Mailman 3 May 2015 - yt-users

Disabling yt info outputs
by Joshua Wall May 11, 2015

May 11, 2015

Dear users, I recently updated yt to the latest verison, and now when I run it in an ipython notebook I get obscene amounts of yt: INFO and yt: WARNING messages. So many that it actually hangs some analysis loops I'm running. How do I turn this output off? Sample from loading a file: yt : [INFO ] 2015-05-11 16:01:16,453 integer runtime parameter checkpointfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-11 16:01:16,455 integer runtime parameter particlefilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-11 16:01:16,456 integer runtime parameter plotfilenumber overwrites a simulation scalar of the same name yt : [INFO ] 2015-05-11 16:01:16,512 Parameters: current_time = 1.80820359458e+12 yt : [INFO ] 2015-05-11 16:01:16,514 Parameters: domain_dimensions = [8 8 8] yt : [INFO ] 2015-05-11 16:01:16,516 Parameters: domain_left_edge = [ -1.29093000e+17 -1.29093000e+17 -1.29093000e+17] yt : [INFO ] 2015-05-11 16:01:16,517 Parameters: domain_right_edge = [ 1.29093000e+17 1.29093000e+17 1.29093000e+17] yt : [INFO ] 2015-05-11 16:01:16,519 Parameters: cosmological_simulation = 0.0 Any assistance is greatly appreciated. I checked the docs, but I was unable to find a way to pass to yt the configuration option which I suspect is the problem, namely one: suppressStreamLogging. Cordially, Joshua Wall Drexel University _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Deposited Particle Data
by Jason Galyardt May 11, 2015

May 11, 2015

Hi all, Has anyone had success accessing deposited particle data generated with FLASH? It appears in the dataset derived field list, but when I go to access it (via ds.all_data()['deposit', 'io_mass']), I get an error concerning zero-length selection. I get the same error when I try to access the 'standard' particle data (from ds.field_list), such as ds.all_data()['io', 'particle_mass']. Does this ring any bells? This very well could be user error, so please let me know if that seems to be the case. I've pasted a basic script to reproduce the error here: http://paste.yt-project.org/show/5538/ I'd rather not post the dataset publicly, but I can send you a link, if you're interested. Cheers, Jason Galyardt _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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PYTHONPATH
by mc knabbits May 6, 2015

May 6, 2015

hi everybody, this question aint very yt specific but more on the python way of treating its PATH variable. since having installed yt I have 2 versions of python on my machine. (the yt one and my previous 2.7.3 with the main scipy packages) I wonder how its possible to have each of them having its own PYTHONPATH variable? so when yt is activated it uses its yt path and when switched off the independend python install uses another. right now even when deactivated the first entry in the PPATH is the yt link to the yt python site packages where numpy etc is stored. but these packeges would not work with the original python version I may want to use as well so that I need to re-source my bashrc or restart the terminal... hope theres a solution to this thanx, phil _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Pressure in Enzo methods
by David Collins May 5, 2015

May 5, 2015

Hi, Everybody! I'm having a little trouble with getting pressure when using HydroMethod=6. For instance, >>> ds0.all_data()['pressure'] Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/dcollins/local-2014-09-24-yt3/src/yt-hg/yt/data_objects/data_containers.py", line 233, in __getitem__ f = self._determine_fields([key])[0] File "/Users/dcollins/local-2014-09-24-yt3/src/yt-hg/yt/data_objects/data_containers.py", line 489, in _determine_fields finfo = self.ds._get_field_info("unknown", fname) File "/Users/dcollins/local-2014-09-24-yt3/src/yt-hg/yt/data_objects/static_output.py", line 482, in _get_field_info raise YTFieldNotFound((ftype, fname), self) yt.utilities.exceptions.YTFieldNotFound: Could not find field '('all', 'pressure')' in data0000. while this works for a run with HydroMethod = 0. Could someone give me the nickel tour of hydro method impacts setting of variables, and where I should look to make sure pressure is defined? Thanks! d. -- -- Sent from a computer. _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Re: [yt-users] Plot 2D magnetic field lines
by Stella Offner May 5, 2015

