<br><br>On Tuesday, August 12, 2014, Britton Smith <<a href="mailto:brittonsmith@gmail.com">brittonsmith@gmail.com</a>> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Cameron, David,<div><br></div><div>Cameron, you are correct, on Mac systems you need to set DYLD_LIBRARY_PATH instead of LD_LIBRARY_PATH. The fact that this causes vi and other things to fail is apparently an OS X bug (I found some discussions of it on the internet) and has nothing to do with yt. I went through a similar thing and had to resort to having a separate terminal for running rockstar that I didn't try to do anything else in. For what it's worth, this behavior seems to have been fixed. I am on OS X 10.8.5 and no longer have the issue of things crashing in a terminal where I have edited DYLD_LIBRARY_PATH.</div>
<div><br></div><div>On the second issue that you both reported, the problem is the way in which one tells yt to run in parallel depends on how you import yt.</div><div><br></div><div>If you do "from yt.mods import *", the parallelism is enabled by adding the --parallel flag on the command line. However, if you do "import yt", then parallelism is enabled by doing "yt.enable_parallelism()" directly below the import statement within your script.</div>
<div><br></div><div>I looked at the latest documentation on parallelism (<a href="http://yt-project.org/doc/analyzing/parallel_computation.html" target="_blank">http://yt-project.org/doc/analyzing/parallel_computation.html</a>) and is discusses the use of yt.enable_parallelism(), but not the old way that works with "from yt.mods import *". There should probably be a short discussion added of how this has changed. Additionally, let's make sure that the yt-rockstar docs get any needed additions there as well.</div>
</div></blockquote><div><br></div><div>This is mentioned on the yt3 differences page. You're right that there should be some discussion in the parallelism docs, though<span></span></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><br></div><div>Britton</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Aug 12, 2014 at 11:52 AM, David Sullivan <span dir="ltr"><<a href="javascript:_e(%7B%7D,'cvml','D.Sullivan@sussex.ac.uk');" target="_blank">D.Sullivan@sussex.ac.uk</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 all,<div><br></div><div>I also get the same error as Cameron when trying to run rockstar with mpi:</div>
<div><br></div><div><a href="http://paste.yt-project.org/show/5019/" target="_blank">http://paste.yt-project.org/show/5019/</a></div><div><br></div><div>I’m using a ramses dataset (not sure if this is supported, but couldn’t see any clear evidence that it isn’t) and the following script:</div>
<div><br></div><div>mpirun -np 4 --mca btl ^openib python run_rockstar.py --parallel</div><div><a href="http://paste.yt-project.org/show/5020/" target="_blank">http://paste.yt-project.org/show/5020/</a></div><div><br></div>
<div>I followed the same install instructions as Cameron, but I’m using a Linux cluster running CentOS. Appreciate any help!</div><div><br></div><div>Cheers,</div><div>David</div><div><br><div><div>On 12 Aug 2014, at 10:04, <a href="javascript:_e(%7B%7D,'cvml','yt-users-request@lists.spacepope.org');" target="_blank">yt-users-request@lists.spacepope.org</a> wrote:</div>
<br><blockquote type="cite"><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Message: 3</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Date: Tue, 12 Aug 2014 02:04:10 -0700</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">From: Sam Skillman <</span><a href="javascript:_e(%7B%7D,'cvml','samskillman@gmail.com');" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">samskillman@gmail.com</a><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">></span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">To: Discussion of the yt analysis package</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;white-space:pre-wrap"> </span><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important"><</span><a href="javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org');" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">yt-users@lists.spacepope.org</a><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">></span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Subject: Re: [yt-users] Problems using Rockstar in yt</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Message-ID:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;word-spacing:0px;white-space:pre-wrap"> </span><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important"><</span><a href="javascript:_e(%7B%7D,'cvml','CAB4%5Cx3d1s1oHK0uPFo88rkSaEa-W6EASMLoyOiEFeniV-xSm6SPaQ@mail.gmail.com');" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">CAB4=1s1oHK0uPFo88rkSaEa-W6EASMLoyOiEFeniV-xSm6SPaQ@mail.gmail.com</a><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">></span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Content-Type: text/plain; charset="utf-8"</span><div>
<div><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Hi Cameron,</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Are you running in MPI? You need to run with at least 3 MPI tasks for</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Rockstar to work properly.</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">Sam</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">On Mon, Aug 11, 2014 at 6:41 PM, Cameron Hummels <</span><a href="javascript:_e(%7B%7D,'cvml','chummels@gmail.com');" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px" target="_blank">chummels@gmail.com</a><span style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;float:none;display:inline!important">> wrote:</span><br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<br style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<blockquote type="cite" style="font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
Hello,<br><br>I'm trying to use Rockstar with the new HaloCatalog functionality in yt<br>3.0, but I'm encountering some problems. For reference, this is an OS X<br>box with the "yt" branch. I've tested it on two OS X systems to the same<br>
result.<br><br>I modified my install_script.py to have it install Rockstar as described<br>here:<br><br><br><a href="http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_finders.html#rockstar-installation" target="_blank">http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_finders.html#rockstar-installation</a><br>
<br>Then, after rerunning my install script for the `yt` branch (ie yt-3.1<br>dev) I tried to run the script provided here in order to generate a halo<br>catalog using HOP:<br><br><br><a href="http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_transition.html#getting-halo-information" target="_blank">http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_transition.html#getting-halo-information</a><br>
<br>It can create the catalog fine with finder_method='hop', but when I change<br>it to finder_method='rockstar', I get failures. This is the traceback:<br><br><a href="http://paste.yt-project.org/show/TE2DW8gc50urchv4JnUk" target="_blank">http://paste.yt-project.org/show/TE2DW8gc50urchv4JnUk</a><br>
<br>In the traceback, it claims that it cannot access librockstar.so, but this<br>library exists in the yt-x86_64/lib directory, which is explicitly in from<br>my $LD_LIBRARY_PATH. I can seemingly get it to work, if I add that path to<br>
my $DYLD_LIBRARY_PATH environment variable, but then a bunch of other<br>things break (like vi). Not sure what to do here.<br><br>But assuming there is no vi problem here, even then, when I run the script<br>above, I get failures. Here is the traceback:<br>
<br><a href="http://paste.yt-project.org/show/rCOT1eVT1szR1T6DEUDb" target="_blank">http://paste.yt-project.org/show/rCOT1eVT1szR1T6DEUDb</a><br><br>I'm not sure what to do here. I've also tried running rockstar external<br>
to yt on an enzo dataset, but it doesn't appear that the version we install<br>as part of yt allows it to work on HDF5 datasets.<br><br>Has anyone run into any of these problems before? I'm at a bit of a loss<br>
as to how to proceed on any of these fronts.<br><br>Cameron<br><br><br>--<br>Cameron Hummels<br>Postdoctoral Researcher<br>Steward Observatory<br>University of Arizona<br><a href="http://chummels.org/" target="_blank">http://chummels.org</a><br>
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