yt Community Survey
by Cameron Hummels
Fellow yt users:
We at the yt development team want to make yt better for you, the user. We
have prepared a short survey to gain your valuable feedback to help us
understand what is working in yt and what is not. Could you please spare 2
minutes to fill out our survey below?
We plan to collect responses and make available a selection of results
by December
10, so please let us know what you think at the following URL:
http://goo.gl/forms/hRNryOWTPO
On behalf of the yt development team,
Cameron
--
Cameron Hummels
Postdoctoral Researcher
Steward Observatory
University of Arizona
http://chummels.org
4 years, 3 months
domain-decomposition for volume rendering huge brick?
by Stuart Levy
Hello all,
We're hoping to use yt parallel volume rendering on a very large generic
brick - it's a simple rectangular unigrid slab, but containing something
like 1.5e11 points, so much too large for load_uniform_grid() to load
into memory in a single machine.
I imagine it wouldn't be hard to do the domain decomposition by hand,
loading a different chunk of grid into each MPI process. But then
what? What would it take to invoke the volume renderer on each piece
and composite them together? Would it help if the chunks were stored
in a KDTree? Is there some example (one of the existing data loaders?)
which I could follow?
4 years, 3 months
Reading athena output
by almog yalin
Hi.
I ran a 2D simulation with Athena and exported the data to vtk files. I was
even able to load the file with yt and inspect some of its elements. What I
would like to do is to compare the density from the simulation to an
analytic solution (which I can evaluate at the grid points). The problem is
I cannot figure out how to extract the relevant information from the
yt.frontends.athena.data_structures.AthenaDataset object. What I expect are
2d arrays of the x coordinate, y coordinate and density.
Thanks in Advance,
Almog
4 years, 3 months
Performance when using derived fields
by Daniel Fenn
Hi everyone. Is it normal for slices to take substantially longer to be
created if they're made from a derived field rather than an intrinsic one?
Specifically, I'm having an issue creating an axis-aligned slice using the
divergence of the velocity field. It's taking around 6.5 minutes just to
make the slice, whereas if I use temperature or density, it takes around 10
seconds or so for the same dataset.
I also notice that the amount of time it takes is not dependent on the
number of processors I'm using. I've used 1, 12, and 24 processors, with
identical results, even though I'm calling enable_parallelism(), and I can
see that all the processes are running.
I read in the docs that slice operations aren't generally done in parallel,
but in this case it seems that maybe it would be beneficial. A similar
operation in VisIt completes much faster, so I'm wondering if I've
misconfigured something, or if there is something I can do to speed things
up.
I'd appreciate any thoughts anyone has on the subject.
Thanks,
Dan
4 years, 3 months
Volume Rendering and Field lines
by Dionysopoulou K.
Dear all,
I would like to ask if there has been any progress on the volume rendering refactoring since late October. In particular, I would like to know if volume rendering and the new camera implementation allows for plotting field lines together with the rendering. If so, are there any examples on the web? Unfortunately, matplotlib contour plots with field lines are not good enough for me.
Thanks in advance,
Kiki
Kyriaki Dionysopoulou
=======================================================
Mathematical Sciences
University of Southampton
Southampton, SO17 1BJ, UK
K.Dionysopoulou(a)soton.ac.uk<mailto:K.Dionysopoulou@soton.ac.uk>
4 years, 3 months
Handling large files
by Adam Jacobs
Is it unreasonable for me to expect yt on a workstation with 4x3GHz cores
and ~20 GB of RAM to be able to handle a ~100 GB dataset? I'm trying to
select out a subset of the dataset using cut_region(), but still seem to
run into hanging or running out of RAM. For example, when I try to do a
write_out() on the cut region yt sucks up all 20 GB of RAM and I have to
kill it. Is there a preferred method for loading in a subset of data? I
don't need near the full 100 GB of data.
I'm using yt dev and looking at BoxLib/Maestro data.
--
Adam Jacobs
Department of Physics and Astronomy, PhD Candidate
Stony Brook University
http://astro.sunysb.edu/amjacobs/
4 years, 3 months
Radial Velocity Projection
by John Regan
Hi All,
I need to set the "center" field parameter for making a projection of the
"radial_velocity".
I see from the docs how to do that for a data container but its not clear
what to do for a
projection.
