Csh environment setting bug
by Alice Coucke
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
6 years, 9 months
yt in macports
by erosenblum
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
6 years, 9 months
error "Zero-length selections are not allowed"
by Jean-Claude Passy
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
6 years, 9 months
matpltolib warning at start
by Jean-Claude Passy
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
6 years, 9 months
particle_mass
by Ali Snedden
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
6 years, 10 months
help
by Nicholas David Tillman
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
6 years, 10 months
opaqueness of iso-surface
by Renyue Cen
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
6 years, 10 months
int/long error
by Stella Offner
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
6 years, 10 months
hg problems in clean yt install on ubuntu?
by Eric Hallman
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!
--
Eric Hallman
Tech-X Corporation hallman(a)txcorp.com
5621 Arapahoe Ave, Suite A Phone: (720) 254-5833
Boulder, CO 80303 Fax: (303) 448-7756
--
6 years, 10 months
