Hi everyone,
I'm having a problem using fields that use ghost zones. The following
simple script:
http://paste.yt-project.org/show/2010/
gives this error:
http://paste.yt-project.org/show/bOikDPScBBtDiUGvH11X/
I am working from the tip, but I get the same behavior from yt/2.3. In
yt/2.2, everything is working. I am working now to narrow that range down
a bit, but does anyone have an idea?
Britton
Hello everyone,
It looks like there is a bug with the csh environment setting. I am a Unix beginner so I might have done an error.
I had to make these modifications to the install script to set up yt in a csh shell OSX Lion machine :
* Disable the install of zlib. The HDF5 build failed because of some sort of version confusion.
* Force the use of gcc over the newer clang compiler by setting :
export CC=gcc
at the top of the install script. Matplotlib-1.1.0 fails to compile with the default Lion cc which is clang based.
Once installed, I had difficulties to run it. I tried to follow the Extremely Simple Data Inspection.
$ yt stats $YT_DEST/src/yt-hg/tests/DD0010/moving7_0010
BUT that is what happens :
yt : [ERROR ] 2012-03-23 11:17:08,651 Couldn't figure out output type for /Users/acoucke/yt-i386:/src/yt-hg/tests/DD0010/moving7_0010
Traceback (most recent call last):
File "/Users/acoucke/yt-i386/bin/yt", line 9, in <module>
load_entry_point('yt==2.3', 'console_scripts', 'yt')()
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 1610, in run_main
sys.exit(YT.main())
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 257, in main
return self.cmd(args)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 280, in cmd
retval = self.onecmd(argv)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 412, in onecmd
return self._dispatch_cmd(handler, argv)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/cmdln.py", line 1100, in _dispatch_cmd
return handler(argv[0], opts, *args)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 256, in arg_iterate
func(self, subcmd, opts, arg)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 627, in do_stats
pf = _fix_pf(arg)
File "/Users/acoucke/yt-i386/src/yt-hg/yt/utilities/command_line.py", line 44, in _fix_pf
raise IOError
IOError
Then if I type :
$ echo $YT_DEST
/Users/acoucke/yt-i386:
It seems that there is an unexpected colon here because :
$ ls /Users/acoucke/yt-i386:
ls: /Users/acoucke/yt-i386:: No such file or directory
I have to use :
setenv YT_DEST /Users/acoucke/yt-i386
to make that works.
Best,
Alice Coucke
Hi all,
I tried using macports to install yt and ran into a couple of issues.
First, there was a conflict because I had hdf5 installed to use flash and yt required hdf5-18. Secondly, after uninstalling hdf5 to see what would happen, I received these errors:
Error: Checksum (md5) mismatch for yt-2.2.tar.gz
Error: Checksum (sha1) mismatch for yt-2.2.tar.gz
Error: Checksum (rmd160) mismatch for yt-2.2.tar.gz
Error: Target org.macports.checksum returned: Unable to verify file checksums
Error: Status 1 encountered during processing.
Any ideas?
Thanks!
Erica
Hi everyone,
I get an error when executing the simple script below:
------------------------------------------------------------------------------
from yt.mods import *
output = 'DD0010/data0010'
pf = load(output)
region = pf.h.region([0.5,0.5,0.5],[0.0,0.0,0.0],[1.0,1.0,1.0])
------------------------------------------------------------------------------
I have pasted the output there:
http://paste.yt-project.org/show/awqlzVK7mAhtiIVihFfC/
I think the problem is that my simulation has only 2 particles (no gas)
and both particles are in subgrids so the root grid is empty:
------------------------------------------------------------------------------
[19:46:54] Obiwan:$ h5ls DD0010/data0010.cpu0000
Grid00000001 Group
Grid00000002 Group
Metadata Group
[19:47:09] Obiwan:$ h5ls DD0010/data0010.cpu0000/Grid00000001
[19:47:15] Obiwan:$ h5ls DD0010/data0010.cpu0000/Grid00000002
particle_index Dataset {2}
particle_mass Dataset {2}
particle_position_x Dataset {2}
particle_position_y Dataset {2}
particle_position_z Dataset {2}
particle_type Dataset {2}
particle_velocity_x Dataset {2}
particle_velocity_y Dataset {2}
particle_velocity_z Dataset {2}
------------------------------------------------------------------------------
I would really appreciate if someone could help me to fix this.
