[Paraview] ParaView thinks that it does not have a wind blade reader

[Sohail Shafii]

Well I guess it's not a problem in the derived functions if I check to see
if MPI is available; if not, call the superclass's version of the virtual
function.

On Tue, Aug 28, 2012 at 11:32 AM, Sohail Shafii <ssshafii at ucdavis.edu>wrote:

> MPI is only used if it's available. It tries to see if there is a
> MPIController available.  If not, then the number of ranks is 1, which
> means that the parallel class calls the super class's requestdata (super
> class is the serial wind blade reader).
>
> However, the parallel class overrides certain functions to make use of
> MPI. So even the parallel instantiation will call the superclass's
> requestdata, the overriden functions that are called from that point on
> assume that MPI is available...this is a problem when the MPI controller is
> not available.
>
> On another note, it appears that the rectilinear grid that I am reading
> (VTK file, structured points I think) is read by the vtkFileSeriesReader,
> which makes use of the vtkPDataSetReader class.  Strange that if I use
> vtkPDataSetReader myself in C++ code that uses VTK and not paraview,
> bounds/cell information is not generated. So I think that ParaView does
> something else besides using that reader...hmmm.
>
>
> On Mon, Aug 27, 2012 at 7:32 PM, Andy Bauer <andy.bauer at kitware.com>wrote:
>
>>
>>
>> On Mon, Aug 27, 2012 at 6:53 PM, Sohail Shafii <ssshafii at ucdavis.edu>wrote:
>>
>>> I see...so if MPI is running then it will create a parallel version of
>>> the class. Otherwise, it will create the normal reader.
>>>
>>
>> Technically, if ParaView is built with MPI enabled it will create the
>> parallel version of the class every time whether or not the client, server,
>> or python scripts are actually run with mpiexec, mpirun, or whatever is
>> used to start the executable. So you can't rely on MPI being initialized
>> and should not initialize it yourself in your class as that can cause
>> problems as well. I think that's what you meant but wanted to be as clear
>> as possible for the implications for the classes.
>>
>>
>>>
>>> As far as the check goes for a multiprocess controller; while it does
>>> call the parent request data in the serial case, the inherited parallel
>>> class overrides some of the methods.  Which is a problem because it refers
>>> to its own file pointer in those methods (it uses MPI_File instead of a
>>> FILE*). Hmm.
>>>
>>> Sohail
>>>
>>>
>>> On Thu, Aug 23, 2012 at 3:20 PM, Andy Bauer <andy.bauer at kitware.com>wrote:
>>>
>>>> Hi Sohail,
>>>>
>>>> Sorry for the slow reply but I wanted to make sure how things should
>>>> work first and that took a bit to figure out. Anyways, this is closer to
>>>> what's needed but the way it is supposed to work in VTK is that we use
>>>> vtkObjectFactory to determine which one should be created when
>>>> vtkWindBladeReader::New() is called. This is done at build time based on
>>>> whether or not VTK is built with MPI. So if VTK and ParaView are built in
>>>> parallel then there is code added that creates a vtkPWindBladeReader when
>>>> vtkWindBladeReader::New() is called. This is regardless of whether or not
>>>> the executable is run with mpi initialized or not. Because of this, the
>>>> parallel version of the reader is responsible for checking whether mpi is
>>>> initialized, ideally by doing
>>>> vtkMultiProcessController::GetGlobalController()->IsA("vtkMPIController")
>>>> is true, and if it isn't it should just call the parent class's methods for
>>>> reading in the files. You may want to look at vtkPNrrdReader and the
>>>> CMakeLists.txt file in that directory to see how they did things. Note
>>>> though that if it's a single process running that it doesn't do any MPI
>>>> calls even in the parallel version so your code will be slightly different
>>>> than theirs.
>>>>
>>>> As for other parts of the email below:
>>>>
>>>> 1) yes, please keep cc'ing the list as there are some details in here
>>>> that will be helpful to other people trying to implement their own parallel
>>>> readers or filters
>>>>
>>>> 2) I'm not sure what's going on with the gradient filter but am
>>>> guessing that it has to do with the multiblock data set and that there
>>>> probably isn't that same array in each block. But that's just a guess. Did
>>>> you try extracting the "air" block and do the vorticity and/or q criterion
>>>> computation on that?
>>>>
>>>> 3) vtkSMReaderFactory may be the class you're looking for to determine
>>>> which reader is getting used. ParaViewReaders.xml has a list of readers
>>>> that it will try to read in a file.
