[Amr] yt inside paraview
Jorge Poco
jorge.poco at kitware.com
Fri Jun 10 15:59:45 EDT 2011
Hi Matt
I have written the StreamFieldHandler and StreamHandler to interact with
Paraview, but I have a couple of questions:
- parent_ids will be change by child masking, right?
- In the function __getitem__ of StreamFieldHandler, could be changed to
receive 2 parameter instead of 1?, these parameters would be index_gridand
field_name, and should return an numpy.array in 3D. In way it's done now
could work, but the array returned will be 1D, so, I think I could handle it
in __getitem__ and return the correct array.
The ProgrammableFilter filter is here http://paste.enzotools.org/show/1695/ I
was using the tests/DD0010/moving7_0010.hierarchy data set.
Regards,
On Fri, Jun 10, 2011 at 3:21 PM, Matthew Turk <matthewturk at gmail.com> wrote:
> As a quick note, the values should all differ by single multiplicative
> factor for each field.
>
> On Fri, Jun 10, 2011 at 12:19 PM, Matthew Turk <matthewturk at gmail.com>
> wrote:
> > Hi Jorge,
> >
> > Yup, we apply the unit conversions to get them back to CGS.
> > Temperature field takes no conversions.
> >
> > -Matt
> >
> > On Fri, Jun 10, 2011 at 12:18 PM, Jorge Poco <jorge.poco at kitware.com>
> wrote:
> >> HI Matt
> >> Another doubt: I'm using the tests/DD0010/moving7_0010 data set. I have
> >> tried to load it using YT and Paraview.
> >> The problem is that grid values are different in both tools except
> >> temperature field. I'm wondering if you
> >> do any conversions in the grid values when you load the data set.
> >> The code I'm using in yt is:
> >>>> pf = load('tests/DD0010/moving7_0010')
> >>>> pf.h.grids[0]['Density'].min()
> >>>> pf.h.grids[0]['Density'].max()
> >> Regards,
> >> On Fri, Jun 10, 2011 at 2:40 PM, George Zagaris <
> george.zagaris at kitware.com>
> >> wrote:
> >>>
> >>> That's great!
> >>>
> >>> Yes the vtkHierarchicalBoxDataSet has IBLANK information that
> >>> can be supplied directly to yt.
> >>>
> >>> Best,
> >>> George
> >>>
> >>> On Fri, Jun 10, 2011 at 2:37 PM, Matthew Turk <matthewturk at gmail.com>
> >>> wrote:
> >>> > Hi Jorge,
> >>> >
> >>> > Nope, it should not be mandatory, although it currently is. It is
> >>> > currently only used to calculate child masking, which I believe we
> can
> >>> > also get from vtkHierarchicalBoxDataSet? I'll make this change later
> >>> > today.
> >>> >
> >>> > -Matt
> >>> >
> >>> >
> >>> >
> >>> > On Fri, Jun 10, 2011 at 11:35 AM, Jorge Poco <jorge.poco at kitware.com
> >
> >>> > wrote:
> >>> >> HI Matt
> >>> >> Looks nice.
> >>> >> In the 'stream' frontends, when the stream.StreamHandler(...) is
> >>> >> create,
> >>> >> one parameter is the parent_ids right? It's really mandatory to send
> >>> >> it?
> >>> >> because the vtkHierarchicalBoxDataSet doesn't save this information,
> >>> >> but we
> >>> >> can compute the parent/child relations.
> >>> >> Regards,
> >>> >>
> >>> >> On Fri, Jun 10, 2011 at 2:19 PM, Matthew Turk <
> matthewturk at gmail.com>
> >>> >> wrote:
> >>> >>>
> >>> >>> Hi Jorge,
> >>> >>>
> >>> >>> I thought this might be of interest to you; I've started keeping
> track
> >>> >>> of how to interface with external codes such as ParaView here:
> >>> >>>
> >>> >>> http://hg.enzotools.org/yt/wiki/InterfacingWithYT
> >>> >>>
> >>> >>> I'll be updating this as need be with information about the
> in-memory
> >>> >>> datasets and so on.