Thanks a lot,
JC
Hi everyone,
nothing dramatic but I get a warning when I start iyt:
---------------------------------------------------------------------------------------------------------------------
[19:25:12] lattice:$ iyt
/home/jcpassy/yt-x86_64/lib/python2.7/site-packages/matplotlib/__init__.py:908:
UserWarning: This call to matplotlib.use() has no effect
because the the backend has already been chosen;
matplotlib.use() must be called *before* pylab, matplotlib.pyplot,
or matplotlib.backends is imported for the first time.
if warn: warnings.warn(_use_error_msg)
Welcome to pylab, a matplotlib-based Python environment [backend: agg].
For more information, type 'help(pylab)'.
==================
| Welcome to yt! |
==================
---------------------------------------------------------------------------------------------------------------------
I did not get this problem before I updated to the most recent
changeset, and I reproduced the warning on two different Linux machines.
If anyone has an idea about how to get rid of it, please let me know.
Cheers,
JC
Hello,
I was trying to get the position and mass information for the dark matter
(and stellar) particles in an Enzo simulation. I have tried a couple of
different ways and I was curious about the units on the following method.
In this case I am presumably accessing the dark matter particles
(particle_type = 1)
*from yt.mods import **
*pf = load("DD0252/DD0252")*
*array = pf.h.find_particles_by_type(ptype=1, max_num=3)*
*print "(%.5f, %.5f, %.5f) = %f\n" %(array['particle_position_x'][0],
array['particle_position_y'][0], array['particle_position_z'][0],
array['particle_mass'][0])*
This returns *(0.01055, 0.01873, 0.00224) = 0.835448. *What are the mass
units on the *0.835448*? I don't think that they are cgs, and there
doesn't appear to be a conversion factor available via pf[' * ']. If I
continue and enter
*print pf.field_info['Density'].get_units()*
*print pf.field_info['particle_mass'].get_units()*
*
*
The 'Density' line returns *\rm{g}/\rm{cm}^3, *but the 'particle_mass'
line returns nothing. So I can't get the units from here. I can, however,
access the same particle (or at least a particle at the same location) by
using
*from yt.mods import **
*pf = load("DD0252/DD0252")*
*dd = pf.h.all_data()*
*print "(%f %f %f) = %f Msun, ptype= %i\n"%(dd["particle_position_x"][0],
dd["particle_pos ition_y"][0], dd["particle_position_z"][0],
dd["ParticleMassMsun"][0],dd["particle_type"][0])*
Which returns *(0.010554 0.018727 0.002239) = 82255596.670652 Msun, ptype=
1*
This seems to give reasonable values. Both methods should be equivalent
ways of to access the particle (both stellar and dark matter) data,
correct? So how do I get my units in solar masses when using *
pf.h.find_particles_by_type()*? Thanks for your time!
~ali
This is my first time using yt so bear with me please...
Every time I try to upload a file as FLASH, I get an error message saying that it couldn't figure out the output type. I even went back and tried using a sample file, still got the same error message.
Thanks,
Nick
Hi,
For iso-density surface I have a primitive question: how do I make certain contour level totally opaque?
I can do " tf.add_gaussian(-25.5, 0.05, [1.0, 0, 0, 1.0])"
but specifying alpha=1.0 in this example does not seem to make that level (red) totally opaque.