The error I am getting at the moment when the "center" is not set is:
File
"/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/data_containers.py",
line 249, in __getitem__
self.get_data(f)
File
"/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/data_objects/data_containers.py",
line 656, in get_data
finfo.check_available(self)
File
"/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/fields/derived_field.py",
line 146, in check_available
validator(data)
File
"/homeappl/home/regan/appl_taito/YT/Dev-3.0/yt/yt/fields/derived_field.py",
line 235, in __call__
raise NeedsParameter(doesnt_have)
yt.fields.field_exceptions.NeedsParameter: (['center'])
Any tips much appreciated!
Cheers,
John
4 years, 3 months
rockstar loading
by Desika Narayanan
Hey All,
I'm trying to get started with basic Rockstar halo finding in yt (I
typically use HOP, though current analysis requires Rockstar). I'm
having trouble with the following line:
>from yt.analysis_modules.halo_finding.rockstar.api import
RockstarHaloFinder
which gives the error: http://paste.yt-project.org/show/5224/
I'm running yt 3.0 (updated this morning). I just installed Rockstar (I
think) by switching on the INST_ROCKSTAR flag in the install script to 1,
and re-running the script. To be sure, I am running in an 'activated' yt,
with the following ld_library_path:
>(yt-x86_64)thundersnow:~ desika$ echo $LD_LIBRARY_PATH
/Users/desika/yt-x86_64/lib:/opt/gsl/lib:
Though I note manually adding the directory:
/Users/desika/yt-x86_64/src/yt-hg/yt/analysis_modules/halo_finding/rockstar/
to my ld_library_path doesn't fix the problem. Is this symptomatic of an
erroneous installation on my part?
thanks
-desika
4 years, 3 months
Fwd: [FLASH-USERS] VisIt 2.7.2 and FLASH 4.2.2
by John ZuHone
Hi yt'ers,
Ivo Seitenzahl, a fellow FLASHer and former UChicago colleague, is having trouble with the install script on a HPC system. His issue is copied below.
It keeps picking up the Intel compilers, even though he specifies the GNU compiler modules to be loaded. At the moment, I've suggested he set CC=gcc and CXX=g++, but I thought I would copy over here to see if anyone else has any ideas.
Best,
John
> From: Ivo Seitenzahl <ivo.seitenzahl(a)anu.edu.au>
> Date: November 23, 2014 at 10:54:09 PM EST
> To: John ZuHone <jzuhone(a)space.mit.edu>
> Subject: Re: [FLASH-USERS] VisIt 2.7.2 and FLASH 4.2.2
>
> Hi John,
> so, no luck. I'm trying to do this on raijin.
>
> http://nci.org.au/nci-systems/national-facility/peak-system/raijin/
>
> After logging in, the following modules are loaded.
>
> [irs120@raijin2 ~]$ module list
> Currently Loaded Modulefiles:
> 1) pbs 4) openmpi/1.6.3 7) hdf5/1.8.10
> 2) intel-fc/12.1.9.293 5) dot
> 3) intel-cc/12.1.9.293 6) szip/2.1
>
> So what I've done is 'module unload intel-fc' and 'module unload intel-cc' and 'module load gcc', after which I get
>
> [irs120@raijin2 ~]$ module list
> Currently Loaded Modulefiles:
> 1) pbs 2) openmpi/1.6.3 3) dot 4) szip/2.1 5) hdf5/1.8.10 6) gcc/system
>
> However, for some reason, I still get the same problem (see below). It seems like that icc is still called, instead of gcc, although I only have the gcc module loaded. Any thoughts?
>
> Thanks,
>
> Ivo
>
> >>>>>>>>>>>
>
> Awesome! Here we go.
>
> Using wget
> Using sha512sum
> Setting YT_DIR=/home/120/irs120/yt-x86_64/src/yt-hg/
> Installing distribute
> Installing pip
> Installing numpy-1.8.2
> Installing matplotlib-1.4.0
> ********************************************
> FAILURE REPORT:
> ********************************************
>
> extern/qhull/qhull_a.h(106): error: expected a ";"
> template <typename T>
> ^
>
> extern/qhull/qhull_a.h(115): warning #12: parsing restarts here after previous syntax error
> void qh_qhull(void);
> ^
>
> compilation aborted for src/qhull_wrap.c (code 2)
> error: command 'icc' failed with exit status 2
>
> ********************************************
> ********************************************
> Failure. Check /home/120/irs120/yt-x86_64/yt_install.log. The last 10 lines are
4 years, 3 months
