Mailman 3 December 2014 - yt-users

Nightly binary builds of yt for Anaconda Python
by John Zuhone 16 Dec '14

16 Dec '14

Hello everyone, I’ve set up some nightly binary builds of yt that are installable via Anaconda Python: https://binstar.org/jzuhone/yt/files These build a binary package of yt from whatever the tip of the main repository is every night. I’m still working the kinks out of scheduling the builds, but there should be very recent versions of yt up there for Linux, Windows, and Mac OS X (all 64-bit only). I’d like folks to test these out at their leisure to see how they hold up under different platforms. If you don’t want to mess up your current Anaconda/yt setup, you can test it out in a separate Anaconda environment on the same machine. To set up a new conda environment, start with Step 1 below. If you’re ok with installing it in the default environment, you can skip to Step 2. Step 1: You can setup a new Anaconda Python environment, completely separate from the default one, using “conda create”, e.g.: conda create -n test_yt python=2.7 numpy=1.8 which will set up a completely new conda environment which can be activated at will. You should see some instructions like this: # # To activate this environment, use: # $ source activate test_yt # # To deactivate this environment, use: # $ source deactivate # After you activate this environment, the prompt will indicate that you are in this new environment (in this example “yt_test”), and anything you do will NOT touch your default install at all. Step 2: Install the yt nightly using: conda install -c https://conda.binstar.org/jzuhone yt==dev And you’re done! Let me know what happens! Best, John Z _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Particles, periodic
by David Collins 16 Dec '14

16 Dec '14

Hi, Everybody- I have a periodic data set and want to run the annotate_particles callback centered on the max. It looks like the particles are cut off for a chunk of my region, as though the weren't rolled around the periodic boundary. There used to be a periodic_region that I think took care of this, but I don't see it any more. Is there an easy work around for this? I apologize if this came up already, I feel like I saw this question go by recently, but couldn't find it. (I might have even asked it. I'm a little dumb these days) d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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cut mask
by David Collins 15 Dec '14

15 Dec '14

Hi, Everybody- I have some old code in which I pulled particle ids from grid objects, and I'm porting it to yt3.0. My old code used a "cut mask" defined like the following: for grid in data._grids: cut_mask= data._get_cut_mask(grid) I see that grids is now handled through chunks, is there a modern equivalent of the cut_mask? Or, is there a new-and-improved method to get particle ids from complex objects? d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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pf.proj docs
by David Collins 15 Dec '14

15 Dec '14

Hi, Everybody-- When getting a projection from a parameter file, like this, >>> proj = pf.proj(0, 'density') the order in the parameters 'axis' and 'field' has switched form yt2.x to yt3.x, but the docs didn't follow suit: >>> help(pf.proj) still has | >>> ds = load("RedshiftOutput0005") | >>> prj = ds.proj(0, "density") | >>> print proj["density"] Am I correct in assuming that this is a hungover docstring? I can submit a fix to that, if that's right. d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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yt basic visualization for gadget output
by Junhwan Choi (최준환) 15 Dec '14

15 Dec '14

Hi yt users and developers: I try to use yt to visualize my gadget output (hdf5 format). I made following simple script: ======================== import matplotlib as matplotlib matplotlib.use('Agg') import matplotlib.pylab as pylab import yt ds = yt.load("snap_agora_100.hdf5") print ds.field_list print ds.derived_field_list pc = yt.ProjectionPlot(ds, "x", ('gas', 'Density')) pc.save("gadget") ========================== But it results in unknown error messages. And, I have searched some documents for yt for gadget, but there is also nothing I can find. Is there any yt gadget documents I can consult ? I have used yt for my enzo simulation analysis. Thanks in advance, Junhwan Choi

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Creating 1-D Radial Profile
by Lu, Yinghe 14 Dec '14

