[yt-users] Loading RAMSES Data into yt.

k.grisdale at surrey.ac.uk k.grisdale at surrey.ac.uk
Wed Oct 30 11:58:56 PDT 2013


Hi Matt,

I updated yt and it now lets me input the data into yt. However when I try to plot a slice I get this error:

>>> slc = SlicePlot(pf, 'z', 'Density').save()
You are running with the wrong number of fields.
Please specify these in the load command.
We are looking for 6 fields.
The last set of field sizes was: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 16, 16, 16, 16, 16, 16]
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 2148, in SlicePlot
    return AxisAlignedSlicePlot(pf, normal, fields, *args, **kwargs)
  File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/visualization/plot_window.py", line 1320, in __init__
    slc.get_data(fields)
  File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/data_objects/data_containers.py", line 531, in get_data
    fluids, self, self._current_chunk)
  File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/geometry/geometry_handler.py", line 520, in _read_fluid_fields
    chunk_size)
  File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/io.py", line 41, in _read_fluid_selection
    rv = subset.fill(content, fields, selector)
  File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py", line 304, in fill
    for level, offset in enumerate(self.domain.hydro_offset):
  File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/ramses/data_structures.py", line 102, in hydro_offset
    hvals = fpu.read_attrs(f, header, "=")
  File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/fortran_utils.py", line 74, in read_attrs
    assert(s1 == s2)
AssertionError.

Is this related or a different problem?

Thanks

Kearn
On 30 Oct 2013, at 17:41, Matthew Turk <matthewturk at gmail.com> wrote:

> Hi Kearn,
> 
> Not a dumb question at all!  You should be able to run this command:
> 
> cd $YT_DEST/src/yt-hg
> hg pull -r tip http://bitbucket.org/yt_analysis/yt-3.0
> hg up -C yt-3.0
> 
> We do have a "yt update" command but I want to make sure it does
> precisely this, so it'd be best if you ran it.
> 
> -Matt
> 
> On Wed, Oct 30, 2013 at 1:37 PM,  <k.grisdale at surrey.ac.uk> wrote:
>> This is probably a dumb question but how do I update yt?
>> 
>> Thanks
>> Kearn
>> 
>>> On 30 Oct 2013, at 17:35, "Matthew Turk" <matthewturk at gmail.com> wrote:
>>> 
>>> Hi Kearn,
>>> 
>>> Did you update yt?  If so, it should have given at least a better error message.
>>> 
>>> cd $YT_DEST/src/yt-hg
>>> hg pull -r tip http://bitbucket.org/yt_analysis/yt-3.0
>>> hg up -C yt-3.0
>>> 
>>> 
>>> -Matt
>>> 
>>>> On Wed, Oct 30, 2013 at 1:29 PM,  <k.grisdale at surrey.ac.uk> wrote:
>>>> Hi,
>>>> 
>>>> I completed a new run in RAMSES using the new version of the code and go the same results again.
>>>> 
>>>>>>> from yt.mods import *
>>>>>>> pf =  load("output_00001/info_00001.txt") Traceback (most recent call last):
>>>> File "<stdin>", line 1, in <module>
>>>> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line 76, in load
>>>>   if c._is_valid(*args, **kwargs): candidates.append(n)
>>>> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/art/data_structures.py", line 427, in _is_valid
>>>>   amr_header_vals = read_attrs(fh, amr_header_struct, '>')
>>>> File "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/fortran_utils.py", line 62, in read_attrs
>>>>   vals = list(struct.unpack(net_format, f.read(size)))
>>>> struct.error: unpack requires a string argument of length 892
>>>> 
>>>> Is there anything else I can try?
>>>> 
>>>> Thanks
>>>> 
>>>> Kearn
>>>>> On 30 Oct 2013, at 17:02, Matthew Turk <matthewturk at gmail.com> wrote:
>>>>> 
>>>>> Hi Kearn,
>>>>> 
>>>>> I think Romain's suggestion is likely going to fix the issue, but I
>>>>> also just pushed a change that will show the error differently and in
>>>>> a more informative way.  ("hg pull
>>>>> http://bitbucket.org/yt_analysis/yt-3.0 && hg up" in your yt-hg
>>>>> directory will fix it.)
>>>>> 
>>>>> -Matt
>>>>> 
>>>>>> On Wed, Oct 30, 2013 at 12:39 PM,  <k.grisdale at surrey.ac.uk> wrote:
>>>>>> Hi,
>>>>>> 
>>>>>> I have been trying to load RAMSES data into yt 2.5. Orginaly it was loading
>>>>>> in but the graphs I was able to produce didn’t make sense.  So I tried to
>>>>>> change to yt3 using the commands
>>>>>> 
>>>>>> cd $YT_DEST/src/yt-hg/
>>>>>> hg pull http://bitbucket.org/yt_analysis/yt-3.0
>>>>>> hg up -C yt-3.0
>>>>>> python2.7 setup.py build_ext -i -f
>>>>>> 
>>>>>> The commands appear to have worked. But when I try to use yt to load in
>>>>>> RAMSES data I now get this error:
>>>>>> 
>>>>>> 
>>>>>> Traceback (most recent call last): File
>>>>>> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/gui/reason/basic_repl.py",
>>>>>> line 81, in execute exec code in self.locals File "", line 1, in File
>>>>>> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/convenience.py", line 76, in
>>>>>> load if c._is_valid(*args, **kwargs): candidates.append(n) File
>>>>>> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/frontends/art/data_structures.py",
>>>>>> line 427, in _is_valid amr_header_vals = read_attrs(fh, amr_header_struct,
>>>>>> '>') File
>>>>>> "/Applications/Code/yt/yt-x86_64/src/yt-hg/yt/utilities/fortran_utils.py",
>>>>>> line 62, in read_attrs vals = list(struct.unpack(net_format, f.read(size)))
>>>>>> error: unpack requires a string argument of length 892
>>>>>> 
>>>>>> 
>>>>>> Any idea what I need to do?
>>>>>> 
>>>>>> Thanks
>>>>>> 
>>>>>> Kearn
>>>>>> 
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