Mailman 3 April 2011 - yt-users

Re: [yt-users] Updated yt module on Kraken and Nautilus
by Harinarayan Krishnan 12 Apr '11

12 Apr '11

No problem. I also added myself to the yt-users mailing list in case any other issues arise and I will try and fix it as soon as possible. Hari On Tue, Apr 12, 2011 at 1:27 PM, Cameron Hummels < chummels(a)astro.columbia.edu> wrote: Excellent! Thanks again for making this happen! Cameron On 4/12/11 4:12 PM, Harinarayan Krishnan wrote: Hi, I apologize for missing that. I forgot to add execute permission to the world in the modulefile. I had a colleague test that yt loads on the kraken's login node. Thanks for catching that! Hari On Tue, Apr 12, 2011 at 1:02 PM, Cameron Hummels < chummels(a)astro.columbia.edu> wrote: > It appears that Harinarayan Krishnan needs to change the permissions on > the yt subdirectory on kraken to be executable by world. I loaded the > yt module and it complains of permissions: > > $ module swap PrgEnv-pgi PrgEnv-gnu > $ module load yt > utility.c(2361):ERROR:50: Cannot open file '/sw/xt/modulefiles/yt/2.1' > for 'reading' > yt(5):ERROR:105: Unable to locate a modulefile for 'yt' > > $ ls -l /sw/xt/modulefiles/ > drwxrwxr-- 2 hkrishna install 4096 2011-04-11 13:31 yt > > Thanks to Stephen, Harinarayan and Matt for making this happen, as > having yt built into the module infrastructure is excellent (especially > with the small amount of $HOME space they give us on kraken = 2GB)! > > Cameron > > On 4/11/11 6:41 PM, Matthew Turk wrote: > > Hi all, > > > > The yt module on Kraken and the one on Nautilus have both been updated > > to yt 2.1. You can use these in lieu of an install script. > > > > On Nautilus: just run "module load yt" and it should default to > > yt/2.1. The 1.7 install is still there and can be loaded using module > > load yt/1.7 > > > > On Kraken run: > > module swap PrgEnv-pgi PrgEnv-gnu > > module load yt > > > > Thanks very much to Harinarayan Krishnan, who maintains these modules. > > If you run into any problems, let me know! > > > > Best, > > > > Matt > > _______________________________________________ > > yt-users mailing list > > yt-users(a)lists.spacepope.org > > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > >

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Updated yt module on Kraken and Nautilus
by Matthew Turk 12 Apr '11

12 Apr '11

Hi all, The yt module on Kraken and the one on Nautilus have both been updated to yt 2.1. You can use these in lieu of an install script. On Nautilus: just run "module load yt" and it should default to yt/2.1. The 1.7 install is still there and can be loaded using module load yt/1.7 On Kraken run: module swap PrgEnv-pgi PrgEnv-gnu module load yt Thanks very much to Harinarayan Krishnan, who maintains these modules. If you run into any problems, let me know! Best, Matt

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volume rendering
by Maike Schmidt 12 Apr '11

12 Apr '11

Hi together, I would like to better understand how the volume rendering works. It is explained here http://yt.spacepope.org/doc/visualizing/volume_rendering.html that the user defines transfer functions in terms of RGB values. >From the description of the add_gaussian function, I understand that these RGB values describe the color value in the interval [0,1]. Now, in the radiative transfer equation on the above website, the emissivity gets multiplied by the path length delta s. I am now wondering how this works: Depending on how big the step size is, one could get extremely large or extremely small intensities that are essentially unrelated to the RGB values that were previously specified. How is it possible that, for example, the color of a density isosurface depends on the density only and not on the cell size? I guess I am missing something. Cheers, Maike -- GMX DSL Doppel-Flat ab 19,99 Euro/mtl.! Jetzt mit gratis Handy-Flat! http://portal.gmx.net/de/go/dsl

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Re: [yt-users] loading halo off disk problem
by Stephen Skory 11 Apr '11

11 Apr '11

Geoffrey, I think we've stumbled upon a h5py bug! Without getting into gritty details, the LoadHaloes() code actually opens, closes, and then re-opens the h5 file when data is read in. For some reason, the re-open wasn't working, and the file was still marked as closed, and therefore trying read data from it wasn't working. I've added a band-aid of sorts which seems to fix the issue. Go ahead and update and let me know if you continue to have problems. (For those of you who get this twice, sorry! I sent the reply to the wrong yt list the first time.) -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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loading halo off disk problem
by gso＠physics.ucsd.edu 11 Apr '11

11 Apr '11

Hi Stephen, I was trying your two examples shown on "Loading Haloes Off Disk" in the documentation, I can do to both: haloes[0].center_of_mass() to find the center of mass coordinate xyz of the 0th halo, but when I tried to get the particle positions by doing haloes[0]["partilcle_position_x"] I succeeded with the first method while the data is still in memory, but fail in the second method when it is loaded off disk, can you verify this? It'll save a lot of time if I have the particle positions without having to run the profiler every time. error pasted at: http://paste.enzotools.org/show/NyLEwvGzl2RGBOcAcfKH From G.S.