14 Dec '14

Hi everyone, I have a question using the create_profile routine. I am currently using yt for analyzing FLASH data (creating 1D radial density profile namely). Now I am encountering trouble where after creating the profile, the field value is outputting a lot of zeros around the domain centre. ds = yt.load(filename) sphere = ds.sphere(ds.domain_center, (300.0, "kpc")) print sphere["density"][1:50].value profile = yt.create_profile(sphere, "radius", "density", weight_field = "cell_volume",units = {'radius': 'kpc'}) print profile["density"][1:50].value After creating the sphere, the field value has no zeros; they only start to occur after creating the profile. I have used other methods to check my simulation and there are no zero densities involved. So I was wondering if there is something in the create_profile routine (maybe the weighting or binning) is causing this, and how could I get rid of the them? Thanks all, Yinghe

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problem running yt in parallel
by Professor Maller 13 Dec '14

13 Dec '14

Hi Everyone, I'm having trouble using yt in parallel. I'm getting an error message; AttributeError: 'module' object has no attribute 'rootLogger' I'm running this simple test script #test_script.py import yt yt.enable_parallelism(suppress_logging=True, communicator=None) # Load the dataset filename='Data/enzo_cosmology_plus/DD0046/DD0046' ds=yt.load(filename) v,c=ds.find_max("density") print v,c this runs fine when just executing python test_script.py, but if I do mpirun -np 4 python test_script.py I get the following yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation enabled: 1 / 4 yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation enabled: 2 / 4 yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation enabled: 3 / 4 yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation enabled: 0 / 4 Traceback (most recent call last): File "create_catalog.py", line 3, in <module> Traceback (most recent call last): File "create_catalog.py", line 3, in <module> Traceback (most recent call last): File "create_catalog.py", line 3, in <module> Traceback (most recent call last): File "create_catalog.py", line 3, in <module> yt.enable_parallelism(suppress_logging=True, communicator=None) File "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 116, in enable_parallelism yt.enable_parallelism(suppress_logging=True, communicator=None) File "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 116, in enable_parallelism yt.enable_parallelism(suppress_logging=True, communicator=None) File "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 116, in enable_parallelism yt.enable_parallelism(suppress_logging=True, communicator=None) File "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", line 116, in enable_parallelism if len(yt.utilities.logger.rootLogger.handlers) > 0: AttributeError: 'module' object has no attribute 'rootLogger' if len(yt.utilities.logger.rootLogger.handlers) > 0: if len(yt.utilities.logger.rootLogger.handlers) > 0: AttributeError: 'module' object has no attribute 'rootLogger' AttributeError: 'module' object has no attribute 'rootLogger' if len(yt.utilities.logger.rootLogger.handlers) > 0: AttributeError: 'module' object has no attribute 'rootLogger' =================================================================================== = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES = EXIT CODE: 1 = CLEANING UP REMAINING PROCESSES = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES =========================================================== Any thoughts would be greatly appreciated. Ari _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Re: [yt-users] yt-users Digest, Vol 82, Issue 31
by Professor Maller 13 Dec '14

