[yt-users] SlicePlot script stuck

Tue Sep 3 08:22:20 PDT 2013

Hi JC,

My initial thought was the same as Jeff's.  However, we do have
something in place to check where things are in the code.  The first
option is to hit Ctrl-C and see where the stack trace is.  The second
is to send SIGUSR1 to the process; this would be done by finding the
PID of the python script:

ps awxu|grep -i python

and doing:

kill -SIGUSR1 that_pid

If you can get a stack trace, it would help us figure out what is up.

-Matt

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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