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spin parameter quantity
by Andrew Davis 11 Apr '11

11 Apr '11

Hi folks, I'm looking at the spin of some objects and have a few questions about the quantities BaryonSpinParameter, and ParticleSpinParameter. I've only measured the spin of DM particles in the past, which is straightfoward compared to the baryons. In looking at the code (posted below from derived_quantities.py) however, I don't think either of the two functions actually calculate the spin parameter as usually defined: spin = | J | sqrt( | Etot | ) / (G M^5/2). In the both the Baryon and Particle Spin Parameter functions, the energy calculated is only the kinetic energy (and it's missing a factor of 0.5), whereas the definition of spin includes the total energy -- for DM this is just potential and kinetic energies. I'm assuming for baryons, it is potential + kinetic + internal energy. Neither functions include the potential energy, or the internal energy. Also, it looks like the second function (ParticleSpinParameter) really is just calculating the spin paramter of the DM particles (or star particles I guess), so it may make more sense just to not include the gas mass in the first line, and then re-word the short description so that it says that it really is just calculating the particle spin, ignoring any gas. If I'm wrong, please let me know -- otherwise, I'd be happy to submit a modified version of the two functions. Cheers, Andrew def _BaryonSpinParameter(data): """ This function returns the spin parameter for the baryons, but it uses the particles in calculating enclosed mass. """ m_enc = data["CellMassMsun"].sum() + data["ParticleMassMsun"].sum() am = data["SpecificAngularMomentum"]*data["CellMassMsun"] j_mag = am.sum(axis=1) e_term_pre = na.sum(data["CellMassMsun"]*data["VelocityMagnitude"]**2.0) weight=data["CellMassMsun"].sum() return j_mag, m_enc, e_term_pre, weight def _combBaryonSpinParameter(data, j_mag, m_enc, e_term_pre, weight): # Because it's a vector field, we have to ensure we have enough dimensions if len(j_mag.shape) < 2: j_mag = na.expand_dims(j_mag, 0) W = weight.sum() M = m_enc.sum() J = na.sqrt(((j_mag.sum(axis=0))**2.0).sum())/W E = na.sqrt(e_term_pre.sum()/W) G = 6.67e-8 # cm^3 g^-1 s^-2 spin = J * E / (M*1.989e33*G) return spin add_quantity("BaryonSpinParameter", function=_BaryonSpinParameter, combine_function=_combBaryonSpinParameter, n_ret=4) def _ParticleSpinParameter(data): """ This function returns the spin parameter for the baryons, but it uses the particles in calculating enclosed mass. """ m_enc = data["CellMassMsun"].sum() + data["ParticleMassMsun"].sum() am = data["ParticleSpecificAngularMomentum"]*data["ParticleMassMsun"] if am.size == 0: return (na.zeros((3,), dtype='float64'), m_enc, 0, 0) j_mag = am.sum(axis=1) e_term_pre = na.sum(data["ParticleMassMsun"] *data["ParticleVelocityMagnitude"]**2.0) weight=data["ParticleMassMsun"].sum() return j_mag, m_enc, e_term_pre, weight add_quantity("ParticleSpinParameter", function=_ParticleSpinParameter, combine_function=_combBaryonSpinParameter, n_ret=4) ************************************************************* ** Andrew J. Davis andrew.davis(a)yale.edu ** ** Dept. of Astronomy 203-432-5119 ** ** Yale University www.astro.yale.edu/adavis ** *************************************************************

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covering grid
by John ZuHone 08 Apr '11

08 Apr '11

Hi all, Does anyone know what the covering grid does if the cell size on the covering grid is larger than the cells on the amr level? Is an average taken? Best, John Z

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Kraken Common Install
by Stephen Skory 08 Apr '11

08 Apr '11

Hi All, I've just updated the common install of yt on Kraken to 2.1, and added an install of the unstable branch. Both are full copies of yt that is kept on lustre in a non-volatile place. This means that it is accessible from both the login nodes and the compute nodes, but unlike most files on Lustre, will not be deleted automatically. If you wish to use yt 2.1, which will only see changes for bug fixes, please set your environment using these settings: YT_DEST => /lustre/scratch/proj/yt_common/2.1 PATH => /lustre/scratch/proj/yt_common/2.1/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/2.1/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/2.1/lib/ If you wish to use the unstable branch, which I'll update on Kraken when I remember to do it (or you can bug me if I haven't): YT_DEST => /lustre/scratch/proj/yt_common/unstable PATH => /lustre/scratch/proj/yt_common/unstable/bin/ PYTHONPATH => /lustre/scratch/proj/yt_common/unstable/lib/python2.7/site-packages/ LD_LIBRARY_PATH => /lustre/scratch/proj/yt_common/unstable/lib/ The older versions of yt at /lustre/scratch/proj/yt_common/2.0 and /lustre/scratch/proj/yt_common/trunk will be deleted within a week or so. -- Stephen Skory s(a)skory.us http://stephenskory.com/ 510.621.3687 (google voice)

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parallel yt on ranger
by Christine Simpson 07 Apr '11