13 Dec '14

Hi Nathan, Thanks, I'll do that. Ari On Sat, Dec 13, 2014 at 3:18 PM, <yt-users-request(a)lists.spacepope.org> wrote: > > Send yt-users mailing list submissions to > yt-users(a)lists.spacepope.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > or, via email, send a message with subject or body 'help' to > yt-users-request(a)lists.spacepope.org > > You can reach the person managing the list at > yt-users-owner(a)lists.spacepope.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of yt-users digest..." > > > Today's Topics: > > 1. problem running yt in parallel (Professor Maller) > 2. Re: problem running yt in parallel (Nathan Goldbaum) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 13 Dec 2014 14:51:18 -0500 > From: Professor Maller <amaller(a)citytech.cuny.edu> > To: yt-users(a)lists.spacepope.org > Subject: [yt-users] problem running yt in parallel > Message-ID: > < > CACCSjdNg9-AZzagbvxaz4PHYj2U6aD7edkuZ5AFA7WJCGA63ig(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Everyone, > > I'm having trouble using yt in parallel. I'm getting an error message; > AttributeError: 'module' object has no attribute 'rootLogger' > > I'm running this simple test script > #test_script.py > import yt > yt.enable_parallelism(suppress_logging=True, communicator=None) > # Load the dataset > filename='Data/enzo_cosmology_plus/DD0046/DD0046' > ds=yt.load(filename) > v,c=ds.find_max("density") > print v,c > > this runs fine when just executing python test_script.py, but if I do > mpirun -np 4 python test_script.py > I get the following > > yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation > enabled: 1 / 4 > yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation > enabled: 2 / 4 > yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation > enabled: 3 / 4 > yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation > enabled: 0 / 4 > Traceback (most recent call last): > File "create_catalog.py", line 3, in <module> > Traceback (most recent call last): > File "create_catalog.py", line 3, in <module> > Traceback (most recent call last): > File "create_catalog.py", line 3, in <module> > Traceback (most recent call last): > File "create_catalog.py", line 3, in <module> > yt.enable_parallelism(suppress_logging=True, communicator=None) > File > > "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", > line 116, in enable_parallelism > yt.enable_parallelism(suppress_logging=True, communicator=None) > File > > "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", > line 116, in enable_parallelism > yt.enable_parallelism(suppress_logging=True, communicator=None) > File > > "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", > line 116, in enable_parallelism > yt.enable_parallelism(suppress_logging=True, communicator=None) > File > > "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", > line 116, in enable_parallelism > if len(yt.utilities.logger.rootLogger.handlers) > 0: > AttributeError: 'module' object has no attribute 'rootLogger' > if len(yt.utilities.logger.rootLogger.handlers) > 0: > if len(yt.utilities.logger.rootLogger.handlers) > 0: > AttributeError: 'module' object has no attribute 'rootLogger' > AttributeError: 'module' object has no attribute 'rootLogger' > if len(yt.utilities.logger.rootLogger.handlers) > 0: > AttributeError: 'module' object has no attribute 'rootLogger' > > > =================================================================================== > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = EXIT CODE: 1 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > =========================================================== > > Any thoughts would be greatly appreciated. > > Ari > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Message: 2 > Date: Sat, 13 Dec 2014 12:08:17 -0800 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] problem running yt in parallel > Message-ID: > <CAJXewOn=ic0nmowA_zP4VXiEpy= > 9uOu1y4GMsJWzOPW7V70vzg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Ari, > > Thanks for the report! This is a genuine bug, due to a pull request that > was merged just a few days ago that removed the rootLogger. > > If you update to the change before the pull request was merged (changeset > hash bca4a05), this issue should go away. Let us know if you need help > updating to the old version. > > I've opened an issue to track this: > > https://bitbucket.org/yt_analysis/yt/issue/956/enable_parallelism-dies-due-… > > If you have a bitbucket account, you can watch the issue to get e-mail > updates. > > Hopefully we should have this fixed soon. > > -Nathan > > > On Sat, Dec 13, 2014 at 11:51 AM, Professor Maller < > amaller(a)citytech.cuny.edu> wrote: > > > > Hi Everyone, > > > > I'm having trouble using yt in parallel. I'm getting an error message; > > AttributeError: 'module' object has no attribute 'rootLogger' > > > > I'm running this simple test script > > #test_script.py > > import yt > > yt.enable_parallelism(suppress_logging=True, communicator=None) > > # Load the dataset > > filename='Data/enzo_cosmology_plus/DD0046/DD0046' > > ds=yt.load(filename) > > v,c=ds.find_max("density") > > print v,c > > > > this runs fine when just executing python test_script.py, but if I do > > mpirun -np 4 python test_script.py > > I get the following > > > > yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation > > enabled: 1 / 4 > > yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation > > enabled: 2 / 4 > > yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation > > enabled: 3 / 4 > > yt : [INFO ] 2014-12-13 14:49:40,188 Global parallel computation > > enabled: 0 / 4 > > Traceback (most recent call last): > > File "create_catalog.py", line 3, in <module> > > Traceback (most recent call last): > > File "create_catalog.py", line 3, in <module> > > Traceback (most recent call last): > > File "create_catalog.py", line 3, in <module> > > Traceback (most recent call last): > > File "create_catalog.py", line 3, in <module> > > yt.enable_parallelism(suppress_logging=True, communicator=None) > > File > > > "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", > > line 116, in enable_parallelism > > yt.enable_parallelism(suppress_logging=True, communicator=None) > > File > > > "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", > > line 116, in enable_parallelism > > yt.enable_parallelism(suppress_logging=True, communicator=None) > > File > > > "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", > > line 116, in enable_parallelism > > yt.enable_parallelism(suppress_logging=True, communicator=None) > > File > > > "/home/amaller/yt-x86_64/src/yt-hg/yt/utilities/parallel_tools/parallel_analysis_interface.py", > > line 116, in enable_parallelism > > if len(yt.utilities.logger.rootLogger.handlers) > 0: > > AttributeError: 'module' object has no attribute 'rootLogger' > > if len(yt.utilities.logger.rootLogger.handlers) > 0: > > if len(yt.utilities.logger.rootLogger.handlers) > 0: > > AttributeError: 'module' object has no attribute 'rootLogger' > > AttributeError: 'module' object has no attribute 'rootLogger' > > if len(yt.utilities.logger.rootLogger.handlers) > 0: > > AttributeError: 'module' object has no attribute 'rootLogger' > > > > > > > =================================================================================== > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > > = EXIT CODE: 1 > > = CLEANING UP REMAINING PROCESSES > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > =========================================================== > > > > Any thoughts would be greatly appreciated. > > > > Ari > > > > > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > http://lists.spacepope.org/pipermail/yt-users-spacepope.org/attachments/201… > > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > > ------------------------------ > > End of yt-users Digest, Vol 82, Issue 31 > **************************************** > _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Cosmological parameters necessary to run synthetic spectrum?
by Nicholas Earl 12 Dec '14

