yt-users September 2015

yt-users@python.org

22 participants
26 discussions

by Muhammad Latif

Hi all, I'm getting the following error while installing yt-3.2.1 latest release. Any idea what is going on here? thanks in advance, cheers Latif Installing nose-1.3.6 Installing python-hglib-1.6 Installing sympy-0.7.6 Doing yt update, wiping local changes and updating to branch stable install_script.sh: line 1025: cd: /home/latif/YT/yt-x86_64/src/yt-hg/: No such file or directory Installing yt ******************************************** FAILURE REPORT: ******************************************** running install_data copying doc/man/isympy.1 -> /home/latif/YT/yt-x86_64/share/man/man1 running install_egg_info Writing /home/latif/YT/yt-x86_64/lib/python2.7/site-packages/sympy-0.7.6-py2.7.egg-info Collecting jinja2 Using cached Jinja2-2.8-py2.py3-none-any.whl Collecting MarkupSafe (from jinja2) Installing collected packages: MarkupSafe, jinja2 Successfully installed MarkupSafe-0.23 jinja2-2.8 /home/latif/YT/yt-x86_64/bin/python2.7: can't open file 'setup.py': [Errno 2] No such file or directory ******************************************** ******************************************** Failure. Check /home/latif/YT/yt-x86_64/yt_install.log. The last 10 lines are above.

4 years

EnzoDatasetInMemory not working in parallel

by Britton Smith

Hi all, I've recently been trying to use yt's inline analysis functionality with Enzo and am having some difficultly getting it to work in parallel. I am using the development tip of yt. In serial, everything works fine, but in parallel, I get the following error: http://paste.yt-project.org/show/5694/ It seems that the issue is that yt is not correctly identifying which grids are available on a given processory for the EnzoDatasetInMemory object. Does anyone have an idea of how to fix this? Has anyone else seen this? For reference, my user_script is just this: import yt from yt.frontends.enzo.api import EnzoDatasetInMemory def main(): ds = EnzoDatasetInMemory() ad = ds.all_data() print ad.quantities.total_quantity("cell_mass") Thanks for any help, Britton

4 years, 1 month

Apply now for the Python in Astronomy 2016 conference! (21-25th March 2016)

by Thomas Robitaille

Dear colleagues, We are very pleased to inform you that applications are now open for the Python in Astronomy 2016 conference: Python in Astronomy University of Washington eScience Institute Seattle, WA, USA 21-25th March 2016 http://python-in-astronomy.github.io/2016/ This meeting aims to bring together researchers, Python developers, users, and educators, and will include presentations, tutorials, unconference sessions, and coding sprints. In addition to sharing information about state-of-the-art Python Astronomy packages, the workshop will also focus on improving interoperability between astronomical Python packages, providing training for new contributors, and developing educational materials for Python in Astronomy. The meeting is therefore aimed not only at current developers, but also users and educators who are interested in being involved in these efforts. Note that this meeting is not intended to be a Python 'boot camp', and we do expect participants to have already at least used Python for some of their projects, even if only at a beginner level. To apply, please go to the following page: http://python-in-astronomy.github.io/2016/ and follow the link to the application form. Applications should be submitted by 9th October 2015 at the latest, and we hope to let you know by mid- to late November whether you have been accepted. Contingent on sponsorship, we hope to offer financial support for travel for a few participants. If you would like to apply for financial support, please indicate this in the last section of the application form. Please forward this email to anyone who may be interested! Best regards, The organizing committee: Kelle Cruz Perry Greenfield Eric Jeschke Mario Juric Stuart Mumford Chanda Prescod-Weinstein Thomas Robitaille Megan Sosey Erik Tollerud Jake Vanderplas

4 years, 5 months

PHOX implementation

by Barbara Ramirez

Hello again John! I'm not sure what you mean with changing the number of chunks in the .yt/config file? I did change the number of chunks and lowered the exposition time to get one photon list, but is that list enough? Don't I need to merge it with another observation? Or you meant changing the photon_per_chunk parameter somewhere else in the yt code? Or perhaps you meant I should try the first option (run it in a machine with more RAM / parallel)? I'll try that right now anyway! Thanks for everything, I'll keep an eye on the patch! Barbara ------------------------------------------------------------------------ Hi Barbara, Any chance you could try the option I mentioned where you change number of chunks in the .yt/config file? That way you might be able to avoid doing merging altogether. This is a bug I fixed yesterday?when I have some way of getting the patch to you I will let you know. This happens when you choose parameters for project_photons that would result in a higher number of photons being drawn than exist in the original set that you generated. I?m going to change this error message so it?s more informative. Best, John

