Problem when run yt dev in parallel on Blue Waters
by Pengfei Chen
Hi all,
I have trouble running yt in parallel on Blue Waters. I installed yt using
miniconda, the version of yt is
~/miniconda/lib $yt version
yt module located at:
/u/sciteam/madcpf/miniconda/lib/python2.7/site-packages/yt-3.3.dev0-py2.7-linux-x86_64.egg
The current version and changeset for the code is:
---
Version = 3.3-dev
Changeset = 90f900be7a36+ yt
Then with miniconda/bin in PATH I installed mpi4py-2.0.0. But when I tried
to make the following simple output in parallel, I get:
import yt
yt.enable_parallelism()
from yt.utilities.parallel_tools.parallel_analysis_interface import\
parallel_objects, communication_system
comm = communication_system.communicators[-1]
print comm.rank, comm.size
0 1
0 1
0 1
0 1
0 1
0 1
0 1
0 1
...
When I run a similar code but with yt-2.x also on Blue Waters, I get what I
expect:
7 16
15 16
6 16
9 16
11 16
8 16
0 16
4 16
...
I'm confused about it. Could anyone give me some suggestions please?
Thanks,
Pengfei
2 years, 7 months
Slice plot in FITS format
by Prateek Gupta
Dear Yt users
I want to save the slice plot in FITS or HDF5 format. How can I do this in
yt once I plot the slice plot of derived field.
Many thanks in advance
Regards
Prateek
2 years, 7 months
Downsampling AMR data for plotting isocontours
by Daniel Fenn
Hi,
I'm trying to figure out the best way to downsample FLASH AMR data for
making isocontours. I'd like to be able to specify the maximum refinement
level that should be used for creating the isocontours.
My first thought was to use a covering grid, but I'm uncertain how to use
that to create a YTSurface object.
If anyone can offer any suggestions, I'd appreciate it.
Thanks,
Dan
2 years, 8 months
loading Gadget outputs
by Molly Peeples
Hi folks,
I am trying to read in a Gadget output that’s split into 16 hdf5 files (fwiw, it’s an EAGLE output, and so “should” be similar to the OWLS format). I need to be able to analyze / render the entire output, not just one of the pieces, but I haven’t been able to figure out how to actually load them (akin to how for Enzo yt figures out that there are a lot of cpu outputs in a directory).
I have taken a look at http://yt-project.org/doc/cookbook/owls_notebook.html#owls-notebook, but even there in the example, it’s just reading in the one output and ignoring the other 7 in the example tarball. And there I was having trouble tracking down what n_ref and over_refine_factor refer to.
Interestingly, if I load just the single hdf5s, I can get ProjectionPlots to work but not SlicePlots (which insist there’s “zero dynamic range” with “Min = Max = 0.00000”.)
FWIW, yt.__version__ gives me 3.3.1. (And major thanks to Nathan for getting that installation to go smoothly!!)
Suggestions?
—Molly
2 years, 8 months
emission weighted temperature profile
by Mateusz Ruszkowski
Hi,
[apologies if you received this twice; I have problems with my e-mail[
I am trying to plot an emission-weighted temperature profile. The relevant part of my script and the error message are attached below. Does anybody have an idea why this is not working?
Thanks,
Mateusz
——— part of yt script ———
from yt.analysis_modules.spectral_integrator.api import add_xray_emissivity_field
[…]
def my_temp(field, data):
return data['flash', 'temp']
ds=yt.load("/nobackupnfs2/mruszkow/halo_hdf5_plt_cnt_%04i"%i)
xray_fields = add_xray_emissivity_field(ds, with_metals=False, constant_metallicity=1.0, e_min=0.5, e_max=10.0, filename="apec_emissivity.h5")
ds.add_field(("flash", "my_temp"), units="code_temperature", function=my_temp)
sp = ds.sphere([0.0,0.0,0.0], rmax)
prof = yt.Profile1D(sp, "radius", xbins, prof_min, prof_max, True, weight_field="xray_emissivity_0.5_10_keV") #"cell_mass")
prof.add_fields(["my_temp"])
——— error message ———
yt : [INFO ] 2016-07-25 17:20:54,022 Parameters: cosmological_simulation = 0.0
yt : [INFO ] 2016-07-25 17:20:54,023 Loading emissivity data from apec_emissivity.h5.
