[yt-users] Loading RAMSES Data into yt.

Matthew Turk matthewturk at gmail.com
Wed Oct 30 12:02:23 PDT 2013 

Yup, this looks like a field count issue.  It looks like you've got
n_fields != 6 -- you can specify this by supplying fields = [ ... ]
(where ... ius the list of fields) to your load() command.

On Wed, Oct 30, 2013 at 2:58 PM,  <k.grisdale at surrey.ac.uk> wrote:
> 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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