4 years, 6 months

Re: [yt-users] optimal resolution for frb

by Slavin, Jonathan

Hi Nathan, Thanks very much for the detailed response. I had no idea that ds.index contains so much information. I've looked at the grid data for a simulation I did and it's quite revealing. Unfortunately for my case, a 2D simulation, it seems that ds.index.get_smallest_dx() includes the third (unused) dimension, which for some reason is given a (very small) thickness in FLASH data. As a result, I get that very small dimension from ds.index.get_smallest_dx(). Nevertheless, it seems that it should possible to get the smallest grid dimension in each direction via the use of ds.index.grids.RightEdge and ds.index.grids.LeftEdge. I'm working on it now. Regards, Jon On Sat, Sep 26, 2015 at 11:25 AM, <yt-users-request(a)lists.spacepope.org> wrote: > Date: Fri, 25 Sep 2015 14:00:13 -0500 > From: Nathan Goldbaum <nathan12343(a)gmail.com> > To: Discussion of the yt analysis package > <yt-users(a)lists.spacepope.org> > Subject: Re: [yt-users] optimal resolution for frb > Message-ID: > <CAJXewO= > 1rW7E+VkFeVqogWV+8Uq_Tq_rkufLDZ3xaA8tWuQzWg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Making it easy to lock the FRB resolution to the simulation resolution or > some factor-of-two multiple would be a great improvement, and something > that would be not too hard I think. Right now you're right that it's not > very obvious how to do this. If you'd be interested in coming up with a UI > for making FRBs that are locked to the simulation resolution, I think that > would be a fun first yt project that many people would like to use. > > One easy way to get the size of the smallest computational element is the > `ds.index.get_smallest_dx()` function, which will return the size of the > smallest cell width in code units. The ds.index object is the main way to > access information about the geometrical or mesh properties of a dataset. > > For patch AMR datasets like FLASH, you can access the grid objects like so: > > for grid in ds.index.grids: > print grid.LeftEdge, grid.RightEdge # left and right edge of the grid > in code units > print grid.ActiveDimensions # the dimensions of the grid patch (i.e. > number of zones along x, y, and z) > print grid.Level # AMR leve > print grid.Children # references to child grid objects, if any > print grid.Parent # reference to parent grid > print grid['dens'] # the on-disk gas density field > > You can access any yt field on the grid object using a dictionary-like > lookup, just like any other yt data object. > > -Nathan > -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

4 years, 6 months

Error updating yt3.1 to yt.3.2.1

by Joshua Wall

Dear YT users, I have yt installed with pip, and it reports being version 3.1. However I'd like to use the new particle plot function, so I tried updating it with sudo pip install -U yt and got the error: Downloading/unpacking yt from https://pypi.python.org/packages/source/y/yt/yt-3.2.1.tar.gz#md5=5cda4af043… Downloading from URL https://pypi.python.org/packages/source/y/yt/yt-3.2.1.tar.gz#md5=5cda4af043… Running setup.py (path:/tmp/pip_build_root/yt/setup.py) egg_info for package yt Cython is a build-time requirement for the source tree of yt. Please either install yt from a provided, release tarball, or install Cython (version 0.22 or higher). You may be able to accomplish this by typing: pip install -U Cython So I did this. Then I checked Cython with cython --version, it reports version 0.23.2, but the same yt install error remains when I attempt an update. I'm guessing there is something I need to refresh, but I'm unsure of how to do this. Thanks for the assistance, Josh -- Joshua Wall Doctoral Candidate Department of Physics Drexel University 3141 Chestnut Street Philadelphia, PA 19104

4 years, 6 months

optimal resolution for frb

by Slavin, Jonathan

Hi all, I've been doing FLASH runs in 2D and using yt to manipulate the data for display -- that is, I've been creating frb objects from slices (which are not really slices since the data is 2D anyways). One thing that bothers me about this is the need to specify the dimensions of the frb. For some reason 800 x 800 seems to be preferred in the yt docs, but it seems to me that there are certain optimal dimensions that depend on the grid structure. For example an frb that uses pixels the size of the smallest resolution element/cell or some integer multiple of that (of course less refined cells would be split into multiple pixels). How would one find what that grid size would be? I guess what I'd need to know is the dimensions of that most refined cell in the computational grid. How does one access the grid structure information in a dataset? Jon -- ________________________________________________________ Jonathan D. Slavin Harvard-Smithsonian CfA jslavin(a)cfa.harvard.edu 60 Garden Street, MS 83 phone: (617) 496-7981 Cambridge, MA 02138-1516 cell: (781) 363-0035 USA ________________________________________________________