May 5, 2015

Many thanks, Nathan! This does annotate the streamlines like I wanted for yt 3.1, and I think it would be useful for the cookbook. Once I reformat it a little, I'm happy to send my version back to you. Stella P.S. Matt, I'm sorry to say the users archive is still 'forbidden' to me. On Mon, May 4, 2015 at 3:01 PM, Nathan Goldbaum <nathan12343(a)gmail.com> wrote: > > > On Mon, May 4, 2015 at 11:43 AM, Stella Offner <offner(a)gmail.com> wrote: > >> Hi, >> >> Is there a way to do annotate streamlines and use get_multi_plot with yt >> 3.1? The single-plot example below works for me, but it doesn't work with >> this example of get_multi_plot (i.e. annotations are not carried over): >> >> http://yt-project.org/docs/3.1/cookbook/complex_plots.html#multipanel-with-… >> > > Hi Stella, > > With a bit of fiddling, I was able to get this to work in the latest > development version of yt, although I think it should work in 3.1 as well, > see: > > http://paste.yt-project.org/show/5532/ > > This is a bit tricky, since it depends sensitively on details of how > matplotlib stores imshow plots and that way we interface with that in the > streamline callback. > > It might be worthwhile to add a new cookbook script using this example - > we'd be very grateful for any docs improvements you might want to make! > > > >> >> Sorry if this was already answered in the mailing list archive somewhere, >> the user discussion archives is still unsearchable: >> Forbidden >> >> You don't have permission to access /pipermail/yt-users-spacepope.org/ >> on this server. >> > Additionally, a 404 Not Found error was encountered while trying to use an >> ErrorDocument to handle the request. >> > > This has come up a few times before although the lack of mailing list > archives might make that hard to discover! It's an issue with our ISP. Matt > has been sending them angry e-mails for a while now.... > > > -Nathan > > >> Thanks! >> Stella >> >> On Tue, Apr 28, 2015 at 9:05 AM, David Collins <dcollins4096(a)gmail.com> >> wrote: >> >>> Hi, Dominik-- >>> >>> What was the yt command you used to make the streamlines and generate >>> the error you sent? I used the following and it was successful: >>> >>> ds = yt.load('DD0004/data0004') >>> >>> proj = yt.ProjectionPlot(ds,2,'density') >>> >>> proj.annotate_streamlines('Bx','By') >>> >>> and it made this image: >>> http://imgur.com/eZQmqTB >>> Can you try the above and let me know if it works? >>> >>> d. >>> >>> >>> On Tue, Apr 28, 2015 at 2:58 AM, Dominik Derigs <derigs(a)ph1.uni-koeln.de >>> > wrote: >>> >>>> Hi together, >>>> >>>> I want to use yt for plotting magnetic field lines in FLASH simulations >>>> from 2D simulations and slices from 3D simulations. >>>> An example of what it could look like can be seen here: >>>> http://aprg.mae.ufl.edu/wp-content/uploads/2014/07/tang_51.png >>>> >>>> I tried to use yt's streamline function, but this does not work for me: >>>> http://yt-project.org/doc/visualizing/streamlines.html >>>> >>>> The error shown is: >>>> ValueError: operands could not be broadcast together with shapes >>>> (9,9,2) (9,9,95) (9,9,2) >>>> >>>> The used FLASH file is attached. >>>> >>>> Thanks a lot >>>> >>>> Dominik >>>> >>>> -- >>>> Dominik Derigs >>>> I. Physikalisches Institut >>>> Universität zu Köln >>>> Zülpicher Straße 77 >>>> 50937 Köln >>>> GERMANY >>>> >>>> Tel. (+49|0) 221 470-8352 >>>> Fax. (+49|0) 221 470-5162 >>>> >>>> Diese Email ist vertraulich und nur für den angegebenen Empfänger >>>> bestimmt. Zugang, Freigabe, die Kopie, die Verteilung oder Weiterleitung >>>> durch jemand anderen außer dem Empfänger selbst ist verboten und kann eine >>>> kriminelle Handlung sein. Bitte löschen Sie die Email, wenn Sie sie durch >>>> einen Fehler erhalten haben und informieren Sie den Absender. >>>> >>>> This email and any files transmitted with it may contain confidential >>>> and/or privileged material and is intended only for the person or entity to >>>> which it is addressed. Any review, retransmission, dissemination or other >>>> use of, or taking of any action in reliance upon, this information by >>>> persons or entities other than the intended recipient is prohibited. If you >>>> have received this email in error, please notify the sender immediately and >>>> delete this material from all known records. >>>> >>>> _______________________________________________ >>>> yt-users mailing list >>>> yt-users(a)lists.spacepope.org >>>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>>> >>>> >>> >>> >>> -- >>> -- Sent from a computer. >>> >>> _______________________________________________ >>> yt-users mailing list >>> yt-users(a)lists.spacepope.org >>> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >>> >>> >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Re: [yt-users] Plot 2D magnetic field lines
by Stella Offner May 4, 2015

