[yt-users] SlicePlot script stuck
Jean-Claude Passy
jcpassy at gmail.com
Wed Sep 4 07:12:11 PDT 2013
Hi Caroline et al.,
ooops, I did not see that thread. Indeed, yt was built with icc. Rebuilding with gcc fixed it.
Thanks for the suggestion!
Cheers,
JC
On Sep 4, 2013, at 12:43 PM, Caroline Van Borm <borm at astro.rug.nl> wrote:
> 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> 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> 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> 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> 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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