> >>> >>>
> >>> >>> Best,
> >>> >>>
> >>> >>> Matt
> >>> >>>
> >>> >>> On Fri, May 27, 2011 at 2:08 PM, Matthew Turk <
> matthewturk at gmail.com>
> >>> >>> wrote:
> >>> >>> > Hi all,
> >>> >>> >
> >>> >>> > I've created a new data frontend in yt entitled "Stream" (the
> name
> >>> >>> > is
> >>> >>> > up for discussion, if someone has a better idea -- Charles
> pointed
> >>> >>> > out
> >>> >>> > today that it might get confused with time series data.) The
> idea
> >>> >>> > behind this is that the user can use it to construct an arbitrary
> >>> >>> > dataset in memory. I've tested this by proxying an existing Enzo
> >>> >>> > dataset:
> >>> >>> >
> >>> >>> >
> >>> >>> >
> >>> >>> >
> http://matthewturk.bitbucket.org/html/ba3fd37b-842c-4641-b21e-2d3f5268eefe-stream_proxy-py.html
> >>> >>> >
> >>> >>> > (downloadable at the top level domain, or by "yt_lodgeit.py
> >>> >>> > --download=1672 if you have a yt stack installed.)
> >>> >>> >
> >>> >>> > You have to construct both a StreamHandler that knows how to pass
> >>> >>> > around the grid geometry and which, although not instantiated
> with
> >>> >>> > them, requires certain attributes to be set. In addition, a
> fields
> >>> >>> > handler has to be created. This script executes to completion
> and
> >>> >>> > passes its tests; projecting and slicing require slightly more
> >>> >>> > effort,
> >>> >>> > because I wanted to pose to the Kitware group how the data should
> be
> >>> >>> > evaluated in terms of units -- should it be assumed to have CGS
> >>> >>> > units
> >>> >>> > already? How should the domain size be handled -- in yt right
> now
> >>> >>> > units are distinct from the code definitions, but I don't know
> how
> >>> >>> > Paraview handles this distinction. (If you want to try setting
> up a
> >>> >>> > PlotCollection, you can, but you will have to set spf.units["cm"]
> =
> >>> >>> > spf.units["unitary"] = 1.0).
> >>> >>> >
> >>> >>> > Hopefully this can be a start, and we can continue to iterate on
> the
> >>> >>> > API necessary to load data in yt from that already loaded in
> >>> >>> > Paraview.
> >>> >>> > This is in the tip of the development yt repository,
> 6d4a5588a550.
> >>> >>> >
> >>> >>> > Best,
> >>> >>> >
> >>> >>> > Matt
> >>> >>> >
> >>> >>> > On Thu, May 26, 2011 at 3:54 PM, Jorge Poco <
> jorge.poco at kitware.com>
> >>> >>> > wrote:
> >>> >>> >> In the meantime I will be working to import yt's data
> structures
> >>> >>> >> inside
> >>> >>> >> vtkHierarchicalBoxDataset using ProgrammableSources inside
> Python.
> >>> >>> >> Regards,
> >>> >>> >>
> >>> >>> >> On Thu, May 26, 2011 at 3:43 PM, Jorge Poco
> >>> >>> >> <jorge.poco at kitware.com>
> >>> >>> >> wrote:
> >>> >>> >>>
> >>> >>> >>> Hi
> >>> >>> >>> YT has some function to access the arrays data in numpy.array
> >>> >>> >>> objects
> >>> >>> >>> (
> >>> >>> >>> pf.h.grids[0]['Density']), using them we can instantiate a
> >>> >>> >>> vtkHierarchicalDataset to be process into paraview.
> >>> >>> >>> On Thu, May 26, 2011 at 2:53 PM, Berk Geveci
> >>> >>> >>> <berk.geveci at kitware.com>
> >>> >>> >>> wrote:
> >>> >>> >>>>
> >>> >>> >>>> Awesome.
> >>> >>> >>>>
> >>> >>> >>>> What about from the other side? If we wanted to pass data
> >>> >>> >>>> structures
> >>> >>> >>>> that yt loaded (from an Enzo file for example) to VTK/ParaView
> >>> >>> >>>> for
> >>> >>> >>>> filtering/rendering?