May 4, 2015

Hi, Is there a way to do annotate streamlines and use get_multi_plot with yt 3.1? The single-plot example below works for me, but it doesn't work with this example of get_multi_plot (i.e. annotations are not carried over): http://yt-project.org/docs/3.1/cookbook/complex_plots.html#multipanel-with-… Sorry if this was already answered in the mailing list archive somewhere, the user discussion archives is still unsearchable: Forbidden You don't have permission to access /pipermail/yt-users-spacepope.org/ on this server. Additionally, a 404 Not Found error was encountered while trying to use an ErrorDocument to handle the request. Thanks! Stella On Tue, Apr 28, 2015 at 9:05 AM, David Collins <dcollins4096(a)gmail.com> wrote: > Hi, Dominik-- > > What was the yt command you used to make the streamlines and generate the > error you sent? I used the following and it was successful: > >>> ds = yt.load('DD0004/data0004') > >>> proj = yt.ProjectionPlot(ds,2,'density') > >>> proj.annotate_streamlines('Bx','By') > > and it made this image: > http://imgur.com/eZQmqTB > Can you try the above and let me know if it works? > > d. > > > On Tue, Apr 28, 2015 at 2:58 AM, Dominik Derigs <derigs(a)ph1.uni-koeln.de> > wrote: > >> Hi together, >> >> I want to use yt for plotting magnetic field lines in FLASH simulations >> from 2D simulations and slices from 3D simulations. >> An example of what it could look like can be seen here: >> http://aprg.mae.ufl.edu/wp-content/uploads/2014/07/tang_51.png >> >> I tried to use yt's streamline function, but this does not work for me: >> http://yt-project.org/doc/visualizing/streamlines.html >> >> The error shown is: >> ValueError: operands could not be broadcast together with shapes (9,9,2) >> (9,9,95) (9,9,2) >> >> The used FLASH file is attached. >> >> Thanks a lot >> >> Dominik >> >> -- >> Dominik Derigs >> I. Physikalisches Institut >> Universität zu Köln >> Zülpicher Straße 77 >> 50937 Köln >> GERMANY >> >> Tel. (+49|0) 221 470-8352 >> Fax. (+49|0) 221 470-5162 >> >> Diese Email ist vertraulich und nur für den angegebenen Empfänger >> bestimmt. Zugang, Freigabe, die Kopie, die Verteilung oder Weiterleitung >> durch jemand anderen außer dem Empfänger selbst ist verboten und kann eine >> kriminelle Handlung sein. Bitte löschen Sie die Email, wenn Sie sie durch >> einen Fehler erhalten haben und informieren Sie den Absender. >> >> This email and any files transmitted with it may contain confidential >> and/or privileged material and is intended only for the person or entity to >> which it is addressed. Any review, retransmission, dissemination or other >> use of, or taking of any action in reliance upon, this information by >> persons or entities other than the intended recipient is prohibited. If you >> have received this email in error, please notify the sender immediately and >> delete this material from all known records. >> >> _______________________________________________ >> yt-users mailing list >> yt-users(a)lists.spacepope.org >> http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org >> >> > > > -- > -- Sent from a computer. > > _______________________________________________ > yt-users mailing list > yt-users(a)lists.spacepope.org > http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org > > _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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PYTHONPATH
by mc knabbits May 3, 2015

May 3, 2015

hi everybody, this question aint very yt specific but more on the python way of treating its PATH variable. since having installed yt I have 2 versions of python on my machine. (the yt one and my previous 2.7.3 with the main scipy packages) I wonder how its possible to have each of them having its own PYTHONPATH variable? so when yt is activated it uses its yt path and when switched off the independend python install uses another. right now even when deactivated the first entry in the PPATH is the yt link to the yt python site packages where numpy etc is stored. but these packeges would not work with the original python version I may want to use as well so that I need to re-source my bashrc or restart the terminal... hope theres a solution to this thanx, phil _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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Pointing yt at a specific version of libstdc++
by Joshua Wall May 2, 2015

May 2, 2015

Hello users, I've installed yt locally under a local install of python2.7 on a local cluster to analyze data after runs. It was installed using a local version of pip, and I installed yt-3.1. However the cluster is running Centos6 which loads with gcc4.4.7 automatically. I have installed gcc4.8 alongside this. When I installed python and pip and yt, unfortunately I hadn't updated the enviromental variables to point at gcc4.8. So now when I load yt I get: ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /home/draco/jwall/usr/local/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/_tri.so) since gcc4.4 doesn't have GLIBCXX_3.4.15. Is there anyway to point yt at the later version of libstdc++ that I have with gcc4.8? Or do I have to reinstall (and if so how far back? Just yt? pip also? python?). Cordially, Joshua Wall _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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How to find densest point in subvolume of Gadget data
by Joseph Smidt May 2, 2015

May 2, 2015

Hey everyone, I am trying to find the densest point in Gadget data in the subvolume with left edge [700]*3 and right edge [800]*3 where 700 and 800 are in code units. This is what I do [1], which was inspired by this page [2], except I try and take the all_data confined to a region. The output [3] says however where you will note the center is not inside the region. It found the densest point in the whole data set, not the region. So how would I do this instead for a subvolume of Gadget data? Thanks. [1] http://pastebin.com/kyUgEi3a [2] http://yt-project.org/doc/cookbook/gadget_notebook.html [3] http://pastebin.com/E4aLb5VC -- ------------------------------------------------------------------------ Joseph Smidt <josephsmidt(a)gmail.com> Theoretical Division P.O. Box 1663, Mail Stop B283 Los Alamos, NM 87545 Office: 505-665-9752 Fax: 505-667-1931 _______________________________________________ yt-users mailing list yt-users(a)lists.spacepope.org http://lists.spacepope.org/listinfo.cgi/yt-users-spacepope.org

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