------------
> WARNING: There are more than one active ports on host 'laozi.ucsc.edu',
> but the
> default subnet GID prefix was detected on more than one of these
> ports.  If these ports are connected to different physical IB
> networks, this configuration will fail in Open MPI.  This version of
> Open MPI requires that every physically separate IB subnet that is
> used between connected MPI processes must have different subnet ID
> values.
>
> Please see this FAQ entry for more details:
>
>   http://www.open-mpi.org/faq/?category=openfabrics#ofa-default-subnet-gid
>
> NOTE: You can turn off this warning by setting the MCA parameter
>       btl_openib_warn_default_gid_prefix to 0.
> --------------------------------------------------------------------------
> Beginning parallel import block.
> --------------------------------------------------------------------------
> An MPI process has executed an operation involving a call to the
> "fork()" system call to create a child process.  Open MPI is currently
> operating in a condition that could result in memory corruption or
> other system errors; your MPI job may hang, crash, or produce silent
> data corruption.  The use of fork() (or system() or other calls that
> create child processes) is strongly discouraged.
>
> The process that invoked fork was:
>
>   Local host:          laozi.ucsc.edu (PID 31958)
>   MPI_COMM_WORLD rank: 0
>
> If you are *absolutely sure* that your application will successfully
> and correctly survive a call to fork(), you may disable this warning
> by setting the mpi_warn_on_fork MCA parameter to 0.
> --------------------------------------------------------------------------
> Traceback (most recent call last):
>   File "test.py", line 7, in <module>
>     from yt.pmods import *
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 364, in
> <module>
>     from yt.mods import *
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 235, in
> __import_hook__
>     m = __load_tail__(q, tail)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 339, in
> __load_tail__
>     m = __import_module__(head, mname, m)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 279, in
> __import_module__
>     m = imp.load_module(fqname, fp, pathname, stuff)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/mods.py", line 142, in
> <module>
>     from yt.visualization.api import \
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 235, in
> __import_hook__
>     m = __load_tail__(q, tail)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 339, in
> __load_tail__
>     m = __import_module__(head, mname, m)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 279, in
> __import_module__
>     m = imp.load_module(fqname, fp, pathname, stuff)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/visualization/api.py",
> line 31, in <module>
>     from color_maps import \
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 234, in
> __import_hook__
>     q, tail = __find_head_package__(parent, name)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 323, in
> __find_head_package__
>     q = __import_module__(head, qname, parent)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 279, in
> __import_module__
>     m = imp.load_module(fqname, fp, pathname, stuff)
>   File
> "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/visualization/color_maps.py",
> line 26, in <module>
>     import matplotlib
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 234, in
> __import_hook__
>     q, tail = __find_head_package__(parent, name)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 328, in
> __find_head_package__
>     q = __import_module__(head, qname, parent)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 279, in
> __import_module__
>     m = imp.load_module(fqname, fp, pathname, stuff)
>   File
> "/share/work1/morgan/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/__init__.py",
> line 130, in <module>
>     from matplotlib.compat import subprocess
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 239, in
> __import_hook__
>     __ensure_fromlist__(m, fromlist)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 357, in
> __ensure_fromlist__
>     submod = __import_module__(sub, subname, m)
>   File "/share/work1/morgan/yt-x86_64/src/yt-hg/yt/pmods.py", line 279, in
> __import_module__
>     m = imp.load_module(fqname, fp, pathname, stuff)
>   File
> "/share/work1/morgan/yt-x86_64/lib/python2.7/site-packages/matplotlib-1.3.0-py2.7-linux-x86_64.egg/matplotlib/compat/subprocess.py",
> line 79, in <module>
>     CalledProcessError = subprocess.CalledProcessError
> AttributeError: 'module' object has no attribute 'CalledProcessError'
> --------------------------------------------------------------------------
> mpirun noticed that the job aborted, but has no info as to the process
> that caused that situation.
> --------------------------------------------------------------------------
> (yt-x86_64)[morgan at laozi ytpar]$
>
> _______________________________________________
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> yt-users at lists.spacepope.org
> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>
>
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