[yt-users] Problems using Rockstar in yt

Nathan Goldbaum nathan12343 at gmail.com
Tue Aug 12 08:37:32 PDT 2014


On Tuesday, August 12, 2014, Britton Smith <brittonsmith at 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 at sussex.ac.uk
> <javascript:_e(%7B%7D,'cvml','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
>> <javascript:_e(%7B%7D,'cvml','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
>> <javascript:_e(%7B%7D,'cvml','samskillman at gmail.com');>>
>> To: Discussion of the yt analysis package
>>  <yt-users at lists.spacepope.org
>> <javascript:_e(%7B%7D,'cvml','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
>> <javascript:_e(%7B%7D,'cvml','CAB4%5Cx3d1s1oHK0uPFo88rkSaEa-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
>> <javascript:_e(%7B%7D,'cvml','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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