4 years, 6 months

Re: [yt-users] yt install help

by Andrew Myers

Hi Daniel, Thanks for telling us about this. We have a pull request <https://bitbucket.org/yt_analysis/yt/pull-requests/1768/improve-check_for_o…> open that should allow the install script to work normally when CC="ccache <compiler>" in the future. Best, Andrew On Thu, Sep 24, 2015 at 12:47 PM, Schwen (Non-US), Daniel < daniel.schwen(a)inl.gov> wrote: > Yeah, it built and installed. I can call > '/opt/moose/miniconda/bin/yt'. It craps out because it does not find > hdf5. I must have missed that dependency. Thanks for your help so far! > Daniel > > On Thu, Sep 24, 2015 at 1:44 PM, Schwen (Non-US), Daniel > <daniel.schwen(a)inl.gov> wrote: > > I think i'm having success with > > > > sudo -E CC=clang CFLAGS="-I/opt/local/include" > > LDFLAGS="-L/opt/local/lib" python setup.py develop > > > > > > > > On Thu, Sep 24, 2015 at 1:43 PM, Schwen (Non-US), Daniel > > <daniel.schwen(a)inl.gov> wrote: > >> and: > >> > >> [10][schwd][~/Downloads/yt-hg]> CC=clang python test.py > >> compiler is: clang > >> filename is: test.c > >> True > >> > >> On Thu, Sep 24, 2015 at 1:42 PM, Schwen (Non-US), Daniel > >> <daniel.schwen(a)inl.gov> wrote: > >>> and: > >>> > >>> [10][schwd][~/Downloads/yt-hg]> CC=gcc python test.py > >>> compiler is: gcc > >>> filename is: test.c > >>> False > >>> [10][schwd][~/Downloads/yt-hg]> which gcc > >>> /opt/moose/gcc_4.9.1/bin/gcc > >>> > >>> > >>> On Thu, Sep 24, 2015 at 1:41 PM, Schwen (Non-US), Daniel > >>> <daniel.schwen(a)inl.gov> wrote: > >>>> compiler is: ccache clang > >>>> filename is: test.c > >>>> Traceback (most recent call last): > >>>> File "test.py", line 47, in <module> > >>>> print check_for_openmp() > >>>> File "test.py", line 37, in check_for_openmp > >>>> stdout=fnull, stderr=fnull) > >>>> File "/opt/moose/miniconda/lib/python2.7/subprocess.py", line 522, > in call > >>>> return Popen(*popenargs, **kwargs).wait() > >>>> File "/opt/moose/miniconda/lib/python2.7/subprocess.py", line 710, > in __init__ > >>>> errread, errwrite) > >>>> File "/opt/moose/miniconda/lib/python2.7/subprocess.py", line 1335, > >>>> in _execute_child > >>>> raise child_exception > >>>> OSError: [Errno 2] No such file or directory > >>>> > >>>> On Thu, Sep 24, 2015 at 1:32 PM, Andrew Myers <atmyers2(a)gmail.com> > wrote: > >>>>> Hi Daniel, > >>>>> > >>>>> Could you try running this python script using the same python > you're trying > >>>>> to install yt with? Does it give you some output, or does it fail > with the > >>>>> same error message? > >>>>> > >>>>> Thanks, > >>>>> Andrew > >>>>> > >>>>> On Thu, Sep 24, 2015 at 12:05 PM, Andrew Myers <atmyers2(a)gmail.com> > wrote: > >>>>>> > >>>>>> Hello yt users, > >>>>>> > >>>>>> I'm working with Daniel Schwen of the MOOSE team to install yt from > >>>>>> source. He is running OS X Yosemite, and trying to install yt over a > >>>>>> miniconda python. After cloning my yt repository, the install > script fails > >>>>>> with the attached traceback. Does anyone have any ideas? > >>>>>> > >>>>>> Thanks, > >>>>>> Andrew > >>>>>> > >>>>>> [10][schwd][~/Downloads/yt-hg]> CFLAGS="-I/opt/local/include" > >>>>>> LDFLAGS="-L/opt/local/lib" python setup.py develop > >>>>>> > >>>>>> > /opt/moose/miniconda/lib/python2.7/site-packages/setuptools-18.3.2-py2.7.egg/setuptools/dist.py:285: > >>>>>> UserWarning: Normalizing '3.3-dev' to '3.3.dev0' > >>>>>> non-existing path in 'yt/utilities/spatial': > 'yt/utilities/spatial/tests' > >>>>>> Traceback (most recent call last): > >>>>>> File "setup.py", line 227, in <module> > >>>>>> setup_package() > >>>>>> File "setup.py", line 222, in setup_package > >>>>>> cmdclass={'build_py': my_build_py, 'build_src': my_build_src}, > >>>>>> File > >>>>>> > "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/distutils/core.py", > >>>>>> line 