yt-users January 2014

yt-users@python.org

32 participants
36 discussions

LightRay Objection Creation - Index Error
by Claire Kopenhafer 12 Jan '14

12 Jan '14

Hello out there, I'm trying to create a LightRay object for an enzo sim. I get this error message: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/data/codes/yt-x86_64/src/yt-hg/yt/analysis_modules/cosmological_observation/light_ray/light_ray.py", line 117, in __init__ redshift_data=redshift_data) File "/data/codes/yt-x86_64/src/yt-hg/yt/analysis_modules/cosmological_observation/cosmology_splice.py", line 119, in create_cosmology_splice cosmology_splice.append({'time': self.simulation[0].current_time, File "/data/codes/yt-x86_64/src/yt-hg/yt/data_objects/time_series.py", line 117, in __getitem__ o = self._pre_outputs[key] IndexError: list index out of range The nearest and farthest redshift are both 0, which is the current redshift of the dataset I was given. This may or may not have any bearing on the problem. Thanks for the help! -Claire Kopenhafer

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Rotations in off_axis_projection
by James Guillochon 10 Jan '14

10 Jan '14

Hi everyone, I have a 3D simulation FLASH that I wish to rotate and then project using YT. I know the transformation matrix needed to rotate the domain such that the projection is correct, depicted in this image: http://i.imgur.com/AOmY6Ao.png. In the image, the dashed lines are the original coordinate system, where the original "north_vector" is the red dashed line, and the original "normal_vector" is a green dashed line that points out of the plane (not visible). The rotated coordinates are shown by the solid lines. The transformation matrix A is: A = 0.0478113 -0.345249 0.937292 0.912293 -0.367011 -0.181724 -0.406737 -0.863774 -0.297421 My question is what should I set "normal_vector" and "north_vector" to to get the proper projection. I tried just doing A.normal and A.north, but the projection I get is not correct. I've also tried multiplying by A_inverse, or just multiplying normal and/or north by A (or A_inverse), and setting the other vector to a trivial direction (such as [0,0,1]), but none of these projections seem to be correct. Another thing I have tried is opening the data in Visit and rotating the domain manually, taking note of what Visit calls the "view normal" and the "up vector". The "up vector" matches the "north vector" I calculate using A.north, but the "view normal" does not match A.normal. Does anyone know the proper way to go about this? Thanks! - James -- James Guillochon Einstein Fellow at the Harvard-Smithsonian CfA jguillochon(a)cfa.harvard.edu

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YT Error on trestles
by Munier Azzam Salem 10 Jan '14

10 Jan '14

Hey Guys, I've just tried installing yt on trestles for the first time (vanilla install of dev version, with scipy and rockstar included). The install seemed to go well, but when I tried to import the modules, it appeared some dependencies were missing: *>>> from yt.mods import ** *Traceback (most recent call last):* * File "<stdin>", line 1, in <module>* * File "/home/msalem/src/yt-x86_64/src/yt-hg/yt/mods.py", line 25, in <module>* * import numpy as na # For historical reasons* * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/__init__.py", line 137, in <module>* * import add_newdocs* * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/add_newdocs.py", line 9, in <module>* * from numpy.lib import add_newdoc* * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/lib/__init__.py", line 13, in <module>* * from polynomial import ** * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 17, in <module>* * from numpy.linalg import eigvals, lstsq, inv* * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 48, in <module>* * from linalg import ** * File "/home/msalem/src/yt-x86_64/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 23, in <module>* * from numpy.linalg import lapack_lite* *ImportError: libquadmath.so.0: cannot open shared object file: No such file or directory* Any insights here? thanks! Munier -- Munier A. Salem // 845.489.6450

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yt-3.0 issues with FLASH
by Alex Bogert 07 Jan '14

07 Jan '14

http://yt-project.org/data/ I ran into an error with the GalaxyClusterMerger example file on the yt-project site. I was attempting to use a covering grid on the data to sub-sample densities. This is with yt-3.0 . Here is the code and error: http://pastie.org/8611073 Thanks, Alex

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Removing Yt and reversing changes to system.
by k.grisdale＠surrey.ac.uk 06 Jan '14

06 Jan '14

Hi, I want to remove yt from my system and reverse the changes that yt made to my python install. What is the best way to achieve this? Thanks Kearn (I am using a Mac with Mavericks incase that is needed)

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YT parallel error
by John Regan 02 Jan '14

02 Jan '14

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)

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yt-users January 2014