Notebook server question
by Andrew Myers
Hello yt users,
I have a (perhaps naive) ssh question related to the yt notebook. I would
like to run a yt notebook server on machine A. However, machine A cannot be
directly accessed via ssh from the wider internet. Instead, I must first
ssh into machine B, and then ssh from B to A. Machine B cannot run the
notebook server itself. Does anyone know how I can configure things -
perhaps by using a more complicated ssh tunnel command - so I that access a
notebook server running on machine A through machine B?
Thanks,
Andrew
4 years, 8 months
Light Cone Projection
by Pengfei Chen
Hi all,
I downloaded the example script of light cone projectoin(
http://yt-project.org/doc/cookbook/cosmological_analysis.html#light-cone-...)
to my laptop and changed the Enzo simulation parameter file and redshifts.
But when I ran it the following error occurred:
File "light_cone_projection.py", line 19, in <module>
find_outputs=False)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/light_cone/light_cone.py",
line 158, in __init__
find_outputs=find_outputs)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py",
line 44, in __init__
find_outputs=find_outputs)
File "/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/convenience.py", line
131, in simulation
find_outputs=find_outputs)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py",
line 81, in __init__
find_outputs=find_outputs)
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/data_objects/time_series.py",
line 343, in __init__
self._parse_parameter_file()
File
"/Users/madcpf/Documents/dev_yt/src/yt-hg/yt/frontends/enzo/simulation_handling.py",
line 273, in _parse_parameter_file
param, vals = (i.strip() for i in line.split("="))
ValueError: need more than 1 value to unpack
Does the parameters "near_redshift" and "far_redshift" in LightCone need to
be the same with "CosmologyFinalRedshift" and "CosmologyInitialRedshift" in
enzo parameter file?
Does anyone know how to solve this?
Thank you all!
Pengfei
4 years, 9 months
YT parallel error
by John Regan
Hi All,
I've started to see a strange error in a simple enough parallel
computation.
I can reproduce it with the script below but with some other scripts where
the code is embedded it runs fine so it may be a race condition.
from yt.mods import *
pf = load("/wrk/regan/H2/Ctrl/DD0035/Data0035")
v, c = pf.h.find_max("Density")
print v, c
Thanks in advance for any help!
Cheers,
John
Error:
Traceback (most recent call last):
P001 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at
0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid
EnzoGrid_1214 at level 18 (3, 3, 2)
Traceback (most recent call last):
File "ptest.py", line 5, in <module>
P003 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at
0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid
EnzoGrid_1214 at level 18 (3, 3, 2)
File "ptest.py", line 5, in <module>
Traceback (most recent call last):
File "ptest.py", line 5, in <module>
P002 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at
0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid
EnzoGrid_1214 at level 18 (3, 3, 2)
Traceback (most recent call last):
P004 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at
0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid
EnzoGrid_1214 at level 18 (3, 3, 2)
Traceback (most recent call last):
File "ptest.py", line 5, in <module>
P005 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at
0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid
EnzoGrid_1214 at level 18 (3, 3, 2)
Traceback (most recent call last):
File "ptest.py", line 5, in <module>
P006 yt : [INFO ] 2013-12-29 09:31:27,756 Max Value is 3.67832e-16 at
0.5025423020124483 0.4896353334188484 0.4947452098131160 in grid
EnzoGrid_1214 at level 18 (3, 3, 2)
Traceback (most recent call last):
File "ptest.py", line 5, in <module>
Traceback (most recent call last):
File "ptest.py", line 5, in <module>
Traceback (most recent call last):
File "ptest.py", line 5, in <module>
File "ptest.py", line 5, in <module>
v, c = pf.h.find_max("Density")
v, c = pf.h.find_max("Density")
v, c = pf.h.find_max("Density")
v, c = pf.h.find_max("Density")
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 51, in find_max
v, c = pf.h.find_max("Density")
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 51, in find_max
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 51, in find_max
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 51, in find_max
v, c = pf.h.find_max("Density")
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 51, in find_max
v, c = pf.h.find_max("Density")
v, c = pf.h.find_max("Density")
v, c = pf.h.find_max("Density")
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 51, in find_max
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 51, in find_max
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 51, in find_max
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 51, in find_max
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 66, in find_max_cell_location
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 66, in find_max_cell_location
File
"/homeappl/home/regan/appl_taito/YT/yt-x86_64/src/yt-hg/yt/data_objects/object_finding_mixin.py",
line 66, in find_max_cell_location
mg, mc, mv, pos = self.find_max_cell_location(field, finest_levels)
4 years, 11 months
TotalQuantity vs. summing manually
by Geoffrey So
Hi all,
I found that using a Enzo dataset I was getting slightly different numbers
when
1) using the list of dark matter particles selected by creation_time < 0.0
In [97]: sph_dm = sph['creation_time'] < 0.0
In [98]: print "%12.12e" % (sph['ParticleMassMsun'][sph_dm]).sum()
1.211311468567e+11
2) compared to summing the dark matter particles inside a 3D container with
TotalQuantity
In [101]: print "%12.12e" %
(sph.quantities['TotalQuantity']('Dark_Matter_Density')[0]*vol/Msun)
1.188937185993e+11
I'm wondering if the field and particles are handled differently when being
counted as inside or outside the 3D container?