135, in setup > >>>>>> config = configuration() > >>>>>> File "setup.py", line 178, in configuration > >>>>>> config.add_subpackage('yt', 'yt') > >>>>>> File > >>>>>> > "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > >>>>>> line 966, in add_subpackage > >>>>>> caller_level = 2) > >>>>>> File > >>>>>> > "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > >>>>>> line 935, in get_subpackage > >>>>>> caller_level = caller_level + 1) > >>>>>> File > >>>>>> > "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > >>>>>> line 872, in _get_configuration_from_setup_py > >>>>>> config = setup_module.configuration(*args) > >>>>>> File "yt/setup.py", line 18, in configuration > >>>>>> config.add_subpackage('utilities') > >>>>>> File > >>>>>> > "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > >>>>>> line 966, in add_subpackage > >>>>>> caller_level = 2) > >>>>>> File > >>>>>> > "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > >>>>>> line 935, in get_subpackage > >>>>>> caller_level = caller_level + 1) > >>>>>> File > >>>>>> > "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > >>>>>> line 872, in _get_configuration_from_setup_py > >>>>>> config = setup_module.configuration(*args) > >>>>>> File "yt/utilities/setup.py", line 161, in configuration > >>>>>> config.add_subpackage("lib") > >>>>>> File > >>>>>> > "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > >>>>>> line 966, in add_subpackage > >>>>>> caller_level = 2) > >>>>>> File > >>>>>> > "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > >>>>>> line 935, in get_subpackage > >>>>>> caller_level = caller_level + 1) > >>>>>> File > >>>>>> > "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/distutils/misc_util.py", > >>>>>> line 872, in _get_configuration_from_setup_py > >>>>>> config = setup_module.configuration(*args) > >>>>>> File "yt/utilities/lib/setup.py", line 57, in configuration > >>>>>> if check_for_openmp() == True: > >>>>>> File "yt/utilities/lib/setup.py", line 37, in check_for_openmp > >>>>>> stdout=fnull, stderr=fnull) > >>>>>> File "/opt/moose/miniconda/lib/python2.7/subprocess.py", line > 522, in > >>>>>> call > >>>>>> return Popen(*popenargs, **kwargs).wait() > >>>>>> File "/opt/moose/miniconda/lib/python2.7/subprocess.py", line > 710, in > >>>>>> __init__ > >>>>>> errread, errwrite) > >>>>>> File "/opt/moose/miniconda/lib/python2.7/subprocess.py", line > 1335, > >>>>>> in _execute_child > >>>>>> raise child_exception > >>>>>> OSError: [Errno 2] No such file or directory > >>>>> > >>>>> > >>>> > >>>> > >>>> > >>>> -- > >>>> Daniel Schwen, PhD > >>>> Staff Scientist, Fuels Modeling & Simulation > >>>> > >>>> Idaho National Laboratory > >>>> P.O. Box 1625, MS 3840 > >>>> Idaho Falls, ID 83415 > >>>> > >>>> Email: daniel.schwen(a)inl.gov > >>>> Phone: (208) 526-4880 > >>> > >>> > >>> > >>> -- > >>> Daniel Schwen, PhD > >>> Staff Scientist, Fuels Modeling & Simulation > >>> > >>> Idaho National Laboratory > >>> P.O. Box 1625, MS 3840 > >>> Idaho Falls, ID 83415 > >>> > >>> Email: daniel.schwen(a)inl.gov > >>> Phone: (208) 526-4880 > >> > >> > >> > >> -- > >> Daniel Schwen, PhD > >> Staff Scientist, Fuels Modeling & Simulation > >> > >> Idaho National Laboratory > >> P.O. Box 1625, MS 3840 > >> Idaho Falls, ID 83415 > >> > >> Email: daniel.schwen(a)inl.gov > >> Phone: (208) 526-4880 > > > > > > > > -- > > Daniel Schwen, PhD > > Staff Scientist, Fuels Modeling & Simulation > > > > Idaho National Laboratory > > P.O. Box 1625, MS 3840 > > Idaho Falls, ID 83415 > > > > Email: daniel.schwen(a)inl.gov > > Phone: (208) 526-4880 > > > > -- > Daniel Schwen, PhD > Staff Scientist, Fuels Modeling & Simulation > > Idaho National Laboratory > P.O. Box 1625, MS 3840 > Idaho Falls, ID 83415 > > Email: daniel.schwen(a)inl.gov > Phone: (208) 526-4880 >

