Re: [yt-users] Problems using Rockstar in yt
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#...
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.ht...
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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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#...
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.ht...
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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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/ 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#... 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-...), 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? 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@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#...
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.ht...
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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org
On Tue, Aug 12, 2014 at 9:15 AM, Cameron Hummels <chummels@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:
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#...
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-...), 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@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#...
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.ht...
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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
-- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org
_______________________________________________ yt-users mailing list yt-users@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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@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
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
On Tue, Aug 12, 2014 at 9:15 AM, Cameron Hummels <chummels@gmail.com> wrote: things 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:
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#...
It also mentions in those docs that in order to deal with simulations
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
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
with perform 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.
but as I said, I am running into problems using the version of rockstar
http://yt-project.org/docs/dev/cookbook/cosmological_analysis.html#plotting-... ), 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 <
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#...
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.ht...
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
D.Sullivan@sussex.ac.uk> 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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-- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org
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I just want to add a little bit of information on why rockstar needs to run in parallel. Natively, rockstar has it's own parallelism in which separate processes are responsible for reading the data (readers), doing the computation and output (writers), and controlling everything (servers). There is always only one server, but the number of readers and writers can be changed with the n_readers and n_writers keywords (which you can add to the finder_kwargs dict in the HaloCatalog). At minimum, you need one server, one reader, and one writer, so rockstar must be run with at least 3 MPI processes. On Tue, Aug 12, 2014 at 3:31 PM, Sam Skillman <samskillman@gmail.com> wrote:
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@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
to fail is apparently an OS X bug (I found some discussions of it on
internet) and has nothing to do with yt. I went through a similar
On Tue, Aug 12, 2014 at 9:15 AM, Cameron Hummels <chummels@gmail.com> wrote: things the 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:
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#...
It also mentions in those docs that in order to deal with simulations
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
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
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
with perform then I 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.
but as I said, I am running into problems using the version of rockstar
http://yt-project.org/docs/dev/cookbook/cosmological_analysis.html#plotting-... ), 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 <
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#...
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.ht...
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
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
D.Sullivan@sussex.ac.uk> traceback: 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@lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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-- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org
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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 <javascript:_e(%7B%7D,'cvml','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 <javascript:_e(%7B%7D,'cvml','yt-users-request@lists.spacepope.org');> wrote:
Message: 3 Date: Tue, 12 Aug 2014 02:04:10 -0700 From: Sam Skillman <samskillman@gmail.com <javascript:_e(%7B%7D,'cvml','samskillman@gmail.com');>> To: Discussion of the yt analysis package <yt-users@lists.spacepope.org <javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org');>> Subject: Re: [yt-users] Problems using Rockstar in yt Message-ID: <CAB4=1s1oHK0uPFo88rkSaEa-W6EASMLoyOiEFeniV-xSm6SPaQ@mail.gmail.com <javascript:_e(%7B%7D,'cvml','CAB4%5Cx3d1s1oHK0uPFo88rkSaEa-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 <javascript:_e(%7B%7D,'cvml','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#...
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.ht...
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@lists.spacepope.org <javascript:_e(%7B%7D,'cvml','yt-users@lists.spacepope.org');> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org
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Hey everyone, Thanks for all of the tips for solving this. To follow up, --OS X needs the $DYLD_LIBRARY_PATH set to the same things that are set by the activation script for $LD_LIBRARY_PATH in order to run Rockstar internal to yt. Setting $DYLD_LIBRARY_PATH to yt's lib dir caused some problems for me initially when I tried to use things like the vi editor, but by reinstalling yt without libpng support, this was resolved. --Rockstar as it is run in yt *requires* parallel operations to work with at least 3 processors. --Running rockstar through yt can be done on datasets using particles with different masses by first applying a filter to isolate the particles of one mass. Use the script that Sam suggested: http://paste.yt-project.org/show/5029/ . Thanks, Sam! I'm going to tweak the docs to take into account these issues, but I wanted to summarize for people reading this at home. Thanks for the help, everyone. Cameron On Tue, Aug 12, 2014 at 8:37 AM, Nathan Goldbaum <nathan12343@gmail.com> wrote:
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#...
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.ht...
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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-- Cameron Hummels Postdoctoral Researcher Steward Observatory University of Arizona http://chummels.org
participants (6)
-
Britton Smith -
Cameron Hummels -
David Sullivan -
Matthew Turk -
Nathan Goldbaum -
Sam Skillman