[Paraview] Status of BoxLib AMR reader

Mon Aug 29 16:12:00 EDT 2016

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/uploads/project/avatar/12/VisitBridge_Icon__3_.png]<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<mailto: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<mailto:utkarsh.ayachit at kitware.com>>
Sent: Monday, August 29, 2016 8:46 AM

To: Gallagher, Timothy P
Cc: paraview at paraview.org<mailto: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/master/databases/visit_readers.xml
[2] https://gitlab.kitware.com/paraview/visitbridge/blob/master/databases/visit_readers.xml#L2562-2565

On Fri, Aug 26, 2016 at 6:26 PM, Gallagher, Timothy P <tim.gallagher at gatech.edu<mailto: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<mailto:paraview-bounces at paraview.org>> on behalf of Gallagher, Timothy P <tim.gallagher at gatech.edu<mailto:tim.gallagher at gatech.edu>>
Sent: Friday, August 26, 2016 11:53 AM
To: Utkarsh Ayachit

Cc: paraview at paraview.org<mailto: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/ParaView/index.php/VisIt_avt_Integration

But then this later one doesn't include it: http://www.paraview.org/Wiki/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<mailto:utkarsh.ayachit at kitware.com>>
Sent: Friday, August 26, 2016 8:35 AM
To: Gallagher, Timothy P
Cc: paraview at paraview.org<mailto: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<mailto: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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