<div dir="ltr"><div><div>Hi Sam, all,<br><br></div>This fixed the problem - thank you! <br><br></div>--Brian<br><br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Aug 5, 2013 at 9:54 AM, Sam Skillman <span dir="ltr"><<a href="mailto:samskillman@gmail.com" target="_blank">samskillman@gmail.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">Err, just to be clear, keep the pf = load(...) line in there before the ts = TimeSeriesData([pf]) line.</div>
<div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Aug 5, 2013 at 8:52 AM, Sam Skillman <span dir="ltr"><<a href="mailto:samskillman@gmail.com" target="_blank">samskillman@gmail.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">Hi Brian,<div><br></div><div>I think what is going on here is that the Rockstar HF expects a TimeSeries object. If you change </div>
<div><div><br></div><div><span style="font-family:arial,sans-serif;font-size:13px">pf = load("DD0057/data0057")</span><br style="font-family:arial,sans-serif;font-size:13px">
<span style="font-family:arial,sans-serif;font-size:13px">rh = RockstarHaloFinder(pf)</span><br></div><div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div></div><div><span style="font-family:arial,sans-serif;font-size:13px">to </span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px"><div>ts = TimeSeriesData([pf])</div><div>rh = RockstarHaloFinder(ts)</div><div>
rh.run()</div><div><br></div><div>I think it should work. Also just for reference, I think Daegene is correct that Rockstar requires at least 3 processors. </div><div><br></div><div>Best,</div><div>Sam</div></span></div>
</div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Aug 4, 2013 at 8:20 PM, Brian O'Shea <span dir="ltr"><<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.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><div>Hi Daegone,<br><br>Sorry, I think my last email was imprecise: after that first email, I am now running in parallel on 4 processors, using the command line:<br>
<br>mpirun -np 4 python ./test_rockstar.py --parallel<br>
<br></div>Rockstar gives a similar error both running on a single core (with mpirun) and in parallel. :-(<span><font color="#888888"><br><br></font></span></div><span><font color="#888888">--Brian<br>
<div><div><br></div></div></font></span></div><div><div><div class="gmail_extra"><br><br><div class="gmail_quote">
On Sun, Aug 4, 2013 at 8:57 PM, Daegene Koh <span dir="ltr"><<a href="mailto:dkoh30@gatech.edu" target="_blank">dkoh30@gatech.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">Hi Brian,<div><br></div><div>If I recall correctly, I believe you need at least 3 processors to get </div><div>Rockstar running properly. And it must always be run in parallel.</div><div>
I'm afraid I don't know much much more beyond that.</div><div><br></div><div>Cheers,</div><div>DK</div><div><br></div><div><div><div><div><div>On Aug 4, 2013, at 7:54 PM, "Brian O'Shea" <<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.com</a>> wrote:</div>
<br></div></div><blockquote type="cite"><div><div><div dir="ltr"><div><div>Hi folks,<br><br>Just a quick followup: I've now run this on a different machine and verified that the reason I couldn't use Rockstar in parallel was due to a MPI problem. *HOWEVER*, I still have the same Rockstar error that I was reporting before when I was using one core (all using the same script as in my previous email):<br>
<br><a href="http://paste.yt-project.org/show/3747/" target="_blank">http://paste.yt-project.org/show/3747/</a><br><br></div>So, it does seem like there is a bug, or I am simply using Rockstar incorrectly...<br><br></div>
--Brian<br><br></div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Sun, Aug 4, 2013 at 6:26 PM, Brian O'Shea <span dir="ltr"><<a href="mailto:bwoshea@gmail.com" target="_blank">bwoshea@gmail.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><div><div>Dear yt-users,<br><br></div>I'm trying to use the Rockstar halo finder within yt, and am encountering some odd problems. I'm using the main development tree (<a href="https://bitbucket.org/yt_analysis/yt" target="_blank">https://bitbucket.org/yt_analysis/yt</a>) with changeset f936432ed45d, and attempting to use Rockstar to find halos on a small server running Ubuntu 12.04. When I call this script:<br>
<br></div><div>---- file test_rockstar.py ----<br></div><div><br>from yt.mods import *<br>from yt.analysis_modules.halo_finding.rockstar.api import RockstarHaloFinder<br><br>pf = load("DD0057/data0057")<br>rh = RockstarHaloFinder(pf)<br>
<br>---<br><br></div>using the command line sequence "mpirun -np 2 python ./test_rockstar.py --parallel", I seem to be getting a seg fault (as can be seen at <a href="http://paste.yt-project.org/show/3745/" target="_blank">http://paste.yt-project.org/show/3745/</a>). However, if I use a single processor (with "mpirun -np 1 python ./test_rockstar.py --parallel"), I get a very different error:<br>
<br>Traceback (most recent call last):<br> File "./test_rockstar.py", line 6, in <module><br> rh = RockstarHaloFinder(pf)<br> File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 230, in __init__<br>
self.pool, self.workgroup = self.runner.setup_pool()<br> File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/rockstar.py", line 112, in setup_pool<br> (self.num_writers, "writers") ]<br>
File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 335, in from_sizes<br> pool.add_workgroup(size, name = name)<br> File "/data/bwoshea/galparttest/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 303, in add_workgroup<br>
group = self.comm.comm.Get_group().Incl(ranks)<br>AttributeError: 'NoneType' object has no attribute 'Get_group'<br><br></div>I'm puzzled about the error, since I can use other parallel yt scripts without any problems (a 4-processor script making projections works just fine). This machine doesn't have infiniband (as warned about at <a href="http://yt-project.org/doc/analysis_modules/running_halofinder.html#rockstar-halo-finding" target="_blank">http://yt-project.org/doc/analysis_modules/running_halofinder.html#rockstar-halo-finding</a>), and both FOF and Hop find several hundred halos with my dataset. I'd just use another halo finder, but I'm trying to do something that requires Rockstar to be run inline with Enzo, so I'm stuck with it...<br>
<br>Does anybody have any idea what might be going on?<br><br>Thanks!<span><font color="#888888"><br><br>Brian<br><br></font></span></div>
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