yt-3.2.1 installation error
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.
2 years, 9 months
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
2 years, 9 months
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
3 years, 2 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
3 years, 2 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
________________________________________________________
3 years, 2 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=5cda4af0...
Downloading from URL
https://pypi.python.org/packages/source/y/yt/yt-3.2.1.tar.gz#md5=5cda4af0...
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
3 years, 2 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
________________________________________________________
3 years, 2 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...>
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
>
3 years, 2 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
3 years, 2 months