> >>> >>> >>>>
> >>> >>> >>>> -berk
> >>> >>> >>>>
> >>> >>> >>>> On Thu, May 26, 2011 at 2:04 PM, Matthew Turk
> >>> >>> >>>> <matthewturk at gmail.com>
> >>> >>> >>>> wrote:
> >>> >>> >>>> > Hi Berk and Jorge,
> >>> >>> >>>> >
> >>> >>> >>>> > Okay, this makes sense.
> >>> >>> >>>> >
> >>> >>> >>>> > I will write up a new code frontend for yt that will act as
> a
> >>> >>> >>>> > generalized system; this will draw upon the current in situ
> >>> >>> >>>> > Enzo
> >>> >>> >>>> > frontend, and will be designed to be instantiated with a
> list
> >>> >>> >>>> > of
> >>> >>> >>>> > arrays and a set of callback functions. We can them
> implement
> >>> >>> >>>> > the
> >>> >>> >>>> > paraview-specific code inside this, or perhaps inside a
> >>> >>> >>>> > ProgrammableFilter inside paraview itself. I'll ping the
> list
> >>> >>> >>>> > back
> >>> >>> >>>> > when I have something up and running.
> >>> >>> >>>> >
> >>> >>> >>>> > Best,
> >>> >>> >>>> >
> >>> >>> >>>> > Matt
> >>> >>> >>>> >
> >>> >>> >>>> > On Thu, May 26, 2011 at 9:15 AM, Berk Geveci
> >>> >>> >>>> > <berk.geveci at kitware.com>
> >>> >>> >>>> > wrote:
> >>> >>> >>>> >> In VTK, an AMR mesh is represented as a collection of
> >>> >>> >>>> >> vtkUniformGrid
> >>> >>> >>>> >> objects. Each vtkUniformGrid has a set of Fortran-ordered
> data
> >>> >>> >>>> >> arrays
> >>> >>> >>>> >> that represent the variables. One exception is how vectors
> are
> >>> >>> >>>> >> stored.
> >>> >>> >>>> >> They are stored in hybrid Fortran - C ordering, i.e. vector
> >>> >>> >>>> >> component
> >>> >>> >>>> >> increases fastest then i, then j, then k. It is
> >>> >>> >>>> >> straightforward to
> >>> >>> >>>> >> pass these to Python and back using NumPy arrays or buffer
> >>> >>> >>>> >> objects
> >>> >>> >>>> >> at
> >>> >>> >>>> >> the lowest level. So we can write Python code to bundle
> these
> >>> >>> >>>> >> arrays
> >>> >>> >>>> >> into any form that yt (and Enzo when we start doing
> in-situ)
> >>> >>> >>>> >> wants. We
> >>> >>> >>>> >> may have to deep-copy the vectors because of the issue I
> >>> >>> >>>> >> described.
> >>> >>> >>>> >>
> >>> >>> >>>> >> On Wed, May 25, 2011 at 7:59 PM, Matthew Turk
> >>> >>> >>>> >> <matthewturk at gmail.com>
> >>> >>> >>>> >> wrote:
> >>> >>> >>>> >>> Hi Jorge,
> >>> >>> >>>> >>>
> >>> >>> >>>> >>> This is really cool!
> >>> >>> >>>> >>>
> >>> >>> >>>> >>> I've been thinking about how to invert this process, and I
> >>> >>> >>>> >>> think
> >>> >>> >>>> >>> we
> >>> >>> >>>> >>> could address it by creating a new hierarchy of objects,
> >>> >>> >>>> >>> similar
> >>> >>> >>>> >>> to
> >>> >>> >>>> >>> the EnzoStaticOutputInMemory family of objects, that
> enables
> >>> >>> >>>> >>> a
> >>> >>> >>>> >>> bi-directional transfer of information. All that's really
> >>> >>> >>>> >>> necessary
> >>> >>> >>>> >>> to get data in is to describe the mesh, describe the
> >>> >>> >>>> >>> parameters
> >>> >>> >>>> >>> of
> >>> >>> >>>> >>> the
> >>> >>> >>>> >>> simulation, and then communicate to yt how to access data.
