[yt-users] SlicePlot y-axis problem

Caroline Van Borm borm at astro.rug.nl
Tue Apr 23 03:13:27 PDT 2013


Hi Matt,

When I tried to build yt with everything set to default values, it was 
not possible to install HDF5. I had someone look at it for me and I 
don't know exactly what they did, but after rebuilding now everything is 
working properly. So I guess it really was a build problem.

Thank you for your help!

Cheers,
Caroline



On 04/18/2013 01:17 PM, Matthew Turk wrote:
> Hi Caroline,
>
> On Thu, Apr 18, 2013 at 6:29 AM, Caroline Van Borm<borm at astro.rug.nl>  wrote:
>> Hi Matthew,
>>
>> I tried both running it from a script and interactively (with iyt). I really
>> only used a minimum of code:
>>
>> from yt.mods import *
>> pf = EnzoStaticOutput("RD0007/RedshiftOutput0007")
>> #I also tried: pf = load("RD0007/RedshiftOutput0007")
>> SlicePlot(pf, 'y', 'Density').save()
>>
>> Sample data to run this on can be found on
>>
>> http://lca.ucsd.edu/software/enzo/data/cookbook/
>>
>> Just download and unpack any of the RD000* folders, for instance RD0007 for
>> the example code above.
>>
>> On the screen, after the SlicePlot command it says
>>
>> yt : [INFO     ] 2013-04-18 12:16:59,830 Getting the binary hierarchy
>> yt : [INFO     ] 2013-04-18 12:16:59,838 Finished with binary hierarchy
>> reading
>>
>> and there it hangs. Pressing Ctrl-C doesn't do anything, I have to kill the
>> process manually from another terminal.
> Interesting.  I've never seen this behavior, and particularly not in a
> way that biases one axis over another for slicing.  One thing we have
> put into yt is the ability to respond to signals like SIGUSR1 ; so if
> instead of "kill [pid]" you do "kill -SIGUSR1 [pid]" (where [pid] is
> the process id) it should -- the next time the event loop hits --
> output where in the python code it is.  But, if it's really hung, this
> probably won't do anything.
>
> Not responding to Ctrl-C indicates it's probably inside C code
> somewhere; a likely candidate for this is in the IO.  Another thing to
> try is this exact same script, but after you put these lines into
> ~/.yt/config
>
> [yt]
> loglevel: 1
>
> this will increase the level of logging, which will tell us a lot
> more.  Other scripts that use different patterns for data access may
> also be illuminating:
>
> pf = load( ... )
> dd = pf.h.all_data()
> print dd["Density"].min(), dd["Density"].max()
>
> for instance.
>
>> I installed yt using the installation script from the website, I don't think
>> I changed any of the settings, or anything after the installation. The only
>> thing I did before installing was "export CC=icc" to get HDF5 to install
>> properly.
> I'm hesitant to say this is a problem, but it may be.  This would mean
> that the entire stack has been built with icc, but possibly only for
> the C code, not the C++ code.  I've not seen a case in the past where
> HDF5 wouldn't compile with GNU (i.e., gcc) and there may be a point
> where matplotlib (C++ code internally) may not be interoperating well.
>   My gut feeling is that rebuilding from scratch with the default
> environment variables is the best bet, just for the purposes of
> reducing the number of possible issues, but I'm not sure.
>
> -Matt
>
>> Thank you very much!
>>
>> Cheers,
>> Caroline
>>
>>
>>
>> On 04/17/2013 01:42 PM, Matthew Turk wrote:
>>
>> Hi Caroline,
>>
>> Thanks for writing, and sorry that it's not working.  Don't worry too
>> much about sending the data.  I'm sorry to hear that it's hanging and
>> not responding, which isn't behavior we have often seen.  Here are a
>> couple questions that will help us figure out how things might have
>> gone wrong.
>>
>>   * Did you run this via a script that you wrote?  If you, could you
>> run the command:
>>
>> yt pastebin that_script.py
>>
>> where "that_script.py" is the filename?  That will give a URL, which
>> you can include in a reply so we can see it.
>>
>>   * What output do you see on screen up to the point where the execution
>> hangs?
>>   * How did you install yt?
>>   * Is there one particular piece of sample data that we can run the
>> script you paste'd (above) on to see the behavior?
>>   * Have you made any changes to your installation -- for instance, to
>> your matplotlib installation?
>>   * When it's hung, if you press Ctrl-C so that execution terminates,
>> what is output to the screen?  It should look like a traceback, where
>> various functions and routines are listed in order and at the bottom
>> it will say something like "KeyboardInterrupt"
>>
>> Thanks very much, and let's see if we can get this working for you.  :)
>>
>> -Matt
>>
>> On Wed, Apr 17, 2013 at 5:51 AM, Caroline Van Borm<borm at astro.rug.nl>
>> wrote:
>>
>> Hi Nathan,
>>
>> I used the Enzo code (version 2.2) and was just running some of the included
>> test problems. There is some example data available at
>> http://lca.ucsd.edu/software/enzo/data/cookbook/  (I believe this is from an
>> earlier version of Enzo), the plotting of which also results in the
>> described problem. This is the first time I'm using yt.
>>
>> Thanks,
>> Caroline
>>
>>
>>
>> On 04/16/2013 11:03 PM, Nathan Goldbaum wrote:
>>
>> Hi Caroline,
>>
>> Sorry to hear you're having trouble.
>>
>> Can you let us know what code generated the dataset you're trying to plot?
>> Have you been able to visualize data produced by this code in the past?
>>
>> If you feel comfortable sharing your data and if it is small enough to be
>> hosted on the web somewhere, it would be great if you could upload your
>> dataset and either reply with a link to the list or send it to me privately
>> so that one of us could try to take a look and see what exactly is going
>> wrong.  I understand that datasets can sometimes be sensitive, however it
>> can be slow and difficult to debug problems like this over e-mail.
>>
>> Cheers,
>>
>> Nathan
>>
>> On Apr 16, 2013, at 6:43 AM, Caroline Van Borm<borm at astro.rug.nl>   wrote:
>>
>> Dear yt users,
>>
>> I have a problem when trying to make a SlicePlot along the y-axis of any
>> data, for any field. yt just hangs and no plot is created. For the x- and
>> z-axes everything works fine, and a ProjectionPlot along the y-axis is also
>> not a problem.
>> I have tried updating yt and installing the current development version,
>> but to no avail.
>>
>> Any help is much appreciated!
>>
>> Best regards,
>> Caroline
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