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:
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:
from yt.utilities.parallel_tools.parallel_analysis_interface import\
comm = communication_system.communicators[-1]
print comm.rank, comm.size
When I run a similar code but with yt-2.x also on Blue Waters, I get what I
I'm confused about it. Could anyone give me some suggestions please?
I'm trying to plot some particle trajectories taken from a FLASH simulation that has particle files. The number of particle files is greater than the checkpoint files. I was wondering if I could use a similar recipe to the yt documentation for particle trajectories but loading data from the particle files instead of using the checkpoints so I have more trajectory points.
Thank you very much!
Dear Suoqing Ji:
Thanks. In the meanwhile can you suggest any alternate function/method in
yt that I can use for my vector plots?
I also have a 3d (streamlines_t000.png) and 2d streamline plot
(UniformGridData_Slice_y_field_x_t000.png), which needs to treated in the
same way. Can you suggest any approach for these plots?
Thanks in advance
On Sat, Apr 30, 2016 at 12:56 PM, <yt-users-request(a)lists.spacepope.org>
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> 1. Re: Camera/Off Axis Options (Suoqing Ji)
> Message: 1
> Date: Fri, 29 Apr 2016 12:35:04 -0700
> From: Suoqing Ji <suoqing(a)physics.ucsb.edu>
> To: Discussion of the yt analysis package
> Subject: Re: [yt-users] Camera/Off Axis Options
> Message-ID: <9D6F4AE6-F3EF-4A4B-A997-32ACA9688E78(a)physics.ucsb.edu>
> Content-Type: text/plain; charset="us-ascii"
> Hi Sushil,
> I was able to reproduce your error and created an issue here:
> Best wishes,
> Suoqing JI
> Ph.D Candidate
> Department of Physics
> University of California, Santa Barbara
> > On Apr 28, 2016, at 7:17 PM, Sushilkumar <sushil.sush19us(a)gmail.com>
> > Dear Suoqing Ji:
> > With a combination of center [0,0,0] and adjusting the width w, I was
> able to eliminate all the warnings mentioned earlier. But the off axis
> slice plots still wont give me a desired result.
> > Plot available on the drive below below.
> > The two plots L(010),N(0,0,1).png and L(101),N(001).png are plotted for
> x-z plane and viewing angle of 45 degrees but both are drastically
> different from each other. In fact the off axis slice plots
> (L(101),N(001).png) is not in the x-z plane either.
> > I am aiming for a plot similar to vector_rotate.png which is same as
> vector_original.png but rotated/viewed at an angle.
> > The vector_rotate.png was created using the python image library. I was
> hoping if yt has any similar options with off axis which would tilt the
> vector plots and fill all the vector grids (which cannot be done using PIL).
> > The script (yt_velocity_fields.py) and sample data file
> (Expl_Bt101.mtx.tar.gz) is available on drive link for your reference.
> > Thanks in advance and my sincere apologies for repeated queries. But
> this is extremely critical in reproducing my result and putting it for
> > https://drive.google.com/open?id=0B4g8shg4DL7oak5PLWVVdG5UMHc <
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*"**Claiming that something can move faster than light is a good
conversation-stopper in physics. People edge away from you in cocktail
parties; friends never return phone calls. You just don’t mess with Albert
I am trying to create a max_dens and max_temp sweep plot in yt. I am using
the following code
for n in range (0,118):
fn = flashFolder+'super3d_hdf5_plt_cnt_%04d' % n
pf = yt.load(fn) # load data
c = pf.h.find_max('temp')
ax = 0 # take a line cut along the x axis
# cutting through the y0,z0 such that we hit the max density
#ray = ds.h.ortho_ray(ax, (c, c))
# ray with start and end point
ray = pf.h.ray([0.,0.,0.],c)
# Sort the ray values by 'x' so there are no discontinuities
# in the line plot
srt = np.argsort(ray['x'])
and getting the the following error:
IOError: [Errno 2] No such file or directory:
Any suggestion on how to fix this error is highly appreciated.
I have installed yt once with no problems, but now I'm trying to install
it on TACC/Stampede, and I'm getting an error message during the Python 2
Fatal: You must get working getaddrinfo() function.
or you can specify "--disable-ipv6"
I don't know what is getaddrinfo() and where I can get it.
I know what ipv6 is, but I don't know where I should specify
"--disable-ipv6" (and whether it is a good thing to do or I better get
working getaddrinfo() function).
If anyone got this error message and knows what to do please help.
Thanks for the response. None of "px", "pdx", "py", and "pdy" work for
me. I perused the code a bit and it's not entirely clear why they don't.
The data_source for the frb in my case is a slice, as I showed and that
slice object does apparently have those fields defined -- for example doing
px = slc['px'] works, though of course the result is a 1D array of values.
It seems to be related to the _determine_fields method of the data_source
(slice) which rather than returning a tuple, in this case returns a
string. In any case, I don't really have time right now to look into it
On Tue, Apr 26, 2016 at 1:53 PM, <yt-users-request(a)lists.spacepope.org>
> Hi Jon,
> This is expected behavior, but it probably isn't what you're looking
> for. dx and dr will be the "pixelized" values of those from the
> simulation, so they will reflect the cells that went into creating the
> FRB, rather than the values as they would be computed in the FRB
> itself. I think what you may be looking for may be accessible in the
> "px" "pdx" "py" and "pdy" fields, which refer to "in the pixel plane"
> and which will be with respect to the FRB.
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