> >>> >>> >>>> >>>
> >>> >>> >>>> >>> What do you think the best mechanism for passing data back
> >>> >>> >>>> >>> and
> >>> >>> >>>> >>> forth
> >>> >>> >>>> >>> is? For in situ viz with Enzo, usually we do this by
> >>> >>> >>>> >>> constructing a
> >>> >>> >>>> >>> new module object in the C code, and then insert into that
> a
> >>> >>> >>>> >>> set
> >>> >>> >>>> >>> of
> >>> >>> >>>> >>> arrays describing the mesh and a dictionary of
> dictionaries
> >>> >>> >>>> >>> of
> >>> >>> >>>> >>> fields,
> >>> >>> >>>> >>> with keys that correspond to grid id and field name. But
> >>> >>> >>>> >>> really,
> >>> >>> >>>> >>> it
> >>> >>> >>>> >>> could be any system, and I'm happy to work on constructing
> >>> >>> >>>> >>> the
> >>> >>> >>>> >>> methods
> >>> >>> >>>> >>> to set this up.
> >>> >>> >>>> >>>
> >>> >>> >>>> >>> Best,
> >>> >>> >>>> >>>
> >>> >>> >>>> >>> Matt
> >>> >>> >>>> >>>
> >>> >>> >>>> >>> On Wed, May 25, 2011 at 5:54 PM, Jorge Poco
> >>> >>> >>>> >>> <jorge.poco at kitware.com>
> >>> >>> >>>> >>> wrote:
> >>> >>> >>>> >>>> Hi Matthew and Berk
> >>> >>> >>>> >>>>
> >>> >>> >>>> >>>> the full stack is
> >>> >>> >>>> >>>> here http://paste.enzotools.org/show/1668/ I'm
> >>> >>> >>>> >>>> trying to
> >>> >>> >>>> >>>> compile paraview with the VTK_USE_SYSTEM_HDF5 but It's
> >>> >>> >>>> >>>> giving me
> >>> >>> >>>> >>>> some
> >>> >>> >>>> >>>> errors, I will try again tomorrow.
> >>> >>> >>>> >>>>
> >>> >>> >>>> >>>> Matthew: Right now, I have written a 'programmable
> source'
> >>> >>> >>>> >>>> script to
> >>> >>> >>>> >>>> read a
> >>> >>> >>>> >>>> file from the system using the yt function 'load'. Then,
> >>> >>> >>>> >>>> create
> >>> >>> >>>> >>>> a
> >>> >>> >>>> >>>> projection
> >>> >>> >>>> >>>> using yt and then the ProjectionPlot object is converted
> >>> >>> >>>> >>>> into a
> >>> >>> >>>> >>>> vtkImageData
> >>> >>> >>>> >>>> to be displayed into paraview.
> >>> >>> >>>> >>>> What I want to do now, is to read a Dataset using
> paraview,
> >>> >>> >>>> >>>> then
> >>> >>> >>>> >>>> create a
> >>> >>> >>>> >>>> 'programmable filter' script to convert the data set into
> >>> >>> >>>> >>>> yt's
> >>> >>> >>>> >>>> data
> >>> >>> >>>> >>>> structure to create a visualization and finally display
> the
> >>> >>> >>>> >>>> image
> >>> >>> >>>> >>>> inside
> >>> >>> >>>> >>>> paraview. What would be the correct way to create yt
> objects
> >>> >>> >>>> >>>> (EnzoHierarchy
> >>> >>> >>>> >>>> and EnzoGrid)?
> >>> >>> >>>> >>>>
> >>> >>> >>>> >>>> Berk: I was trying to find a way to get access to camera
> >>> >>> >>>> >>>> information
> >>> >>> >>>> >>>> from
> >>> >>> >>>> >>>> the 'programmable filter' to send this information to yt
> >>> >>> >>>> >>>> but I
> >>> >>> >>>> >>>> didn't found
> >>> >>> >>>> >>>> anything useful. Is it possible?
