<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<p>Dear Nathan,</p>
<p>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.</p>
<p>Best,</p>
<p>Ariadna</p>
<br>
<br>
<div style="color: rgb(0, 0, 0);">
<hr style="display:inline-block; width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De:</b> yt-users <yt-users-bounces@lists.spacepope.org> en nombre de Nathan Goldbaum <nathan12343@gmail.com><br>
<b>Enviado:</b> viernes, 26 de agosto de 2016 12:46 p. m.<br>
<b>Para:</b> Discussion of the yt analysis package<br>
<b>Asunto:</b> Re: [yt-users] Loading particles</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>Ah, your error file included the information I needed:</div>
<div><br>
</div>
<div>Traceback (most recent call last):<br>
</div>
<div>
<div> File "particle_trajectories.py", line 105, in <module></div>
<div> 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])</div>
<div>KeyError: 'traj_664882'</div>
</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Hope that's helpful,</div>
<div><br>
</div>
<div>Nathan</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Aug 26, 2016 at 12:37 PM, Ariadna Murguia <span dir="ltr">
<<a href="mailto:doggies012@hotmail.com" target="_blank">doggies012@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt; color:#000000; background-color:#ffffff; font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Dear Nathan,</p>
<p>What I mean is that the loading part doesn't finish, attached is the error file.</p>
<p>Thanks!</p>
<p>Ariadna</p>
<br>
<br>
<div style="color:rgb(0,0,0)">
<hr style="display:inline-block; width:98%">
<div dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De:</b> yt-users <<a href="mailto:yt-users-bounces@lists.spacepope.org" target="_blank">yt-users-bounces@lists.<wbr>spacepope.org</a>> en nombre de Nathan Goldbaum <<a href="mailto:nathan12343@gmail.com" target="_blank">nathan12343@gmail.com</a>><br>
<b>Enviado:</b> viernes, 26 de agosto de 2016 12:29 p. m.<br>
<b>Para:</b> Discussion of the yt analysis package<br>
<b>Asunto:</b> Re: [yt-users] Loading particles</font>
<div> </div>
</div>
<div>
<div class="h5">
<div>
<div dir="ltr"><br>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Fri, Aug 26, 2016 at 12:16 PM, Ariadna Murguia <span dir="ltr">
<<a href="mailto:doggies012@hotmail.com" target="_blank">doggies012@hotmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt; color:#000000; background-color:#ffffff; font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Dear yt users,</p>
<p><br>
</p>
</div>
</div>
</blockquote>
<div><br>
</div>
<div>Hi Ariadna,</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt; color:#000000; background-color:#ffffff; font-family:Calibri,Arial,Helvetica,sans-serif">
<p></p>
<p>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. <span style="font-size:12pt">I'm getting the following error:</span></p>
<p><br>
</p>
<p>/pfs/sw/python/yt/yt-x86_64/sr<wbr>c/yt-hg/yt/units/yt_array.py:<wbr>793: RuntimeWarning: invalid value encountered in divide return YTArray(super(YTArray, self).__div__(ro))<br>
</p>
<p>/pfs/sw/python/yt/yt-x86_64/sr<wbr>c/yt-hg/yt/utilities/math_util<wbr>s.py:861: RuntimeWarning: invalid value encountered in arccos return np.arccos( JdotCoords / np.sqrt(np.sum(coords**2,axis=<wbr>0)) )<br>
</p>
<p><br>
</p>
</div>
</div>
</blockquote>
<div>These are just warnings, which might indicate that something is going wrong but also might not.<br>
</div>
<div><br>
</div>
<div>When you say it crashes, how does it crash? Does it print any error message or traceback? If so, can you share those?</div>
<div> </div>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex; border-left:1px #ccc solid; padding-left:1ex">
<div dir="ltr">
<div style="font-size:12pt; color:#000000; background-color:#ffffff; font-family:Calibri,Arial,Helvetica,sans-serif">
<p></p>
<p>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?</p>
<p>Thank you very much in advance</p>
<p><br>
</p>
<p>All the best,</p>
<p>Ariadna</p>
<div style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:12.8px">
----------------</div>
<div style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:12.8px">
Ariadna Murguia Berthier</div>
<div style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:12.8px">
University of California, Santa Cruz</div>
<p></p>
<div style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:12.8px">
Department of Astronomy and Astrophysics</div>
<p></p>
</div>
</div>
<br>
______________________________<wbr>_________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org" target="_blank">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/lis<wbr>tinfo.cgi/yt-users-spacepope.<wbr>org</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
______________________________<wbr>_________________<br>
yt-users mailing list<br>
<a href="mailto:yt-users@lists.spacepope.org">yt-users@lists.spacepope.org</a><br>
<a href="http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org" rel="noreferrer" target="_blank">http://lists.spacepope.org/<wbr>listinfo.cgi/yt-users-<wbr>spacepope.org</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
</body>
</html>