[yt-users] error on pmods import

[Morgan MacLeod]

Yes, a huge thanks to Nathan for helping me diagnose (and fix!) this.

A more general question: is importing "mods" versus "pmods" generally
preferred, or was this a special case?

Morgan


On Sun, Oct 6, 2013 at 12:44 AM, Nathan Goldbaum <nathan12343 at gmail.com>wrote:

> 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]$
>>
>> _______________________________________________
>> yt-users mailing list
>> yt-users at lists.spacepope.org
>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
>>
>>
>
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