> >>> >>> >>>> >>>>
> >>> >>> >>>> >>>>
> >>> >>> >>>> >>>> Regards,
> >>> >>> >>>> >>>>
> >>> >>> >>>> >>>> On Wed, May 25, 2011 at 3:10 PM, Berk Geveci
> >>> >>> >>>> >>>> <berk.geveci at kitware.com>
> >>> >>> >>>> >>>> wrote:
> >>> >>> >>>> >>>>>
> >>> >>> >>>> >>>>> If I understood what Matt is saying, the problem may be
> >>> >>> >>>> >>>>> fixed
> >>> >>> >>>> >>>>> by
> >>> >>> >>>> >>>>> having ParaView use an external HDF5, the one that yt
> uses.
> >>> >>> >>>> >>>>> I
> >>> >>> >>>> >>>>> believe
> >>> >>> >>>> >>>>> that the variable is something like
> >>> >>> >>>> >>>>> PARAVIEW_USE_SYSTEM_HDF5
> >>> >>> >>>> >>>>> (or
> >>> >>> >>>> >>>>> VTK_,
> >>> >>> >>>> >>>>> not sure) in CMake.
> >>> >>> >>>> >>>>>
> >>> >>> >>>> >>>>> On Wed, May 25, 2011 at 10:49 AM, Matthew Turk
> >>> >>> >>>> >>>>> <matthewturk at gmail.com>
> >>> >>> >>>> >>>>> wrote:
> >>> >>> >>>> >>>>> > Hi Jorge,
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> > Wow, I didn't know that YT-embedding had taken off
> quite
> >>> >>> >>>> >>>>> > so
> >>> >>> >>>> >>>>> > much!
> >>> >>> >>>> >>>>> > This is great news.
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> > On Wed, May 25, 2011 at 9:48 AM, Jorge Poco
> >>> >>> >>>> >>>>> > <jorge.poco at kitware.com>
> >>> >>> >>>> >>>>> > wrote:
> >>> >>> >>>> >>>>> >> Hi
> >>> >>> >>>> >>>>> >> sorry my last email was sent incomplete
> >>> >>> >>>> >>>>> >> I have been trying to use YT inside the Paraview's
> >>> >>> >>>> >>>>> >> python
> >>> >>> >>>> >>>>> >> shell.
> >>> >>> >>>> >>>>> >> Initially I
> >>> >>> >>>> >>>>> >> have had some problems which are now identified. It
> is
> >>> >>> >>>> >>>>> >> not
> >>> >>> >>>> >>>>> >> the
> >>> >>> >>>> >>>>> >> best
> >>> >>> >>>> >>>>> >> solution but I at least solve temporally these
> problems:
> >>> >>> >>>> >>>>> >>
> >>> >>> >>>> >>>>> >> argv problem:
> >>> >>> >>>> >>>>> >>
> >>> >>> >>>> >>>>> >> Sentence: 'from yt.mods import *'
> >>> >>> >>>> >>>>> >> Error: for any reason paraview's python shell has not
> >>> >>> >>>> >>>>> >> defined
> >>> >>> >>>> >>>>> >> the
> >>> >>> >>>> >>>>> >> variable
> >>> >>> >>>> >>>>> >> 'sys.argv'
> >>> >>> >>>> >>>>> >> Temporal solution: comment yt code where the sys.argv
> >>> >>> >>>> >>>>> >> variable
> >>> >>> >>>> >>>>> >> is used:
> >>> >>> >>>> >>>>> >>
> >>> >>> >>>> >>>>> >> yt/funcs.py: lines 439-453
> >>> >>> >>>> >>>>> >>
> >>> >>> >>>> >>>>> >>
> yt/utilities/parallel_tools/parallel_analysis_interface.py:
> >>> >>> >>>> >>>>> >> lines 47
> >>> >>> >>>> >>>>> >> and 48
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> > We can likely get around this on the yt side, although
> >>> >>> >>>> >>>>> > when
> >>> >>> >>>> >>>>> > embedding
> >>> >>> >>>> >>>>> > yt in Enzo we've escaped this by using the command
> >>> >>> >>>> >>>>> > PySys_SetArgv(argc,
> >>> >>> >>>> >>>>> > argv) immediately after calling Py_Initialize. Does
> >>> >>> >>>> >>>>> > Partiview
> >>> >>> >>>> >>>>> > report
> >>> >>> >>>> >>>>> > a different executable name, by any chance? If so we
> can
> >>> >>> >>>> >>>>> > use
> >>> >>> >>>> >>>>> > that as
> >>> >>> >>>> >>>>> > a signal to avoid requesting argv.