yt : [INFO ] 2016-07-25 17:20:54,023 b'X-ray emissivity data calculated with APEC v. 2.0.2 on 06/24/2014 by John ZuHone.'
yt : [INFO ] 2016-07-25 17:20:54,023 X-ray emissivity data version: 1.
yt : [WARNING ] 2016-07-25 17:20:56,114 Could not find a field for "H_number_density". Assuming primordial H mass fraction.
Traceback (most recent call last):
File "temperature2.py", line 64, in <module>
prof = yt.Profile1D(sp, "radius", xbins, prof_min, prof_max, True, weight_field="xray_emissivity_0.5_10_keV") #"cell_mass")
File "/home3/mruszkow/yt/yt/data_objects/profiles.py", line 410, in __init__
super(Profile1D, self).__init__(data_source, weight_field)
File "/home3/mruszkow/yt/yt/data_objects/profiles.py", line 92, in __init__
weight_field = self.data_source._determine_fields(weight_field)[0]
File "/home3/mruszkow/yt/yt/data_objects/data_containers.py", line 985, in _determine_fields
finfo = self.ds._get_field_info("unknown", fname)
File "/home3/mruszkow/yt/yt/data_objects/static_output.py", line 616, in _get_field_info
raise YTFieldNotFound((ftype, fname), self)
yt.utilities.exceptions.YTFieldNotFound: Could not find field '('io', 'xray_emissivity_0.5_10_keV')' in halo_hdf5_plt_cnt_0010.
2 years, 8 months
not able to see anything in notebook
by Ritam Mallick
Dear Users,
I have installed yt in my desktop. however when I am trying to import yt
and load or see anything in the notebook app I cannot see anything. The
message is as follows ..
ritam@ritam:~/yt/doc/source/quickstart$ yt notebook
/home/ritam/yt-conda/lib/python2.7/site-packages/IPython/html.py:14:
ShimWarning: The `IPython.html` package has been deprecated. You should
import from `notebook` instead. `IPython.html.widgets` has moved to
`ipywidgets`.
"`IPython.html.widgets` has moved to `ipywidgets`.", ShimWarning)
You must choose a password so that others cannot connect to your notebook.
Enter password:
Verify password:
If you would like to use this password in the future,
place a line like this inside the [yt] section in your
yt configuration file at ~/.yt/config
notebook_password =
sha1:1631cf9cf288:25f1cbe46746e0d25aed15a26deec2d048ff3570
***************************************************************
The notebook is now live at:
http://127.0.0.1:8888/
Recall you can create a new SSH tunnel dynamically by pressing
~C and then typing -L8888:localhost:8888
where the first number is the port on your local machine.
If you are using 8888 on your machine already, try -L8889:localhost:8888
***************************************************************
[I 10:37:04.487 NotebookApp] Serving notebooks from local directory:
/home/ritam/yt/doc/source/quickstart
[I 10:37:04.487 NotebookApp] 0 active kernels
[I 10:37:04.487 NotebookApp] The Jupyter Notebook is running at:
http://localhost:8888/
[I 10:37:04.487 NotebookApp] Use Control-C to stop this server and shut
down all kernels (twice to skip confirmation).
import yt
ds = yt.load("IsolatedGalaxy/galaxy0030/galaxy0030")
It is just running and running and not showing anything.
Friends, please help me in this regard.
Thanks in advance.
Ritam
2 years, 8 months
installation problem
by Ritam Mallick
Dear all,
I am trying to install yt in my desktop (Ubuntu 15.04). However it shows
this error (last few lines of the yt_install.log)
running install_scripts
copying build/scripts-2.7/hg -> /home/ritam/yt-x86_64/bin
changing mode of /home/ritam/yt-x86_64/bin/hg to 775
running install_egg_info
Writing
/home/ritam/yt-x86_64/lib/python2.7/site-packages/mercurial-3.4-py2.7.egg-info
using https://bitbucket.org/yt_analysis/yt-supplemental/
sending capabilities command
abort: No module named _ssl!
using https://bitbucket.org/yt_analysis/yt/
sending capabilities command
abort: No module named _ssl!
abort: repository /home/ritam/yt-x86_64/src/yt-hg/ not found!
