<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Caroline et al.,<div><br></div><div>ooops, I did not see that thread. Indeed, yt was built with icc. Rebuilding with gcc fixed it.</div><div>Thanks for the suggestion!</div><div><br></div><div>Cheers,</div><div><br></div><div>JC</div><div><br><div><div>On Sep 4, 2013, at 12:43 PM, Caroline Van Borm <<a href="mailto:borm@astro.rug.nl">borm@astro.rug.nl</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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<div class="moz-cite-prefix">Hi JC,<br>
<br>
I think I had the same problem a while ago, see
<a class="moz-txt-link-freetext" href="http://lists.spacepope.org/htdig.cgi/yt-users-spacepope.org/2013-April/003560.html">http://lists.spacepope.org/htdig.cgi/yt-users-spacepope.org/2013-April/003560.html</a>
<br>
For me, it turned out to be a build problem as I had used icc
instead of gcc to build everything. Is it possible that something
similar occurred in your situation? If yes, then perhaps
rebuilding with gcc could solve your problem.<br>
<br>
Cheers,<br>
Caroline<br>
<br>
<br>
Op 4/09/2013 12:42, Jean-Claude Passy schreef:<br>
</div>
<blockquote cite="mid:8754FC1E-FF0C-43D1-9D0D-D0954AC20993@gmail.com" type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
Hi guys,
<div><br>
</div>
<div>sorry for my late reply.</div>
<div><br>
</div>
<div>Jeff, so I ran the script you suggested:</div>
<div><br>
</div>
<div><i>------------------------------------------</i></div>
<div><i>from yt.mods import *</i></div>
<div>
<div><i>this_file = 'DD0000/CE0000'</i></div>
<div><i>pf = load(this_file)</i></div>
<div><i>print "loading ", this_file</i></div>
</div>
<div>
<div><i>s = SlicePlot(pf, 2, 'Density')</i></div>
<div><i>s.save()</i></div>
</div>
<div>
<div><i>------------------------------------------</i></div>
<div><br>
</div>
<div>It works when the axis of the slice is either 0 or 2.
However when it is 1, it gets stuck there:</div>
<div><br>
</div>
<div>
<div><i>--------------------------------------------------------------------------------------------------------------------------------</i></div>
</div>
<div>
<div><i>[ 3:21:00] seawolf1:$ python2.7
~/Enzo/python/script.py -d Agg</i></div>
<div><i>yt : [INFO ] 2013-09-04 03:21:20,355 Parameters:
current_time = 0</i></div>
<div><i>yt : [INFO ] 2013-09-04 03:21:20,355 Parameters:
domain_dimensions = [32 32 32]</i></div>
<div><i>yt : [INFO ] 2013-09-04 03:21:20,356 Parameters:
domain_left_edge = [ 0. 0. 0.]</i></div>
<div><i>yt : [INFO ] 2013-09-04 03:21:20,357 Parameters:
domain_right_edge = [ 1. 1. 1.]</i></div>
<div><i>yt : [INFO ] 2013-09-04 03:21:20,358 Parameters:
cosmological_simulation = 0.0</i></div>
<div><i>loading DD0000/CE0000</i></div>
<div><i>Parsing Hierarchy100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00 </i></div>
<div><i>yt : [INFO ] 2013-09-04 03:21:20,369 Gathering a
field list (this may take a moment.)</i></div>
<div><i>yt : [INFO ] 2013-09-04 03:21:20,408 Adding
unknown field Grav_Potential to list of fields</i></div>
</div>
<div><i><br>
</i></div>
<div>
<div><i>--------------------------------------------------------------------------------------------------------------------------------</i></div>
</div>
<div><br>
</div>
<div>Matt, I am having trouble getting a stack trace. 'kill
-SIGUSR1 job_id ' does not kill my job or output anything, and
I am sure the job_id is correct because a simple 'kill job_id'
kills the job but does not give me more info. I tried using
nohup, but still did not work. I will try to submit the job on
the queue instead of running it interactively.</div>
<div><br>
</div>
<div>Thanks again,</div>
<div><br>
</div>
<div>JC</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>On Sep 3, 2013, at 5:22 PM, j s oishi <<a moz-do-not-send="true" href="mailto:jsoishi@gmail.com">jsoishi@gmail.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div dir="ltr">JC,
<div><br>
</div>
<div>Can you try a simpler script without command line
options? Maybe just</div>
<div><br>
</div>
<div>from yt.mods import *</div>
<div><br>
</div>
<div>pf = load(<DATASET OF DOOM>)</div>
<div>
<br>
</div>
<div>sp = SlicePlot(pf, 2, "Density")</div>
<div>sp.save()</div>
<div><br>
</div>
<div>and then run that with </div>
<div><br>
</div>
<div>python script.py -d Agg</div>
<div><br>
</div>
<div>?</div>
<div><br>
</div>
<div>j</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, Sep 3, 2013 at 11:30 AM,
Jean-Claude Passy <span dir="ltr"><<a moz-do-not-send="true" href="mailto:jcpassy@gmail.com" target="_blank">jcpassy@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Jeff,
<div><br>
</div>
<div>thanks for your quick reply.</div>
<div>Nope, ii still gets stuck at the same place.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>JC</div>
<div>
<div class="h5">
<div><br>
</div>
<div>
<div>On Sep 3, 2013, at 5:09 PM, j s oishi
<<a moz-do-not-send="true" href="mailto:jsoishi@gmail.com" target="_blank">jsoishi@gmail.com</a>>
wrote:</div>
<br>
<blockquote type="cite">
<div dir="ltr">Hi JC,
<div><br>
</div>
<div>the first thing that comes to mind is
the matplotlib backend you are using is
trying to open a window remotely (even
if it doesn't actually use it for
anything or ever even display it). Can
you try doing</div>
<div><br>
</div>
<div>python script.py -d Agg</div>
<div><br>
</div>