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> >>
> >>> >>> >>>> >>>>> >> :
> >>> >>> >>>> >>>>> >>
> >>> >>> >>>> >>>>> >> Sentence: "pf = load('tests/DD0010/moving7_0010')"
> >>> >>> >>>> >>>>> >> Error: python shell does not complete the load
> function
> >>> >>> >>>> >>>>> >> and
> >>> >>> >>>> >>>>> >> paraview
> >>> >>> >>>> >>>>> >> keeps
> >>> >>> >>>> >>>>> >> waiting.
> >>> >>> >>>> >>>>> >> Temporal solution: When I debug paraview and
> interrupt
> >>> >>> >>>> >>>>> >> its
> >>> >>> >>>> >>>>> >> execution
> >>> >>> >>>> >>>>> >> the
> >>> >>> >>>> >>>>> >> backtrace shows sem_wait(). It happens inside the
> load
> >>> >>> >>>> >>>>> >> function
> >>> >>> >>>> >>>>> >> when
> >>> >>> >>>> >>>>> >> tries
> >>> >>> >>>> >>>>> >> to identify the candidates for input file
> >>> >>> >>>> >>>>> >> (convenience.py
> >>> >>> >>>> >>>>> >> line
> >>> >>> >>>> >>>>> >> 74).
> >>> >>> >>>> >>>>> >> There
> >>> >>> >>>> >>>>> >> are 11 possible candidates and gives error for 2 of
> >>> >>> >>>> >>>>> >> them:
> >>> >>> >>>> >>>>> >> ChomboStaticOutput
> >>> >>> >>>> >>>>> >> and FlashStaticOutput. Skipping those candidates
> solve
> >>> >>> >>>> >>>>> >> temporally the
> >>> >>> >>>> >>>>> >> problem: (yt/convenienve.py line 75) inside the loop
> >>> >>> >>>> >>>>> >> add if
> >>> >>> >>>> >>>>> >> n ==
> >>> >>> >>>> >>>>> >> 'ChomboStaticOutput' or n == 'FlashStaticOutput':
> >>> >>> >>>> >>>>> >> continue;
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> > This is interesting. What those two routines have in
> >>> >>> >>>> >>>>> > common
> >>> >>> >>>> >>>>> > is
> >>> >>> >>>> >>>>> > that
> >>> >>> >>>> >>>>> > they are the only two that try opening the file using
> >>> >>> >>>> >>>>> > h5py.
> >>> >>> >>>> >>>>> > HDF5
> >>> >>> >>>> >>>>> > has
> >>> >>> >>>> >>>>> > a number of error handling routines, which in the past
> >>> >>> >>>> >>>>> > I've
> >>> >>> >>>> >>>>> > seen
> >>> >>> >>>> >>>>> > issues with when embedding one app in another -- h5py
> for
> >>> >>> >>>> >>>>> > instance
> >>> >>> >>>> >>>>> > handles error handling, but that can conflict with
> other
> >>> >>> >>>> >>>>> > mechanisms
> >>> >>> >>>> >>>>> > that are attempting to handle those errors.
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> > Another solution that would avoid digging into the
> source
> >>> >>> >>>> >>>>> > code
> >>> >>> >>>> >>>>> > would
> >>> >>> >>>> >>>>> > be to remove the types from the actual type registry:
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> > from yt.convenience import output_type_registry
> >>> >>> >>>> >>>>> > del output_type_registry["ChomboStaticOutput"]
> >>> >>> >>>> >>>>> > del output_type_registry["FlashStaticOutput"]
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> > I'm more interested in figuring out how to fix the
> >>> >>> >>>> >>>>> > interplay
> >>> >>> >>>> >>>>> > between
> >>> >>> >>>> >>>>> > hdf5-paraview and h5py, though. Do you happen to have
> a
> >>> >>> >>>> >>>>> > full
> >>> >>> >>>> >>>>> > stack
> >>> >>> >>>> >>>>> > trace?