2016-07-22 17:28:23 URL:https://bootstrap.pypa.io/get-pip.py
[1524722/1524722] -> "get-pip.py" [1]
Traceback (most recent call last):
File "get-pip.py", line 19177, in <module>
main()
File "get-pip.py", line 194, in main
bootstrap(tmpdir=tmpdir)
File "get-pip.py", line 82, in bootstrap
import pip
File "/tmp/tmpDR_d0M/pip.zip/pip/__init__.py", line 16, in <module>
File "/tmp/tmpDR_d0M/pip.zip/pip/vcs/subversion.py", line 9, in <module>
File "/tmp/tmpDR_d0M/pip.zip/pip/index.py", line 30, in <module>
File "/tmp/tmpDR_d0M/pip.zip/pip/wheel.py", line 39, in <module>
File "/tmp/tmpDR_d0M/pip.zip/pip/_vendor/distlib/scripts.py", line 14, in
<module>
File "/tmp/tmpDR_d0M/pip.zip/pip/_vendor/distlib/compat.py", line 31, in
<module>
ImportError: cannot import name HTTPSHandler
Hope to get some help.
2 years, 8 months
Clump surface pressure
by John Regan
Hi All,
I was hoping to calculate the surface pressure on the surface of a clump. I
see that there is a way to do this with surfaces at the moment in YT
probably by doing something like:
mysurf.calculate_isocontour_flux(*"density"*, *some_value*, *r_x*, *r_y*,
*r_z*, *"pressure"*)
So while that has a fair chance of working for a surface? Is there any way
to get a clump to do the same?
Any tips/advice greatly appreciated!
Cheers,
John
2 years, 8 months
yt parallelism with mpi4py at OLCF
by Max Katz
Hi all,
I'm trying to get yt parallelism enabled to run on the visualization
cluster at OLCF. I am using a conda environment for the yt prerequisites
but I have the development branch of yt installed from source. To get the
parallelism working I tried installing mpi4py both using pip and building
it from source (with the latter, explicitly telling it that the MPI-enabled
C compiler is the wrapper cc). However, the statement "from mpi4py import
MPI" that yt uses to initialize the session fails with:
>>> from mpi4py import MPI
[Sun Jul 17 03:52:10 2016] [unknown] Fatal error in PMPI_Init_thread: Other
MPI error, error stack:
MPIR_Init_thread(547):
MPID_Init(203).......: channel initialization failed
MPID_Init(584).......: PMI2 init failed: 1
Aborted
Some googling suggests that this is potentially an issue specific to the
way Cray sets up their MPI installation. At any rate, although this is not
necessarily a yt-specific issue, if anyone has relevant experience or knows
a workaround, please let me know, thanks!
Max Katz
Ph.D. Candidate, Department of Physics and Astronomy
Stony Brook University
http://astro.sunysb.edu/mkatz/
2 years, 8 months
Re: [yt-users] Using AMR with inline python
by Azton Wells
Thanks Matt for your reply.
I am using
rho = na.asarray(enzo.grid_data[enzo.grid_data.keys()[0]]["Density"])
to access the density, and then insert values into another field, so I'm
not using them for plotting or anything. So after checking the density of
a cell and setting the value 'emis' accordingly, I use
enzo.grid_data[enzo.grid_data.keys()[0]][field][cellx][celly][cellz]=enzo.grid_data[enzo.grid_data.keys()[0]][field][cellx][celly][cellz]+emis
to modify a field within the simulation. Unfortunately, the value 'emis'
that I am generating is volume dependent, so I need a method to find the
volume of the cell (in a way consistent with the two methods above, if
possible). Failing finding the volume, if I could find the AMR level, I
would automatically know the volume. Is this possible using the enzo
object?
Sorry if this is an obvious one, I am relatively new to enzo & yt.
Best,
Azton
2 years, 8 months
