Mailman 3 March 2012 - yt-users

int/long error
by Stella Offner 22 Mar '12

22 Mar '12

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

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hg problems in clean yt install on ubuntu?
by Eric Hallman 21 Mar '12

21 Mar '12

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 --

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yt install script package version updates
by Matthew Turk 20 Mar '12

20 Mar '12

Hi all, In the development branch of yt, we have recently updated the versions of several packages. In IRC last night ( #yt on irc.freenode.net, http://yt-project.org/irc.html ) the idea was tossed around of notifying the mailing list when this happens, so I'm testing that out. If you want to install new versions, you just have to run the latest version of the install script -- no need to remove any previous versions except for space considerations! Below I have noted the versions of the new packages, as well as any yt-related changes that they have brought with them. (The original packages themselves have long changelogs you can also consult.) h5py -- recently upgraded to 2.0.1 from 1.3.1. This fixes some issues a few people have seen of segfaults in the Enzo frontend. IPython -- recently upgraded to 0.12 from 0.10. If you've ever seen "<dict> has no len()!" this will fix it. PyX -- now optionally included! Thanks, and as always, let us know if you run into any problems. We're (tentatively) aiming for a late April / early May release of yt 2.4, at which point the install script in the development branch will be merged back into the stable branch. -Matt

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error when analyzing flash data
by Cien Shang 19 Mar '12

19 Mar '12

Hello, all, I am a rookie in yT, and am trying to analyze some FLASH data with yT. The data load process encountered an error which reads: >>> from yt.mods import * >>>pf=load("flash_data") yt : [WARNING ] 2012-03-18 21:39:56,039 Setting 1.0 in code units to be 1.0 cm yt : [WARNING ] 2012-03-18 21:39:56,039 No time units. Setting 1.0 = 1 second. yt : [INFO ] 2012-03-18 21:39:56,039 Parameters: current_time = 5.0538751323e+15 yt : [ERROR ] 2012-03-18 21:39:56,039 Missing domain_dimensions in parameter file definition! yt : [INFO ] 2012-03-18 21:39:56,040 Parameters: domain_left_edge = [ -3.08600000e+24 -3.08600000e+24 -3.08600000e+24] yt : [INFO ] 2012-03-18 21:39:56,040 Parameters: domain_right_edge = [ 3.08600000e+24 3.08600000e+24 3.08600000e+24] yt : [INFO ] 2012-03-18 21:39:56,040 Parameters: cosmological_simulation = 0.0 yt : [WARNING ] 2012-03-18 21:39:56,040 Setting 1.0 in code units to be 1.0 cm yt : [WARNING ] 2012-03-18 21:39:56,040 No time units. Setting 1.0 = 1 second. I guess to fix it, I'll have to insert the domain-dimensions into the file. but I am not sure how exactly to do it. i opened the file with IDL, and the data are 4 dimensional matrices, something like [16,16,16, 40**]. does anyone know what went wrong, and how i could fix it? Your help will be greatly appreciated! Many thanks, Cien

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how do you build mpi4py on a cray
by Semeraro, B David 15 Mar '12

15 Mar '12

Hi, Yt installs easily on our cray system. However, mpi4py seems to depend on there being an mpi wrapper which we don't have. Has anyone built mpi4py on on a Cray system in the context of YT. I assume someone has since it is installed on Kraken. I could do the usual thing and flounder around for a couple of days on my own but I thought I would break with tradition and ask the benevolent list how to do this. Thanks, Dave Semeraro

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hop circles
by Eric Hallman 13 Mar '12

13 Mar '12

Sorry I've been on a tear with yt lately, but on two machines I've noticed that the hop circles have only been showing up on the upper left quad of the image. Not sure what happened, but I'm just using the standard recipe from the yt docs… -- 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 --

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shine through images
by Elizabeth Tasker 13 Mar '12

13 Mar '12

Hi, Is there a way to create an image that, rather than being a projection, shows the maximum or minimum point of a field? Elizabeth

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Power spectrum
by Miguel Angel González 12 Mar '12

12 Mar '12

Hi, I’m working in Enzo and I’d would like to know if it generates its own power spectrum or if I have to configure it. Thanks.

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kraken yt module
by Eric Hallman 12 Mar '12

12 Mar '12

So I've been out of the loop on NICS Kraken for a while. Are the yt modules on kraken fully functional and set to use? Thanks! Eric -- 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 --

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Support for FLASH particle files
by Nathan Goldbaum 09 Mar '12

09 Mar '12

Hi all, I asked this question on yt-dev but didn't receive any responses, I figure there's a wider FLASH user readership on this list. I'm trying to add support for FLASH particle files. However, the particle files I have are nonstandard and so the particle reader I've come up with may not work with the default particle types that come with FLASH. I'm curious if anyone would like to share a more vanilla particle file dataset so I can test my yt modifications. Thanks very much, Nathan Goldbaum Graduate Student Astronomy & Astrophysics, UCSC goldbaum(a)ucolick.org http://www.ucolick.org/~goldbaum

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