[Paraview] Status of BoxLib AMR reader

Wed Sep 7 09:08:42 EDT 2016

Tim,
Sorry, no I didn't get a chance to look at it yet.

Utkarsh

On Tue, Sep 6, 2016 at 2:52 PM, Gallagher, Timothy P <
tim.gallagher at gatech.edu> wrote:

> Hi Utkarsh,
>
>
> Have you had a chance to take a look at this yet? I will have some time
> later this week to pick it back up -- just wanted to check if there was
> anything new about it before I dove back in.
>
>
> Thanks,
>
>
> Tim
>
>
> ------------------------------
> *From:* Utkarsh Ayachit <utkarsh.ayachit at kitware.com>
> *Sent:* Tuesday, August 30, 2016 7:51 AM
>
> *To:* Gallagher, Timothy P
> *Cc:* paraview at paraview.org
> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>
> Thanks, Tim. I'll take a look in next few days.
>
> Utkarsh
>
> On Mon, Aug 29, 2016 at 4:12 PM, Gallagher, Timothy P <
> tim.gallagher at gatech.edu> wrote:
>
>> I have to throw in the towel on this one for now and get back to some
>> other deadlines... but, I put what I have so far online and created a merge
>> request with information about the error and an example dataset attached.
>>
>>
>> Hopefully somebody better with VTK than I am can take a look and figure
>> out what I'm missing. I tried comparing the files for Chombo against the
>> original Visit source files to see if any special modifications were
>> required and none are (the only changes are HDF5 related). It looks like
>> the Chombo reader is from Visit 2.7.0 -- the Boxlib files I added are from
>> 2.10.3, but I tried it with the Boxlib reader from Visit 2.7.0 also and
>> it's the same issue.
>>
>>
>> If anybody has a chance to take a look, I'd appreciate it. Hopefully it's
>> something simple. If not, I'll try to pick it back up in a few days. I
>> apologize for the hacked CMakeLists to link against the library, I will fix
>> it to do it properly once everything else works!
>>
>> Tim
>>
>>
>> ------------------------------
>> *From:* ParaView <paraview-bounces at paraview.org> on behalf of Gallagher,
>> Timothy P <tim.gallagher at gatech.edu>
>> *Sent:* Monday, August 29, 2016 12:41 PM
>>
>> *To:* Utkarsh Ayachit
>> *Cc:* paraview at paraview.org
>> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>>
>>
>> Thanks for the quick response, the case didn't match between the two
>> files and that was the issue. I'm able to use the reader to select the file
>> and it sees the names of the variables in it properly, but when I hit Apply
>> it throws:
>>
>>
>> ERROR: In /data4/PVBoxLibTest/paraview/VTK/Common/DataModel/vtkAMRInformation.cxx,
>> line 573
>> vtkAMRInformation (0x44210f0): Invalid grid description for a
>> vtkUniformGrid
>>
>>
>> I have a feeling this might get beyond my paraview knowledge to fix.
>>
>>
>> One potential source of the problem -- what version of Visit are the
>> other readers pulled from? I have the Boxlib files from the latest version,
>> but looking at some of the other readers, they are from older versions.
>>
>> The latest date I see in the copyright for existing readers is 2013 and
>> looking through the Visit Release notes, the last release in 2013 says it
>> was upgraded to use VTK-6.0.
>>
>>
>> Is it possible the bridge is based on Visit before that major VTK upgrade
>> and I need to pull the reader code from a version earlier than that?
>>
>>
>> Thanks for your help. If I can't find something I know how to fix soon, I
>> can create a merge request and see if anybody else can get it the rest of
>> the way.
>>
>>
>> Tim
>>
>> ------------------------------
>> *From:* Utkarsh Ayachit <utkarsh.ayachit at kitware.com>
>> *Sent:* Monday, August 29, 2016 12:17 PM
>> *To:* Gallagher, Timothy P
>> *Cc:* paraview at paraview.org
>> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>>
>> Tim,
>>
>> It doesn't know what the class is. Multiple things could have gone wrong:
>> 1. is there call to ADD_VISIT_READER() for the new reader?
>> 2. does the case match between the XML's class="" and the name specified
>> in 1?
>>
>> If it makes it easier, create a MR on the https://gitlab.kitware.com
>> /paraview/visitbridge repo with your changes, and I can do the necessary
>> fixes.
>> <https://gitlab.kitware.com/paraview/visitbridge>
>> ParaView / VisItBridge <https://gitlab.kitware.com/paraview/visitbridge>
>> gitlab.kitware.com
>> Bridge between VisIt and ParaView to use VisIt readers in ParaView.
>>
>> Utkarsh
>>
>> On Mon, Aug 29, 2016 at 12:06 PM, Gallagher, Timothy P <
>> tim.gallagher at gatech.edu> wrote:
>>
>>> Utkarash,
>>>
>>>
>>> Thanks, I had added it to the xml file, but I didn't reconfigure (just
>>> rebuilt) so it didn't get added to the list.
>>>
>>>
>>> I'm making some progress it seems, it is picking the right reader now.
>>> But it is crashing with a rather unhelpful message:
>>>
>>>