>>>>
>>>> Andy
>>>>
>>>>
>>>> On Tue, Aug 21, 2012 at 7:11 PM, Sohail Shafii <ssshafii at ucdavis.edu>wrote:
>>>>
>>>>>  <sent via another e-mail address; yahoo prevents me from uploading
>>>>> stuff because it's stupid>
>>>>>
>>>>> Here's the first version.  Do you want me to keep ccing the list? Not
>>>>> sure if that's necessary at this point because this is related to the
>>>>> development of ParaView and not help.
>>>>>
>>>>> I've run it with an older version of the master, and it seems to read
>>>>> in a test .wind file just fine.  For now I had to store the
>>>>> vtkPWindBladeReader* files into VTK/Parallel/MPI since I don't have
>>>>> VTK/IO/MPIParallel module yet.  Now when I run the gradient filter after
>>>>> the field, the gradient filter thinks that the input array does not have
>>>>> the appropriate number of components for Q criterion or vorticity...but it
>>>>> should (UVW does have three components per tuple).  Might be my outdated
>>>>> copy of the git repo.  Haven't debugged that gradient code yet.
>>>>>
>>>>> *I was wondering if this is the type of code that you want?  Or
>>>>> should the classes be designed differently?*  Also, I have only run
>>>>> it parallel because if I try to instantiate it inside of the python shell
>>>>> in serial it tries to run RequestInformation (which assumes that the file
>>>>> path exists but does not).  It's a work-in-progress but it's a start.
>>>>>
>>>>> A random question: if ParaView reads a file, where would I put a
>>>>> breakpoint that tells me which reader it ends up picking??  I have some
>>>>> separate VTK code that reads in a rectilinear grid, but does not generate
>>>>> cell/bounds information. ParaView does generate information about the
>>>>> bounds though.
>>>>>
>>>>> Sohail
>>>>>
>>>>>   ------------------------------
>>>>> *From:* David E DeMarle <dave.demarle at kitware.com>
>>>>> *To:* Sohail Shafii <sohailshafii at yahoo.com>
>>>>> *Cc:* Andy Bauer <andy.bauer at kitware.com>; "migichen at gmail.com" <
>>>>> migichen at gmail.com>; "paraview at paraview.org" <paraview at paraview.org>;
>>>>> "Woodring, Jonathan L" <woodring at lanl.gov>
>>>>> *Sent:* Friday, July 20, 2012 10:02 AM
>>>>> *Subject:* Re: [Paraview] ParaView thinks that it does not have a
>>>>> wind blade reader
>>>>>
>>>>> Thanks.
>>>>>
>>>>> In today's git master it now sits in
>>>>> VTK/IO/Parallel/vtkWindbladeReader.
>>>>>
>>>>> The serial version should go in VTK/IO/Geometry.
>>>>>
>>>>> The MPI version should go in a new module VTK/IO/MPIParallel.
>>>>> (VTK/IO/Parallel depends only on vtkSocketController now and should
>>>>> not depend on vtkMPIController).
>>>>>
>>>>> Finally when that is done we can remove the flag in paraview's xml
>>>>> that prevents it from being used in serial.
>>>>>
>>>>> David E DeMarle
>>>>> Kitware, Inc.
>>>>> R&D Engineer
>>>>> 21 Corporate Drive
>>>>> Clifton Park, NY 12065-8662
>>>>> Phone: 518-881-4909
>>>>>
>>>>>
>>>>> On Thu, Jul 19, 2012 at 7:08 PM, Sohail Shafii <sohailshafii at yahoo.com>
>>>>> wrote:
>>>>> > Well it seems like #1 and #2 can be solved by writing a new parallel
>>>>> wind
>>>>> > blade reader class. I had similar experience by creating distributed
>>>>> > versions of class that I created in other vtk directories. The
>>>>> normal wind
>>>>> > blade reader would have no parallel calls, which would address #1.
>>>>> >
>>>>> > What I find interesting is that in your directories, the wind blade
>>>>> reader
>>>>> > is located in VTK/IO/Parallel. For the ParaView snapshot that I
>>>>> downloaded,
>>>>> > as well as the 3.14 source, it's still in VTK/Parallel.  No Parallel
>>>>> folder
>>>>> > in VTK/IO. Is this a recent change?
