Ah, your error file included the information I needed:

Traceback (most recent call last):
  File "particle_trajectories.py", line 105, in <module>
    globals()['dset%s' % key_list.index(key)+'_Particle_%s'%int(j-1)] = globals()['Particle_%s' % int(j-1)].create_dataset(key[1], data=globals()['traj_%s' % int(j-1)][key])
KeyError: 'traj_664882'

So you seem to be trying to access a trajectory that doesn't appear in the output. I might be able to say more if you can share your script.

It might also help to try to run with the aid of a debugger in an interactive session on hyades, or on eudora or the hyades head node. You can start an interactive session from the command line on hyades with "qsub -I", there are some examples of this in the hyades documentation.

Hope that's helpful,

Nathan

On Fri, Aug 26, 2016 at 12:37 PM, Ariadna Murguia <doggies012@hotmail.com> wrote:

Dear Nathan,

What I mean is that the loading part doesn't finish, attached is the error file.

Thanks!

Ariadna



De: yt-users <yt-users-bounces@lists.spacepope.org> en nombre de Nathan Goldbaum <nathan12343@gmail.com>
Enviado: viernes, 26 de agosto de 2016 12:29 p. m.
Para: Discussion of the yt analysis package
Asunto: Re: [yt-users] Loading particles
 


On Fri, Aug 26, 2016 at 12:16 PM, Ariadna Murguia <doggies012@hotmail.com> wrote:

Dear yt users,



Hi Ariadna,
 

I'm trying to load a set of particles (a bunch of particles, so I'm running it in the hyades cluster). I have their positions and velocities. What I'm doing is just defining a box as the domain of my simulation, the data as a dictionary of velocities and positions, and just saying yt.load_particles(data=data, bbox=bbox). I tried it for some particle files that I'm using, and it works, but for others, it crashes. I'm getting the following error:


/pfs/sw/python/yt/yt-x86_64/src/yt-hg/yt/units/yt_array.py:793: RuntimeWarning: invalid value encountered in divide  return YTArray(super(YTArray, self).__div__(ro))

/pfs/sw/python/yt/yt-x86_64/src/yt-hg/yt/utilities/math_utils.py:861: RuntimeWarning: invalid value encountered in arccos  return np.arccos( JdotCoords / np.sqrt(np.sum(coords**2,axis=0)) )


These are just warnings, which might indicate that something is going wrong but also might not.

When you say it crashes, how does it crash? Does it print any error message or traceback? If so, can you share those?
 

I tried it in my computer with less particles,and it works perfectly. Am I loading the particles wrong or is there a way to fix this error?

Thank you very much in advance


All the best,

Ariadna

----------------
Ariadna Murguia Berthier
University of California, Santa Cruz

Department of Astronomy and Astrophysics


_______________________________________________
yt-users mailing list
yt-users@lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org



_______________________________________________
yt-users mailing list
yt-users@lists.spacepope.org
http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org