[yt-users] Problems using Rockstar in yt

[Britton Smith]

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.

Britton


On Tue, Aug 12, 2014 at 11:52 AM, David Sullivan <D.Sullivan at 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 at lists.spacepope.org wrote:
>
> Message: 3
> Date: Tue, 12 Aug 2014 02:04:10 -0700
> From: Sam Skillman <samskillman at gmail.com>
> To: Discussion of the yt analysis package
> <yt-users at lists.spacepope.org>
> Subject: Re: [yt-users] Problems using Rockstar in yt
> Message-ID:
> <CAB4=1s1oHK0uPFo88rkSaEa-W6EASMLoyOiEFeniV-xSm6SPaQ at 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 at 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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