07 Apr '11

Hi all, I'm trying to run yt in parallel on ranger. I gather from previous messages to this list that others have had issues in the past, but I haven't been able to find something that works from those posts. I'm trying to run a test script that does a simple projection. First I tried this (from the yt docs): ibrun mpirun -np 8 python2.7 test_parallel_yt.py --parallel I got this output in the output file: TACC: Setting memory limits for job 1896644 to unlimited KB TACC: Dumping job script: -------------------------------------------------------------------------------- # Submit this script using the "qsub" command. # Use the "qstat" command to check the status of a job. # #$-l h_rt=00:05:00 #$-pe 8way 16 #$-N test_parallel_yt #$-o $JOB_NAME.o$JOB_ID #$-q development #$-M csimpson(a)astro.columbia.edu #$-m be #$-V #$-cwd ibrun mpirun -np 8 python2.7 test_parallel_yt.py --parallel -------------------------------------------------------------------------------- TACC: Done. TACC: Starting up job 1896644 TACC: Setting up parallel environment for MVAPICH ssh-based mpirun. TACC: Setup complete. Running job script. TACC: starting parallel tasks... Warning: Command line arguments for program should be given after the program name. Assuming that test_parallel_yt.py is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that test_parallel_yt.py is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that test_parallel_yt.py is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that test_parallel_yt.py is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that test_parallel_yt.py is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that test_parallel_yt.py is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that test_parallel_yt.py is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that test_parallel_yt.py is a command line argument for the program. Warning: Command line arguments for program should be given after the program name. Assuming that --parallel is a command line argument for the program. Missing: program name Program python2.7 either does not exist, is not executable, or is an erroneous argument to mpirun. Warning: Command line arguments for program should be given after the program name. Assuming that --parallel is a command line argument for the program. TACC: MPI job exited with code: 1 TACC: Shutting down parallel environment. TACC: Shutdown complete. Exiting. TACC: Cleaning up after job: 1896644 TACC: Done. I also tried this: ibrun mpi4py -np 8 python2.7 test_parallel_yt.py --parallel and got this output: TACC: Setting memory limits for job 1896674 to unlimited KB TACC: Dumping job script: -------------------------------------------------------------------------------- #!/bin/sh # # Submit this script using the "qsub" command. # Use the "qstat" command to check the status of a job. # #$-l h_rt=00:05:00 #$-pe 8way 16 #$-N test_parallel_yt #$-o $JOB_NAME.o$JOB_ID #$-q development #$-M csimpson(a)astro.columbia.edu #$-m be #$-V #$-cwd ibrun mpi4py -np 8 python2.7 test_parallel_yt.py --parallel -------------------------------------------------------------------------------- TACC: Done. TACC: Starting up job 1896674 TACC: Setting up parallel environment for MVAPICH ssh-based mpirun. TACC: Setup complete. Running job script. TACC: starting parallel tasks... TACC: MPI job exited with code: 1 TACC: Shutting down parallel environment. TACC: Shutdown complete. Exiting. TACC: Cleaning up after job: 1896674 TACC: Done. Any ideas? I guess in the first instance it is not finding python, but the test script I run works fine on the command line and doing -V should import the same environment settings, right? I guess in the second instance I'm using the wrong mpi call. I found info on that call in some old posts to the email list. Christine

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yt 2.1 Release Announcement
by Sam Skillman 06 Apr '11

06 Apr '11

We are proud to announce the release of yt version 2.1. This release includes several new features, bug fixes, and numerous improvements to the code base and documentation. At the yt homepage, http://yt.enzotools.org/ , an installation script, a cookbook, documentation and a guide to getting involved can be found. yt is an analysis and visualization toolkit for Adaptive Mesh Refinement data. yt provides full support for Enzo, Orion, and FLASH codes, with preliminary support for RAMSES, ART, Chombo, CASTRO and MAESTRO codes. It can be used to create many common types of data products such as: * Slices * Projections * Profiles * Arbitrary Data Selection * Cosmological Analysis * Halo finding * Parallel AMR Volume Rendering * Gravitationally Bound Objects Analysis There are a few major additions since yt-2.0 (Released January 17, 2011), including: * Streamlines for visualization and querying * A treecode implementation to calculate binding energy * Healpix / all-sky parallel volume rendering * A development bootstrap script, for getting going with modifying and contributing * CASTRO particles * Time series analysis Documentation: http://yt.enzotools.org/doc/ Installation: http://yt.enzotools.org/doc/advanced/installing.html#installing-yt Cookbook: http://yt.enzotools.org/doc/cookbook/recipes.html Get Involved: http://yt.enzotools.org/doc/advanced/developing.html#contributing-code If you can’t wait to get started, install with: $ wget http://hg.enzotools.org/yt/raw/stable/doc/install_script.sh $ bash install_script.sh Development has been sponsored by the NSF, DOE, and University funding. We invite you to get involved with developing and using yt! Please forward this announcement to interested parties. Sincerely, The yt development team: David Collins Oliver Hahn Cameron Hummels Stefan Klemer Chris Malone Christopher Moody Andrew Myers Jeff Oishi Britton Smith Devin Silvia Sam Skillman Stephen Skory Matthew Turk John Wise John ZuHone

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