4 years, 6 months

yt install help

by Andrew Myers

Hello yt users, I'm working with Daniel Schwen of the MOOSE team to install yt from source. He is running OS X Yosemite, and trying to install yt over a miniconda python. After cloning my yt repository, the install script fails with the attached traceback. Does anyone have any ideas? Thanks, Andrew [10][schwd][~/Downloads/yt-hg]> CFLAGS="-I/opt/local/include" LDFLAGS="-L/opt/local/lib" python setup.py develop /opt/moose/miniconda/lib/python2.7/site-packages/setuptools-18.3.2-py2.7.egg/setuptools/dist.py:285: UserWarning: Normalizing '3.3-dev' to '3.3.dev0' non-existing path in 'yt/utilities/spatial': 'yt/utilities/spatial/tests' Traceback (most recent call last): File "setup.py", line 227, in <module> setup_package() File "setup.py", line 222, in setup_package cmdclass={'build_py': my_build_py, 'build_src': my_build_src}, File "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/ distutils/core.py", line 135, in setup config = configuration() File "setup.py", line 178, in configuration config.add_subpackage('yt', 'yt') File "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/ distutils/misc_util.py", line 966, in add_subpackage caller_level = 2) File "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/ distutils/misc_util.py", line 935, in get_subpackage caller_level = caller_level + 1) File "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/ distutils/misc_util.py", line 872, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "yt/setup.py", line 18, in configuration config.add_subpackage('utilities') File "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/ distutils/misc_util.py", line 966, in add_subpackage caller_level = 2) File "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/ distutils/misc_util.py", line 935, in get_subpackage caller_level = caller_level + 1) File "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/ distutils/misc_util.py", line 872, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "yt/utilities/setup.py", line 161, in configuration config.add_subpackage("lib") File "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/ distutils/misc_util.py", line 966, in add_subpackage caller_level = 2) File "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/ distutils/misc_util.py", line 935, in get_subpackage caller_level = caller_level + 1) File "/opt/moose/miniconda/lib/python2.7/site-packages/numpy/ distutils/misc_util.py", line 872, in _get_configuration_from_setup_py config = setup_module.configuration(*args) File "yt/utilities/lib/setup.py", line 57, in configuration if check_for_openmp() == True: File "yt/utilities/lib/setup.py", line 37, in check_for_openmp stdout=fnull, stderr=fnull) File "/opt/moose/miniconda/lib/python2.7/subprocess.py", line 522, in call return Popen(*popenargs, **kwargs).wait() File "/opt/moose/miniconda/lib/python2.7/subprocess.py", line 710, in __init__ errread, errwrite) File "/opt/moose/miniconda/lib/python2.7/subprocess.py", line 1335, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory

4 years, 6 months

Change in SPH kernel behavior

by Matthew Turk

Hi all, I wanted to bring to your attention a change in the SPH smoothing kernel behavior. This has landed on the development version on yt, but *not* the stable, and will not be backported to stable until the next major release (3.3). Previously, a kernel normalization was applied to smoothed grid cells. This could result in mass conservation not being 100% preserved; some cases were worse than others. (Cosmology was typically fine.) The recent change has removed the normalization step. Here are some relevant PRs: https://bitbucket.org/yt_analysis/yt/pull-requests/1740/remove-normalizatio… https://bitbucket.org/yt_analysis/yt/pull-requests/1721/allow-for-neighbors… -Matt

4 years, 6 months

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yt-users September 2015