Thanks,
Renyue
Hi,
I'm encountering an int/long error in a new installation of yt,
python, computer cluster etc:
(yt-x86_64)[pjumper@hpcmanage ~]$ python covering_grid_test.py
yt : [WARNING ] 2012-03-19 18:42:59,135 Setting 1.0 in code units to
be 1.0 cm
yt : [WARNING ] 2012-03-19 18:42:59,135 No time units. Setting 1.0 =
1 second.
yt : [INFO ] 2012-03-19 18:42:59,136 Parameters:
current_time = 2.26390632737e+14
yt : [INFO ] 2012-03-19 18:42:59,136 Parameters:
domain_dimensions = [256, 256, 256]
yt : [INFO ] 2012-03-19 18:42:59,136 Parameters:
domain_left_edge = [ -3.09000000e+18 -3.09000000e+18
-3.09000000e+18]
yt : [INFO ] 2012-03-19 18:42:59,136 Parameters:
domain_right_edge = [ 3.09000000e+18 3.09000000e+18
3.09000000e+18]
yt : [INFO ] 2012-03-19 18:42:59,228 Adding unknown field density
to list of fields
yt : [INFO ] 2012-03-19 18:42:59,228 Adding unknown field xmom to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,228 Adding unknown field ymom to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,228 Adding unknown field zmom to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,229 Adding unknown field eden to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,229 Adding unknown field frac1 to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,229 Adding unknown field rhof1 to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,229 Adding unknown field rhofe1
to list of fields
yt : [INFO ] 2012-03-19 18:42:59,229 Adding unknown field phi to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,229 Adding unknown field phicorr
to list of fields
yt : [INFO ] 2012-03-19 18:42:59,230 Adding unknown field test0 to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,230 Adding unknown field test1 to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,230 Adding unknown field test2 to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,230 Adding unknown field log_den
to list of fields
yt : [INFO ] 2012-03-19 18:42:59,230 Adding unknown field pressure
to list of fields
yt : [INFO ] 2012-03-19 18:42:59,230 Adding unknown field xvel to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,231 Adding unknown field yvel to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,231 Adding unknown field zvel to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,231 Adding unknown field ieng to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,231 Adding unknown field keng to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,231 Adding unknown field cvt to
list of fields
yt : [INFO ] 2012-03-19 18:42:59,296 Setting right_edge to [1.0,
1.0, 1.0]
Traceback (most recent call last):
File "covering_grid_test.py", line 20, in <module>
dims=[128,128,128],
File "/usr/local/yt/yt-x86_64/src/yt-hg/yt/data_objects/
data_containers.py", line 3331, in __init__
self._refresh_data()
File "/usr/local/yt/yt-x86_64/src/yt-hg/yt/data_objects/
data_containers.py", line 3348, in _refresh_data
AMR3DData._refresh_data(self)
File "/usr/local/yt/yt-x86_64/src/yt-hg/yt/data_objects/
data_containers.py", line 307, in _refresh_data
self.get_data()
File "/usr/local/yt/yt-x86_64/src/yt-hg/yt/data_objects/
data_containers.py", line 3355, in get_data
self._get_list_of_grids()
File "/usr/local/yt/yt-x86_64/src/yt-hg/yt/data_objects/
data_containers.py", line 3343, in _get_list_of_grids
self.right_edge + buffer, self.level)
File "/usr/local/yt/yt-x86_64/src/yt-hg/yt/data_objects/
object_finding_mixin.py", line 214, in get_box_grids_below_level
self.grid_levels, mask)
File "misc_utilities.pyx", line 91, in
yt.utilities.amr_utils.get_box_grids_below_level (yt/utilities/
amr_utils.c:58776)
ValueError: Buffer dtype mismatch, expected 'int32_t' but got 'long'
It is possible to partially get around this by declaring all the input
ints (e.g. dims=[128, 128, 128]) to covering_grid as type int32.
However, doing this for all yt calls seems tedious. Is there an easier
way of dealing with this issue?
Thanks!
Stella
Has anyone seen this error after clean install of yt on ubuntu? I went through lists online to see what is going on, and it appears to be a compile of python without ssl support. I'm not sure how to fix it however. This is using the mercurial build from the install script.
$hg pull
abort: Python SSL support not found
Is it an Ubuntu problem? Or do I need to rebuild python from the install script with some other flags?
Thanks!
--
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Tech-X Corporation hallman(a)txcorp.com
5621 Arapahoe Ave, Suite A Phone: (720) 254-5833
Boulder, CO 80303 Fax: (303) 448-7756
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