[yt-users] Problems using Rockstar in yt

Sam Skillman samskillman at gmail.com
Tue Aug 12 07:31:36 PDT 2014 

This worked for me recently:
http://paste.yt-project.org/show/5029/

With mpirun -np 3 python script.py

Sam


On Tue, Aug 12, 2014 at 7:21 AM, Matthew Turk <matthewturk at gmail.com> wrote:

> On Tue, Aug 12, 2014 at 9:15 AM, Cameron Hummels <chummels at gmail.com>
> wrote:
> > Hi Britton, Sam, and David,
> >
> > Thanks for the insights into this problem.  I've made it farther, but I'm
> > still getting problems.  I'll make sure that when we've resolved this,
> I'll
> > write it up and put it in the docs for other people trying to use
> Rockstar
> > with yt, as I think this may be a common occurrance since rockstar is now
> > the preferred halo finder with yt above hop and fof.  A few comments:
> >
> >> 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.
> >
> >
> > That's odd, since I'm also using OS X 10.8.5 on both machines where I'm
> > getting this vi failure.  And strangely, it appears to be somewhat
> related
> > to yt, according to the failure message when I try to run 'vi' from the
> > command-line seen here:
> >
> > http://paste.yt-project.org/show/5022/
>
> Looks like a conflict between system libpng and the yt stack's libpng.
> Might be fixable with an install where libpng is disabled.
>
> >
> > Anyway, as you suggest, I can just run rockstar in a new terminal without
> > doing anything else, but I thought you might have seen this error before.
> >
> >>
> >> 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.
> >
> >
> > OK, so one needs to run rockstar in parallel.  I thought in reading the
> > rockstar docs, there was a way of running it with one processor, but OK,
> I
> > can run it in parallel.  When I do that on this particular dataset,
> Enzo_64,
> > it fails because there are particles in the simulation of two separate
> > masses (stars and DM).  I know that is a problem with this version of
> > rockstar as described in the docs here:
> >
> >
> http://yt-project.org/docs/dev/analyzing/analysis_modules/halo_finders.html#rockstar-halo-finding
> >
> > It also mentions in those docs that in order to deal with simulations
> with
> > multiple particle masses, "In simulations where the highest-resolution
> > particles all have the same mass (ie: zoom-in grid based simulations),
> one
> > can set up a particle filter to select the lowest mass particles and
> perform
> > the halo finding only on those."
> > I have tried a few things here to make this work.  One, as suggested I
> > created a particle filter to just look at one mass of particles, and
> then I
> > applied it to the dataset, but I'm not sure how to pass that particle
> filter
> > to the Halo Catalog object.  Here is my attempt:
> >
> > http://paste.yt-project.org/show/5023/
> >
> > And the corresponding failure traceback:
> >
> > http://paste.yt-project.org/show/4IWCE1hZS1KGpTWztokW
> >
> > Alternatively, I see that the Halo Catalog object does take a
> "data_source"
> > kwarg, so I made a cut_region of all_data just selecting particles that
> were
> > the most massive, and again, I get the same failure.  So I'm curious how
> to
> > use Rockstar to find halos on simulations that have multiple masses.  I
> > guess I'm just missing something stupid here, as I know there are people
> who
> > have done this in the past.  Does anyone have an example script or some
> hint
> > for me here?  Here is my script using the cut region to get only the most
> > massive particles of a single mass, but it fails the same way as above:
> >
> > http://paste.yt-project.org/show/5027/
> >
> > Alternatively, it seems like the yt docs advocate using rockstar
> external to
> > yt, and then just using the output halos file for doing things (e.g.
> >
> http://yt-project.org/docs/dev/cookbook/cosmological_analysis.html#plotting-halos
> ),
> > but as I said, I am running into problems using the version of rockstar
> that
> > comes with yt on enzo (or any hdf5) datasets.  Does anyone know how to
> use
> > this standalone rockstar with an enzo dataset to produce such a halo file
> > for later use within yt?
>
> Hm, news to me about the docs suggesting that.  My understanding is
> that we're mostly going in the opposite way -- avoiding using
> Rockstar's parallelism completely (to avoid the issues you note) and
> instead feeding in FOF groups found by yt.  This didn't get finished
> in time for the 3.0 release, and I wouldn't recommend trying it right
> now.
>
> For multiple masses, I think your first inclination (using particle
> filters) is the best.  Seems like it should just be fixable by
> allowing the Halo Catalog to accept a particle filter.
>
> >
> > Sorry for the long email, but I've tried lots of things.  Thank you very
> > much for the help so far!
> >
> > Cameron
> >
> >
> >>
> >> 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
> >>>
> >>> _______________________________________________
> >>> yt-users mailing list
> >>> yt-users at lists.spacepope.org
> >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> yt-users mailing list
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> >>>
> >>
> >>
> >> _______________________________________________
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> >>
> >
> >
> >
> > --
> > Cameron Hummels
> > Postdoctoral Researcher
> > Steward Observatory
> > University of Arizona
> > http://chummels.org
> >
> > _______________________________________________
> > yt-users mailing list
> > yt-users at lists.spacepope.org
> > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
> >
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