On Tuesday, August 12, 2014, Britton Smith <brittonsmith@gmail.com> wrote:

Hi Cameron, David,

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.

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.

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.

I looked at the latest documentation on parallelism (http://yt-project.org/doc/analyzing/parallel_computation.html) 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.

This is mentioned on the yt3 differences page.  You're right that there should be some discussion in the parallelism docs, though

 

Britton

On Tue, Aug 12, 2014 at 11:52 AM, David Sullivan <D.Sullivan@sussex.ac.uk> wrote:

Hi all,

I also get the same error as Cameron when trying to run rockstar with mpi:

http://paste.yt-project.org/show/5019/

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:

mpirun -np 4 --mca btl ^openib python run_rockstar.py --parallel

http://paste.yt-project.org/show/5020/

I followed the same install instructions as Cameron, but I’m using a Linux cluster running CentOS. Appreciate any help!

Cheers,

David

On 12 Aug 2014, at 10:04, yt-users-request@lists.spacepope.org wrote:

Message: 3
Date: Tue, 12 Aug 2014 02:04:10 -0700
From: Sam Skillman <samskillman@gmail.com>
To: Discussion of the yt analysis package
<yt-users@lists.spacepope.org>
Subject: Re: [yt-users] Problems using Rockstar in yt
Message-ID:
<CAB4=1s1oHK0uPFo88rkSaEa-W6EASMLoyOiEFeniV-xSm6SPaQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Cameron,

Are you running in MPI?  You need to run with at least 3 MPI tasks for
Rockstar to work properly.

Sam


On Mon, Aug 11, 2014 at 6:41 PM, Cameron Hummels <chummels@gmail.com> wrote:

Hello,

I'm trying to use Rockstar with the new HaloCatalog functionality in yt
3.0, but I'm encountering some problems.  For reference, this is an OS X
box with the "yt" branch.  I've tested it on two OS X systems to the same
result.

I modified my install_script.py to have it install Rockstar as described
here:


http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_finders.html#rockstar-installation

Then, after rerunning my install script for the `yt` branch (ie yt-3.1
dev) I tried to run the script provided here in order to generate a halo
catalog using HOP:


http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_transition.html#getting-halo-information

It can create the catalog fine with finder_method='hop', but when I change
it to finder_method='rockstar', I get failures.  This is the traceback:

http://paste.yt-project.org/show/TE2DW8gc50urchv4JnUk

In the traceback, it claims that it cannot access librockstar.so, but this
library exists in the yt-x86_64/lib directory, which is explicitly in from
my $LD_LIBRARY_PATH.  I can seemingly get it to work, if I add that path to
my $DYLD_LIBRARY_PATH environment variable, but then a bunch of other
things break (like vi).  Not sure what to do here.

But assuming there is no vi problem here, even then, when I run the script
above, I get failures.  Here is the traceback:

http://paste.yt-project.org/show/rCOT1eVT1szR1T6DEUDb

I'm not sure what to do here.  I've also tried running rockstar external
to yt on an enzo dataset, but it doesn't appear that the version we install
as part of yt allows it to work on HDF5 datasets.

Has anyone run into any of these problems before?  I'm at a bit of a loss
as to how to proceed on any of these fronts.

Cameron


--
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org

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