>>> ERROR: In /data4/PVBoxLibTest/paraview/ParaViewCore/ServerImplementation/Core/vtkSIProxy.cxx,
>>> line 310
>>> vtkSISourceProxy (0x3e87420): Failed to create vtkVisItBoxlib2DReader.
>>> Aborting for debugging purposes.
>>>
>>> I thought compiling with a Debug build type would give more verbose
>>> messages, but it's the same.
>>>
>>>
>>> Is there documentation or suggestions on debugging paraview? Is there a
>>> way to get more verbose output on why it isn't able to create the reader?
>>>
>>>
>>> Thanks again,
>>>
>>>
>>> Tim
>>>
>>> ------------------------------
>>> *From:* Utkarsh Ayachit <utkarsh.ayachit at kitware.com>
>>> *Sent:* Monday, August 29, 2016 8:46 AM
>>>
>>> *To:* Gallagher, Timothy P
>>> *Cc:* paraview at paraview.org
>>> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>>>
>>> Tim,
>>>
>>> Did you also add it to visit_readers.xml [1]? The proxy definition
>>> should also have a  <hints> section like so [2].
>>>
>>> Utkarsh
>>>
>>> [1] https://gitlab.kitware.com/paraview/visitbridge/blob/mas
>>> ter/databases/visit_readers.xml
>>> [2] https://gitlab.kitware.com/paraview/visitbridge/blob/mas
>>> ter/databases/visit_readers.xml#L2562-2565
>>>
>>>
>>>
>>> On Fri, Aug 26, 2016 at 6:26 PM, Gallagher, Timothy P <
>>> tim.gallagher at gatech.edu> wrote:
>>>
>>>> I took a stab at adding the Boxlib reader from the visit source to the
>>>> VisitBridge internal readers. I managed to get everything to compile and
>>>> link, Paraview built fine, but I can't seem to figure out how to make
>>>> Paraview aware the reader exists.
>>>>
>>>>
>>>> There isn't an option for Boxlib in the dropdown for the file type when
>>>> I try to open a file, and it doesn't appear as an available reader when I
>>>> try to select the file -- although all the others from the VisitBridge
>>>> appear. I missed a configuration file somewhere to make the file loading
>>>> aware of the reader.
>>>>
>>>>
>>>> Any suggestions on what I missed? I added a section in the
>>>> Utilities/VisItBridge/databases/visit_readers.xml file, but that
>>>> wasn't enough I guess.
>>>>
>>>>
>>>> Thanks,
>>>>
>>>>
>>>> Tim
>>>>
>>>>
>>>> ------------------------------
>>>> *From:* ParaView <paraview-bounces at paraview.org> on behalf of
>>>> Gallagher, Timothy P <tim.gallagher at gatech.edu>
>>>> *Sent:* Friday, August 26, 2016 11:53 AM
>>>> *To:* Utkarsh Ayachit
>>>>
>>>> *Cc:* paraview at paraview.org
>>>> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>>>>
>>>>
>>>> Hi Utkarsh,
>>>>
>>>>
>>>> I just checked with the latest head of the git repo and when I compile
>>>> with the VisitBridge, there are no readers for BoxLib built.
>>>>
>>>>
>>>> This page lists it as supported: http://www.paraview.org/ParaVi
>>>> ew/index.php/VisIt_avt_Integration
>>>>
>>>>
>>>> But then this later one doesn't include it: http://www.paraview.org/Wi
>>>> ki/VisIt_Database_Bridge
>>>>
>>>>
>>>> I have a dataset for you, I will send it off-list.
>>>>
>>>>
>>>> Thanks,
>>>>
>>>>
>>>> Tim
>>>>
>>>>
>>>> ------------------------------
>>>> *From:* Utkarsh Ayachit <utkarsh.ayachit at kitware.com>
>>>> *Sent:* Friday, August 26, 2016 8:35 AM
>>>> *To:* Gallagher, Timothy P
>>>> *Cc:* paraview at paraview.org
>>>> *Subject:* Re: [Paraview] Status of BoxLib AMR reader
>>>>
>>>> Tim,
>>>>
>>>> I am not exactly sure what's the status of the reader, but I can
>>>> certainly look it up. Do you have a sample dataset also to test that
>>>> it's working (or not)?
>>>>
>>>> Utkarsh
>>>>
>>>> On Thu, Aug 25, 2016 at 2:22 PM, Gallagher, Timothy P
>>>> <tim.gallagher at gatech.edu> wrote:
>>>> > Hi,
>>>> >
>>>> >
>>>> > Our code is moving away from traditional structured grids towards an
>>>> AMR
>>>> > capability using BoxLib. That means, unfortunately, that all of the
>>>> > development we have done to make our code Paraview and CoProcessing
>>>> friendly
>>>> > is not usable with the BoxLib file format.
>>>> >
>>>> >
>>>> > I have seen some information on various websites about using the
>>>> VisitBridge
>>>> > to add the readers from Visit into Paraview, but when I build with
>>>> it, the
>>>> > BoxLib reader was not included in the list of formats I could use for
>>>> files
>>>> > -- even though it is listed online.
>>>> >
>>>> >
>>>> > Does anybody know what the status is of the reader in PV and if it is
>>>> > usable? Or is there a different format we can try to write out from
>>>> our code
>>>> > that would be usable? I really don't want to lose the work we've done
>>>> with
>>>> > PV and I would rather spend time writing code to get things working
>>>> again
>>>> > for PV than learn to use new software!
>>>> >
>>>> >
>>>> > Thanks,
>>>> >
>>>> >
>>>> > Tim
>>>> >
>>>> >
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>>>
>>>
>>
>
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