From
G.S.
4 years, 11 months
Re: [yt-users] [enzo-users] Visualizing Tracer Particles
by John ZuHone
Hi Brandon,
Sorry for the delayed reply!
I'm cross-posting this over to the yt-users list since at this point it is really a yt problem.
> Ideally, the type of plot I would like to end up with would be to use the grid/data from an Enzo data dump then overplot the tracer particles. For example:
>
> pf = ("TP0000/TPDD0000.h5", "r")
> pf2 = load("DD0000/data0000)
>
> slc = SlicePlot(pf2, "z", "Density")
> slc.annotate_particles(from_pf)
>
> Is there a function that would allow that?
At the moment, we don't have an _easy_ way to do this (unless I am mistaken). But we should, frankly.
There's a somewhat convoluted way to do this, and I can try to have a script that shows how to do that to you by tomorrow.
Best,
John
4 years, 12 months
RAMSES field autodetection
by Matthew Turk
Hi all,
I just pulled in Sam Geen's fix to make RAMSES fields be autodetected.
If you are manually specifying fields you should not have to change
anything, but it might work now if you don't try specifying them.
-Matt
4 years, 12 months
radmc3d exporter
by Mike Butler
Hi all,
I've been trying to export some of my Enzo data to radmc3d input files and
have run into an issue with the amr grid writer - it writes the
amr_grid.inp file in units of kpc, rather than cgs like radmc3d wants. Is
there a way to fix this short of modifying the .inp file manually afterward?
Thanks a lot,
Mike
4 years, 12 months
Radial velocity Projections
by John Regan
Hi All,
I was trying to make an OffAxis radial projection. Naively using
proj = OffAxisProjectionPlot(pf, L, "RadialVelocityKMS", center='max',
width=(width, 'pc'),
depth=depth)
fails with a message of type
yt.data_objects.field_info_container.NeedsParameter: (['center'])
The RadialVelocity probably isn't the field to use here and requires some
manipulation to be a quantity suitable for plotting.
Any suggestions on the best way forward would be much appreciated.
Cheers,
John
4 years, 12 months
Running Rockstar Halo Finder to create a merger tree
by Hilary Egan
Hi all,
I'm quite confused on a number of points related to running the rockstar
halo finder, so I hope its alright that I put all these questions into this
one email!
1. I can't seem to run the rockstar halo finder at all without getting this
error followed by a segmentation fault and crash.
[Warning] Network IO Failure (PID XXXXXX): Connection reset by peer
[Network] Packet receive retry count at: 1
It sort of seems like this issue (
http://lists.spacepope.org/htdig.cgi/yt-dev-spacepope.org/2012-November/0...)
but I couldn't really figure out what the resolution was from the thread.
Im attempting to run this on kraken and it doesn't matter if I use a single
compute node or multiple, I get the same error. (I hope this isn't the
infiniband issue the docs warned about, I couldn't figure out if that is
how kraken is connected and I got an error that the suggested flag doesn't
exist so I didn't press the issue.)
2. Whenever I finally do get the halo finder to work, I need the results to
be in a form that the merger tree can use. It seems as though the
MergerTree needs the results in the same form as the other halo finders
give, so would getting the halo list and then dumping it as usual be the
appropriate strategy? Ie:
rh.run()
halo_list = rh.halo_list()
halo_list.dump('MergerHalos')
2.5. The docs sort of give mixed messages on whether or not I could just be
calling MergerTree with the argument halo_finder_function =
RockstarHaloFinder. At this point I've pretty thoroughly convinced myself
that I can't, but it would be nice if that was clarified. (Just a
thoroughly overwhelmed new user's perspective!)
3. I'm a little confused as to whether or not I have to use a
TimeSeriesData object rather than the usual single time output when
instantiating the halo finder. Under "Rockstar Halo Finding" it uses
TimeSeriesData, unlike the rest of the examples, but under the subheading
"Output Analysis" it just uses pf. The "Output Analysis" example also
doesn't call the run() method, which leads me to believe something else
entirely is going on, but its not quite clear.
Thanks!
-Hilary
4 years, 12 months
Install yt in oak ridge system with system python package
by Junhwan Choi (최준환)
Hi yt user,
Here, I have a naive question on installing yt.
I try to install yt in the oak ridge super computer system particularly lens.
People at the help desk suggest to use system python package in case I
launch the analysis tool through the queueing system.
What python package do I need to ask them?
Can I simply turn on the default python in the system and install yt
on my home directory?
Or I need to request particular python package with numpy, matplotlib,
scipy and so on.
In addition, I would like to also use mpi4py since I will use large
simulation data.
Thank you,
Junhwan
5 years
