[yt-users] SlicePlot script stuck
Caroline Van Borm
borm at astro.rug.nl
Wed Sep 4 03:43:53 PDT 2013
Hi JC,
I think I had the same problem a while ago, see
http://lists.spacepope.org/htdig.cgi/yt-users-spacepope.org/2013-April/003560.html
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.
Cheers,
Caroline
Op 4/09/2013 12:42, Jean-Claude Passy schreef:
> Hi guys,
>
> sorry for my late reply.
>
> Jeff, so I ran the script you suggested:
>
> /------------------------------------------/
> /from yt.mods import */
> /this_file = 'DD0000/CE0000'/
> /pf = load(this_file)/
> /print "loading ", this_file/
> /s = SlicePlot(pf, 2, 'Density')/
> /s.save()/
> /------------------------------------------/
>
> It works when the axis of the slice is either 0 or 2. However when it
> is 1, it gets stuck there:
>
> /--------------------------------------------------------------------------------------------------------------------------------/
> /[ 3:21:00] seawolf1:$ python2.7 ~/Enzo/python/script.py -d Agg/
> /yt : [INFO ] 2013-09-04 03:21:20,355 Parameters: current_time
> = 0/
> /yt : [INFO ] 2013-09-04 03:21:20,355 Parameters:
> domain_dimensions = [32 32 32]/
> /yt : [INFO ] 2013-09-04 03:21:20,356 Parameters: domain_left_edge
> = [ 0. 0. 0.]/
> /yt : [INFO ] 2013-09-04 03:21:20,357 Parameters:
> domain_right_edge = [ 1. 1. 1.]/
> /yt : [INFO ] 2013-09-04 03:21:20,358 Parameters:
> cosmological_simulation = 0.0/
> /loading DD0000/CE0000/
> /Parsing Hierarchy100%
> |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| Time:
> 00:00:00 /
> /yt : [INFO ] 2013-09-04 03:21:20,369 Gathering a field list (this
> may take a moment.)/
> /yt : [INFO ] 2013-09-04 03:21:20,408 Adding unknown field
> Grav_Potential to list of fields/
> /
> /
> /--------------------------------------------------------------------------------------------------------------------------------/
>
> 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.
>
> Thanks again,
>
> JC
>
>
> On Sep 3, 2013, at 5:22 PM, j s oishi <jsoishi at gmail.com
> <mailto:jsoishi at gmail.com>> wrote:
>
>> JC,
>>
>> Can you try a simpler script without command line options? Maybe just
>>
>> from yt.mods import *
>>
>> pf = load(<DATASET OF DOOM>)
>>
>> sp = SlicePlot(pf, 2, "Density")
>> sp.save()
>>
>> and then run that with
>>
>> python script.py -d Agg
>>
>> ?
>>
>> j
>>
>>
>> On Tue, Sep 3, 2013 at 11:30 AM, Jean-Claude Passy <jcpassy at gmail.com
>> <mailto:jcpassy at gmail.com>> wrote:
>>
>> Hi Jeff,
>>
>> thanks for your quick reply.
>> Nope, ii still gets stuck at the same place.
>>
>> Cheers,
>>
>> JC
>>
>> On Sep 3, 2013, at 5:09 PM, j s oishi <jsoishi at gmail.com
>> <mailto:jsoishi at gmail.com>> wrote:
>>
>>> Hi JC,
>>>
>>> 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
>>>
>>> python script.py -d Agg
>>>
>>> and see if that works remotely?
>>>
>>> j
>>>
>>>
>>> On Tue, Sep 3, 2013 at 11:18 AM, Jean-Claude Passy
>>> <jcpassy at gmail.com <mailto:jcpassy at gmail.com>> wrote:
>>>
>>> Hi all,
>>>
>>> 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.
>>> 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.
>>>
>>> Does anyone have a suggestion?