12 Dec '14

Hey everyone, Is there a way to fake the cosmological parameters that the synthetic spectrum generator looks for in a simulation? Or rather, a "sanctioned" way? Having the package reference hardcoded values when the parameters themselves are not found yields other missing fields like 'creation_time'. I am wondering if this is a consequence of the simulation not being inherently cosmological? I am using yt 2.x currently, as I'm aware that there seems to be an issue with the generator in the 3.0 release. Thanks for your time, Nick

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parallel_objects with projection hanging
by Semyeong Oh 11 Dec '14

11 Dec '14

Hi yt, I have two questions on using parallel_objects. I am using yt 2.6. 1. I have a problem of parallel_objects hanging at the end. def do(i, pf): cube = pf.h.region(..) proj = pf.h.proj(…., source=cube) frb = proj.to_frb(..) …. objects = [list of indices] pf = load(..) for i in parallel_objects(objects): do(i, pf) and I run the script as mpirun -np Nprocs python myscripy.py —parallel When I tested with a simple print operation in do instead of proj, the parallel_objects seem to handle cases when Nobjects is not divisible by Nprocs just fine. But with my real script that has proj in do, it seems to hang at the end. For example, if Nobjects is 3 and Nprocs is 2, the first two objects goes without problem, but the projection of the third completes, but the process sort of hangs there. Why so? 2. Is it possible to use a portion of Nprocs assigned? Also playing around with simple print operation, it seems that because of the way parallel_objects divide work, the work is duplicated. e..g, when I do mpirun -np 5 but have parallal_objects(objects, njobs=3) rank i_object 0 1 1 1 2 2 3 2 4 3 … so object 1 would still run simultaneously on rank 0 and 1. To prevent this, would something like below work? size = MPI.COMM_WORLD.Get_size() rank = MPI.COMM_WORLD.Get_rank() njobs = 3 for ind in parallel_objects(objects, njobs): if rank % int(size/njobs) != 0: continue else: do(ind) Thanks, Semyeong

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