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> > Thanks very much for these reports -- this is very
> >>> >>> >>>> >>>>> > exciting,
> >>> >>> >>>> >>>>> > and
> >>> >>> >>>> >>>>> > I'm
> >>> >>> >>>> >>>>> > eager to help out!
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> > Best,
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> > Matt
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> >>
> >>> >>> >>>> >>>>> >> Any of you have a better way to solve the problems
> >>> >>> >>>> >>>>> >> above?
> >>> >>> >>>> >>>>> >> Regards,
> >>> >>> >>>> >>>>> >> On Wed, May 25, 2011 at 9:43 AM, Jorge Poco
> >>> >>> >>>> >>>>> >> <jorge.poco at kitware.com>
> >>> >>> >>>> >>>>> >> wrote:
> >>> >>> >>>> >>>>> >>>
> >>> >>> >>>> >>>>> >>> Hi
> >>> >>> >>>> >>>>> >>> I have been trying to use YT inside the Paraview's
> >>> >>> >>>> >>>>> >>> python
> >>> >>> >>>> >>>>> >>> shell.
> >>> >>> >>>> >>>>> >>> Initially
> >>> >>> >>>> >>>>> >>> I have had some problems which are now identified.
> It
> >>> >>> >>>> >>>>> >>> is
> >>> >>> >>>> >>>>> >>> not
> >>> >>> >>>> >>>>> >>> the
> >>> >>> >>>> >>>>> >>> smart solution but I at least solve temporally these
> >>> >>> >>>> >>>>> >>> problems:
> >>> >>> >>>> >>>>> >>>
> >>> >>> >>>> >>>>> >>> argv problem:
> >>> >>> >>>> >>>>> >>>
> >>> >>> >>>> >>>>> >>> Sentence: 'from yt.mods import *'
> >>> >>> >>>> >>>>> >>> Error: for any reason paraview's python shell has
> not
> >>> >>> >>>> >>>>> >>> defined
> >>> >>> >>>> >>>>> >>> the
> >>> >>> >>>> >>>>> >>> variable
> >>> >>> >>>> >>>>> >>> 'sys.argv'
> >>> >>> >>>> >>>>> >>> Temporal solution: comment yt code where the
> sys.argv
> >>> >>> >>>> >>>>> >>> variable
> >>> >>> >>>> >>>>> >>> is
> >>> >>> >>>> >>>>> >>> used:
> >>> >>> >>>> >>>>> >>>
> >>> >>> >>>> >>>>> >>> yt/funcs.py: lines 439-453
> >>> >>> >>>> >>>>> >>>
> >>> >>> >>>> >>>>> >>>
> yt/utilities/parallel_tools/parallel_analysis_interface.py:
> >>> >>> >>>> >>>>> >>> lines 47
> >>> >>> >>>> >>>>> >>> and
> >>> >>> >>>> >>>>> >>> 48
> >>> >>> >>>> >>>>> >>>
> >>> >>> >>>> >>>>> >>> pa:
> >>> >>> >>>> >>>>> >>>
> >>> >>> >>>> >>>>> >>> Sentence: "pf = load('tests/DD0010/moving7_0010')"
> >>> >>> >>>> >>>>> >>> Error: python shell does not complete the load
> function
> >>> >>> >>>> >>>>> >>> and
> >>> >>> >>>> >>>>> >>> paraview
> >>> >>> >>>> >>>>> >>> keeps
> >>> >>> >>>> >>>>> >>> waiting.
> >>> >>> >>>> >>>>> >>> Temporal solution: When I debug paraview and
> interrupt
> >>> >>> >>>> >>>>> >>> its
> >>> >>> >>>> >>>>> >>> execution
> >>> >>> >>>> >>>>> >>> the
> >>> >>> >>>> >>>>> >>> backtrace shows sem_wait(). It happens inside the
> load
> >>> >>> >>>> >>>>> >>> function
> >>> >>> >>>> >>>>> >>> when
> >>> >>> >>>> >>>>> >>> tries
> >>> >>> >>>> >>>>> >>> to identify the candidates for input file
> >>> >>> >>>> >>>>> >>> (convenience.py
> >>> >>> >>>> >>>>> >>> line
> >>> >>> >>>> >>>>> >>> 74).