<div>and see if that works remotely?</div>
<div><br>
</div>
<div>j</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, Sep 3,
2013 at 11:18 AM, Jean-Claude Passy <span dir="ltr"><<a moz-do-not-send="true" href="mailto:jcpassy@gmail.com" target="_blank">jcpassy@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div>Hi all,</div>
<div><br>
</div>
<div>I am running a simple script
using SlicePlot (see attached) on
a small dataset (only ~ 200k
cells). While it works without any
problem on my laptop OS X 10.8.4,
it gets stuck after saving the
first slice (see below) on a
remote Linux machine. </div>
<div>I have run the script on the
same data on both machines, have
installed the latest dev version
of yt, even removed the *.yt
files. But it did not help. </div>
<div><br>
</div>
<div>Does anyone have a suggestion?</div>
<div>
<br>
</div>
<div>Thanks a lot,</div>
<div><br>
</div>
<div>JC</div>
<div><br>
</div>
</div>
<br>
<div style="word-wrap:break-word">
<div><br>
</div>
<div><i>-------------------------------------------------------------------------------------------------------------------------------------------------</i></div>
<div><i>[ 7:48:12] seawolf2:$
python2.7
~/Enzo/python/PlotEnzoDataMultiple.py
0 0 1.0 </i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,165 Parameters:
current_time = 0</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,165 Parameters:
domain_dimensions = [32
32 32]</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,166 Parameters:
domain_left_edge = [ 0.
0. 0.]</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,167 Parameters:
domain_right_edge = [ 1.
1. 1.]</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,168 Parameters:
cosmological_simulation = 0.0</i></div>
<div><i>loading DD0000/CE0000</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,174 Getting the binary
hierarchy</i></div>
<div><i>Parsing Hierarchy100%
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Time: 00:00:00 </i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,181 Gathering a field
list (this may take a moment.)</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,220 Adding unknown
field Grav_Potential to list of
fields</i></div>
<div><i>level # grids #
cells # cells^3</i></div>
<div><i>----------------------------------------------</i></div>
<div><i> 0 1
32768 31</i></div>
<div><i> 1 1
13824 23</i></div>
<div><i> 2 6
56320 38</i></div>
<div><i> 3 14
85936 44</i></div>
<div><i>----------------------------------------------</i></div>
<div><i> 22
188848</i></div>
<div><i><br>
</i></div>
<div><i><br>
</i></div>
<div><i>t = 0.00000000e+00 =
0.00000000e+00 s =
0.00000000e+00 years</i></div>
<div><i><br>
</i></div>
<div><i>Smallest Cell:</i></div>
<div><i> Width: 4.431e-14 Mpc</i></div>
<div><i> Width: 4.431e-14 mpc</i></div>
<div><i> Width: 4.431e-11 kpc</i></div>
<div><i> Width: 4.431e-08 pc</i></div>
<div><i> Width: 3.906e-03 1</i></div>
<div><i> Width: 3.906e-03 aye</i></div>
<div><i> Width: 3.906e-03
unitary</i></div>
<div><i> Width: 9.139e-03 au</i></div>
<div><i> Width: 1.966e+00
rsun</i></div>
<div><i> Width: 8.495e+05
miles</i></div>
<div><i> Width: 1.367e+06 km</i></div>
<div><i> Width: 1.367e+11 cm</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,600 xlim = 0.000000
1.000000</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,600 ylim = 0.000000
1.000000</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,600 Making a fixed
resolution buffer of (Density)
800 by 800</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,610 xlim = 0.000000
1.000000</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,610 ylim = 0.000000
1.000000</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,610 Making a fixed
resolution buffer of (Density)
800 by 800</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:34,619 Making a fixed
resolution buffer of (Density)
800 by 800</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:35,467 Getting
particle_position_y using
ParticleIO</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:35,471 Getting
particle_position_z using
ParticleIO</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:35,669 Getting
particle_position_y using
ParticleIO</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:35,674 Getting
particle_position_z using
ParticleIO</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:35,681 Making a fixed
resolution buffer of (Density)
800 by 800</i></div>
<div>
<i>yt : [INFO ] 2013-09-03
07:48:35,881 Getting
particle_position_y using
ParticleIO</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:35,885 Getting
particle_position_z using
ParticleIO</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:35,892 Making a fixed
resolution buffer of (Density)
800 by 800</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:36,091 Getting
particle_position_y using
ParticleIO</i></div>
<div><i>yt : [INFO ] 2013-09-03
07:48:36,095 Getting
particle_position_z using
ParticleIO</i></div>
<div><b><i>yt : [INFO ]
2013-09-03 07:48:36,102 Saving
plot
Plots/Density/x-axis/CE0000_Slice_x_Density.png</i></b></div>
<div><b><i><br>
</i></b></div>
<div><i>-------------------------------------------------------------------------------------------------------------------------------------------------</i></div>
</div>
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