>>>
>>> Thanks a lot,
>>>
>>> JC
>>>
>>>
>>>
>>> /-------------------------------------------------------------------------------------------------------------------------------------------------/
>>> /[ 7:48:12] seawolf2:$ python2.7
>>> ~/Enzo/python/PlotEnzoDataMultiple.py 0 0 1.0 /
>>> /yt : [INFO ] 2013-09-03 07:48:34,165 Parameters:
>>> current_time = 0/
>>> /yt : [INFO ] 2013-09-03 07:48:34,165 Parameters:
>>> domain_dimensions = [32 32 32]/
>>> /yt : [INFO ] 2013-09-03 07:48:34,166 Parameters:
>>> domain_left_edge = [ 0. 0. 0.]/
>>> /yt : [INFO ] 2013-09-03 07:48:34,167 Parameters:
>>> domain_right_edge = [ 1. 1. 1.]/
>>> /yt : [INFO ] 2013-09-03 07:48:34,168 Parameters:
>>> cosmological_simulation = 0.0/
>>> /loading DD0000/CE0000/
>>> /yt : [INFO ] 2013-09-03 07:48:34,174 Getting the binary
>>> hierarchy/
>>> /Parsing Hierarchy100%
>>> ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
>>> Time: 00:00:00 /
>>> /yt : [INFO ] 2013-09-03 07:48:34,181 Gathering a field
>>> list (this may take a moment.)/
>>> /yt : [INFO ] 2013-09-03 07:48:34,220 Adding unknown
>>> field Grav_Potential to list of fields/
>>> /level # grids # cells # cells^3/
>>> /----------------------------------------------/
>>> / 0 1 32768 31/
>>> / 1 1 13824 23/
>>> / 2 6 56320 38/
>>> / 3 14 85936 44/
>>> /----------------------------------------------/
>>> / 22 188848/
>>> /
>>> /
>>> /
>>> /
>>> /t = 0.00000000e+00 = 0.00000000e+00 s = 0.00000000e+00 years/
>>> /
>>> /
>>> /Smallest Cell:/
>>> / Width: 4.431e-14 Mpc/
>>> / Width: 4.431e-14 mpc/
>>> / Width: 4.431e-11 kpc/
>>> / Width: 4.431e-08 pc/
>>> / Width: 3.906e-03 1/
>>> / Width: 3.906e-03 aye/
>>> / Width: 3.906e-03 unitary/
>>> / Width: 9.139e-03 au/
>>> / Width: 1.966e+00 rsun/
>>> / Width: 8.495e+05 miles/
>>> / Width: 1.367e+06 km/
>>> / Width: 1.367e+11 cm/
>>> /yt : [INFO ] 2013-09-03 07:48:34,600 xlim = 0.000000
>>> 1.000000/
>>> /yt : [INFO ] 2013-09-03 07:48:34,600 ylim = 0.000000
>>> 1.000000/
>>> /yt : [INFO ] 2013-09-03 07:48:34,600 Making a fixed
>>> resolution buffer of (Density) 800 by 800/
>>> /yt : [INFO ] 2013-09-03 07:48:34,610 xlim = 0.000000
>>> 1.000000/
>>> /yt : [INFO ] 2013-09-03 07:48:34,610 ylim = 0.000000
>>> 1.000000/
>>> /yt : [INFO ] 2013-09-03 07:48:34,610 Making a fixed
>>> resolution buffer of (Density) 800 by 800/
>>> /yt : [INFO ] 2013-09-03 07:48:34,619 Making a fixed
>>> resolution buffer of (Density) 800 by 800/
>>> /yt : [INFO ] 2013-09-03 07:48:35,467 Getting
>>> particle_position_y using ParticleIO/
>>> /yt : [INFO ] 2013-09-03 07:48:35,471 Getting
>>> particle_position_z using ParticleIO/
>>> /yt : [INFO ] 2013-09-03 07:48:35,669 Getting
>>> particle_position_y using ParticleIO/
>>> /yt : [INFO ] 2013-09-03 07:48:35,674 Getting
>>> particle_position_z using ParticleIO/
>>> /yt : [INFO ] 2013-09-03 07:48:35,681 Making a fixed
>>> resolution buffer of (Density) 800 by 800/
>>> /yt : [INFO ] 2013-09-03 07:48:35,881 Getting
>>> particle_position_y using ParticleIO/
>>> /yt : [INFO ] 2013-09-03 07:48:35,885 Getting
>>> particle_position_z using ParticleIO/
>>> /yt : [INFO ] 2013-09-03 07:48:35,892 Making a fixed
>>> resolution buffer of (Density) 800 by 800/
>>> /yt : [INFO ] 2013-09-03 07:48:36,091 Getting
>>> particle_position_y using ParticleIO/
>>> /yt : [INFO ] 2013-09-03 07:48:36,095 Getting
>>> particle_position_z using ParticleIO/
>>> */yt : [INFO ] 2013-09-03 07:48:36,102 Saving plot
>>> Plots/Density/x-axis/CE0000_Slice_x_Density.png/*
>>> */
>>> /*
>>> /-------------------------------------------------------------------------------------------------------------------------------------------------/
>>>
>>> _______________________________________________
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