[yt-users] error on pmods import

Morgan MacLeod mmacleod at ucolick.org
Sun Oct 6 00:26:42 PDT 2013


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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