> >>> >>> >>>> >>>>> >>> There
> >>> >>> >>>> >>>>> >>> are 11 possible candidates and gives error for 2 of
> >>> >>> >>>> >>>>> >>> them:
> >>> >>> >>>> >>>>> >>> ChomboStaticOutput
> >>> >>> >>>> >>>>> >>> and FlashStaticOutput. Skipping those candidates
> solve
> >>> >>> >>>> >>>>> >>> temporally the
> >>> >>> >>>> >>>>> >>> problem:
> >>> >>> >>>> >>>>> >>
> >>> >>> >>>> >>>>> >>
> >>> >>> >>>> >>>>> >> _______________________________________________
> >>> >>> >>>> >>>>> >> Amr mailing list
> >>> >>> >>>> >>>>> >> Amr at public.kitware.com
> >>> >>> >>>> >>>>> >>
> http://public.kitware.com/cgi-bin/mailman/listinfo/amr
> >>> >>> >>>> >>>>> >>
> >>> >>> >>>> >>>>> >>
> >>> >>> >>>> >>>>> > _______________________________________________
> >>> >>> >>>> >>>>> > Amr mailing list
> >>> >>> >>>> >>>>> > Amr at public.kitware.com
> >>> >>> >>>> >>>>> >
> http://public.kitware.com/cgi-bin/mailman/listinfo/amr
> >>> >>> >>>> >>>>> >
> >>> >>> >>>> >>>>> _______________________________________________
> >>> >>> >>>> >>>>> Amr mailing list
> >>> >>> >>>> >>>>> Amr at public.kitware.com
> >>> >>> >>>> >>>>> http://public.kitware.com/cgi-bin/mailman/listinfo/amr
> >>> >>> >>>> >>>>
> >>> >>> >>>> >>>>
> >>> >>> >>>> >>>> _______________________________________________
> >>> >>> >>>> >>>> Amr mailing list
> >>> >>> >>>> >>>> Amr at public.kitware.com
> >>> >>> >>>> >>>> http://public.kitware.com/cgi-bin/mailman/listinfo/amr
> >>> >>> >>>> >>>>
> >>> >>> >>>> >>>>
> >>> >>> >>>> >>> _______________________________________________
> >>> >>> >>>> >>> Amr mailing list
> >>> >>> >>>> >>> Amr at public.kitware.com
> >>> >>> >>>> >>> http://public.kitware.com/cgi-bin/mailman/listinfo/amr
> >>> >>> >>>> >>>
> >>> >>> >>>> >>
> >>> >>> >>>> > _______________________________________________
> >>> >>> >>>> > Amr mailing list
> >>> >>> >>>> > Amr at public.kitware.com
> >>> >>> >>>> > http://public.kitware.com/cgi-bin/mailman/listinfo/amr
> >>> >>> >>>> >
> >>> >>> >>>> _______________________________________________
> >>> >>> >>>> Amr mailing list
> >>> >>> >>>> Amr at public.kitware.com
> >>> >>> >>>> http://public.kitware.com/cgi-bin/mailman/listinfo/amr
> >>> >>> >>>
> >>> >>> >>
> >>> >>> >>
> >>> >>> >
> >>> >>> _______________________________________________
> >>> >>> Amr mailing list
> >>> >>> Amr at public.kitware.com
> >>> >>> http://public.kitware.com/cgi-bin/mailman/listinfo/amr
> >>> >>
> >>> >>
> >>> > _______________________________________________
> >>> > Amr mailing list
> >>> > Amr at public.kitware.com
> >>> > http://public.kitware.com/cgi-bin/mailman/listinfo/amr
> >>> >
> >>> _______________________________________________
> >>> Amr mailing list
> >>> Amr at public.kitware.com
> >>> http://public.kitware.com/cgi-bin/mailman/listinfo/amr
> >>
> >>
> >
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://public.kitware.com/pipermail/amr/attachments/20110610/a88a6f2b/attachment-0001.htm>
More information about the Amr
mailing list