That is weird, Eric. I think you can possibly disable usetex to get
rid of the tex.cache file, but I'm not entirely sure. This might be
an issue to isolate, by removing yt.mods and importing the individual
matplotlib items that throw the error in a script, and then raise it
with matplotlib-users.
-Matt
On Wed, Sep 5, 2012 at 3:59 PM, Eric Hallman
Matt, it's weird, but in serial or in parallel on a single node I see no problems. I run interactively on one node and it skips right through this part. I don't get it.
On Sep 5, 2012, at 3:55 PM, Matthew Turk wrote:
Hi Eric,
The tex.cache issue seems to tbe the big one here. Can you try, in serial, launching a single job that imports yt? I think it just needs to be bootstrapped once.
-Matt
On Wed, Sep 5, 2012 at 3:50 PM, Eric Hallman
wrote: Well the earlier traceback I posted below is a good start. Seriously if I
post the current error list it's going to be 10M of text. I'll see what I
can come up with in the short term and we can try later on IRC or something.
Thanks
Eric
On Sep 5, 2012, at 3:45 PM, Nathan Goldbaum wrote:
I'm sorry you're having so much trouble. Unfortunately I'm probably not the
best person to advise since I've never run jobs on Kraken. Others on the
list might be more helpful.
One thing that would aid tracking down the problem is if you could paste the
errors you're seeing somewhere so that one of us can take a look at it in
detail.
Cheers,
Nathan
On Sep 5, 2012, at 12:42 PM, Eric Hallman wrote:
Nathan,
usings pmods in the import leads to an error explosion in the matplotlib
imports. It's even worse than the original test.
Eric
On Sep 5, 2012, at 12:42 PM, Nathan Goldbaum wrote:
Hi Eric,
Exactly right. This is a drop-in replacement for yt.mods on high-latency
parallel filesystems (like Kraken, unfortunately).
There's some discussion on the dev mailing list:
http://lists.spacepope.org/htdig.cgi/yt-dev-spacepope.org/2012-January/00176...
Unfortunately this isn't covered in the docs (except for a note in the
changelog) but it should be in there.
Cheers,
Nathan
On Sep 5, 2012, at 9:40 AM, Eric Hallman wrote:
Nathan,
I've been off yt for a while, I'm unaware of pmods. It's specific to
parallel I'm guessing?
Eric
On Sep 5, 2012, at 12:38 PM, Nathan Goldbaum wrote:
Hi Eric,
Have you tried from yt.pmods import * instead of the normal yt.mods?
Cheers,
Nathan
On Sep 5, 2012, at 9:37 AM, Eric Hallman wrote:
Hey everyone,
so this issue seems like one I've had before, but I searched the lists and
don't find this exact issue.
On batch jobs on kraken, attempting to do halo finding, I get an almost
immediate crash (with an eternal hang until the time limit is reached) due
to matplotlib. I've been unable to reproduce it in the interactive queue on
kraken, which is frustrating. I'm hoping someone has seen it and can
comment.
this is with yt/dev on kraken, and I set env variables to MPLCONFIGDIR like
so:
export MPLCONFIGDIR=${PBS_O_WORKDIR}/.matplotlib/
[ ! -d ${MPLCONFIGDIR} ] && mkdir ${MPLCONFIGDIR}
because if you don't, it fails immediately with perm issues.
Anyway, it's a simple script and call
aprun -n 12 python halo_finding.py --parallel
but the details of the script are not too important, since the job fails
when yt is imported, as so:
Traceback (most recent call last):
File "halo_finding.py", line 1, in <module>
from yt.mods import *
File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/mods.py",
line 115, in <module>
from yt.visualization.api import \
File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visualization/api.py",
line 34, in <module>
from plot_collection import \
File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/yt-2.4dev-py2.7-linux-x86_64.egg/yt/visualization/plot_collection.py",
line 26, in <module>
from matplotlib import figure
File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/matplotlib/figure.py",
line 18, in <module>
from axes import Axes, SubplotBase, subplot_class_factory
File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/matplotlib/axes.py",
line 18, in <module>
import matplotlib.contour as mcontour
File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/matplotlib/contour.py",
line 21, in <module>
import matplotlib.texmanager as texmanager
File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/matplotlib/texmanager.py",
line 72, in <module>
class TexManager:
File
"/lustre/scratch/proj/sw/yt/dev/lib/python2.7/site-packages/matplotlib/texmanager.py",
line 92, in TexManager
os.mkdir(texcache)
OSError: [Errno 17] File exists:
'/lustre/scratch/hallman/gigaCubes/run1024/.matplotlib/tex.cache'
In each case, I have deleted tex.cache before I restart, thinking an old
version persisted there, but the same error happens. The most irritating
thing is that the job does not kick out of the batch system, so the time
continues to run on however many processors you have until the limit is
reached (eternal hang!).
I hope this is something obvious and I'm just dumb. Let me know.
Eric
--
Eric Hallman
Tech-X Corporation hallman@txcorp.com
5621 Arapahoe Ave, Suite A Phone: (720) 254-5833
Boulder, CO 80303 Fax: (303) 448-7756
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5621 Arapahoe Ave, Suite A Phone: (720) 254-5833
Boulder, CO 80303 Fax: (303) 448-7756
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Tech-X Corporation hallman@txcorp.com
5621 Arapahoe Ave, Suite A Phone: (720) 254-5833
Boulder, CO 80303 Fax: (303) 448-7756
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Tech-X Corporation hallman@txcorp.com
5621 Arapahoe Ave, Suite A Phone: (720) 254-5833
Boulder, CO 80303 Fax: (303) 448-7756
--
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