[yt-users] SlicePlot script stuck

Jean-Claude Passy jcpassy at gmail.com
Wed Sep 4 03:42:14 PDT 2013


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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