Dear Nathan, What I mean is that the loading part doesn't finish, attached is the error file. Thanks! Ariadna ________________________________ De: yt-users en nombre de Nathan Goldbaum 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 mailto: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.orgmailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

Dear Nathan, Thanks! That's super helpful! I'll try the interactive session, in the meantime, here is my script. I'm using it to read from FLASH particle files. I also added one of the files with less particles. Best, Ariadna ________________________________ De: yt-users en nombre de Nathan Goldbaum Enviado: viernes, 26 de agosto de 2016 12:46 p. m. Para: Discussion of the yt analysis package Asunto: Re: [yt-users] Loading particles 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 mailto: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 mailto:yt-users-bounces@lists.spacepope.org> en nombre de Nathan Goldbaum mailto: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 mailto: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.orgmailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org _______________________________________________ yt-users mailing list yt-users@lists.spacepope.orgmailto:yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org