>>>>> >
>>>>> > So maybe the ideal folder layout would be:
>>>>> >
>>>>> > VTK/IO/WindBladeReader.*
>>>>> >
>>>>> > VTK/IO/Parallel/DistributedWindBladeReader.*
>>>>> >
>>>>> > I can make changes to the WindBladeReader to remove the MPI-IO calls
>>>>> and
>>>>> > make a distributed wind blade reader class in case you want to add
>>>>> them to
>>>>> > the repository. The one template I have for the parallel/serial
>>>>> split is the
>>>>> > vtkStreamTracer and its distributed counterparts so I can use those
>>>>> as a
>>>>> > guide.  If you have better recommendations please let me know.
>>>>> >
>>>>> > Sohail
>>>>> >
>>>>> > ________________________________
>>>>> > From: David E DeMarle <dave.demarle at kitware.com>
>>>>> > To: Sohail Shafii <sohailshafii at yahoo.com>
>>>>> > Cc: Andy Bauer <andy.bauer at kitware.com>; "migichen at gmail.com"
>>>>> > <migichen at gmail.com>; "paraview at paraview.org" <paraview at paraview.org
>>>>> >;
>>>>> > "Woodring, Jonathan L" <woodring at lanl.gov>
>>>>> > Sent: Thursday, July 19, 2012 3:20 PM
>>>>> >
>>>>> > Subject: Re: [Paraview] ParaView thinks that it does not have a wind
>>>>> blade
>>>>> > reader
>>>>> >
>>>>> > Two issues need to be fixed.
>>>>> > 1) that behavior in 3.14 is there because of this fix which we had to
>>>>> > rush in just before the 3.14 release.
>>>>> >
>>>>> > Committer: Utkarsh Ayachit <utkarsh.ayachit at kitware.com>  2012-02-08
>>>>> > 17:12:18
>>>>> > Parent: e401d569f6e54c49c3497852463f6b13a01da8b6 (Update version
>>>>> after
>>>>> > 3.14.0-RC1 tag.)
>>>>> > Child:  99fdb1aeb5997c29b43393f45a478c4b53a23109 (Merge topic
>>>>> > 'fix_windblade_segfault')
>>>>> > Branches: many (31)
>>>>> > Follows: v3.14.0-RC1
>>>>> > Precedes: v3.14.0-RC2
>>>>> >
>>>>> >    Fix segfault with ParaView built with MPI when opening *.vtr
>>>>> files.
>>>>> >
>>>>> >    The problem was that vtkWindBlade reader was getting created to
>>>>> test
>>>>> >    "CanReadFile" and that would cause segfault unless MPI was
>>>>> initialized.
>>>>> >
>>>>> >    Solved the problem by added support to vtkSMReaderFactory to
>>>>> respect the
>>>>> >    ProcessSupport flag on SourceProxy and change windblade reader XML
>>>>> > to say that
>>>>> >    it only works in parallel.
>>>>> >
>>>>> > In other words, Windblade reader's Constructor should not take it
>>>>> upon
>>>>> > itself to initialize MPI.
>>>>> >
>>>>> > Once that is fixed, we get to issue 2 before paraview 4.0
>>>>> >
>>>>> > 2) VTK's new modularization has the rule that no module can behave
>>>>> > differently with parallel (or most other cmake config options) turned
>>>>> > configured on or off. This is so because it makes it very hard to
>>>>> > package VTK when the libs behave differently in different situations.
>>>>> >
>>>>> > Ie, we can't have any more
>>>>> > #ifdef VTK_USE_MPI
>>>>> > do something
>>>>> > #else
>>>>> > do something different
>>>>> > #endif
>>>>> > in VTK classes.
>>>>> >
>>>>> > Now if we want a class to behave differently when MPI is turned on or
>>>>> > off we have to make a serial only version in a non MPI dependent
>>>>> > module and a subclass of that in an MPI dependent module.
>>>>> >
>>>>> > David E DeMarle
>>>>> > Kitware, Inc.
>>>>> > R&D Engineer
>>>>> > 21 Corporate Drive
>>>>> > Clifton Park, NY 12065-8662
>>>>> > Phone: 518-881-4909
>>>>> >
>>>>> >
>>>>> > On Thu, Jul 19, 2012 at 3:52 PM, Sohail Shafii <
>>>>> sohailshafii at yahoo.com>
>>>>> > wrote:
>>>>> >> When running serially, vtkSMReaderFactory::CanReadFile sees that the
>>>>> >> session
>>>>> >> has a single process.  As such, on line 660 it realizes that the
>>>>> source
>>>>> >> proxy's process support (in this case the source is a
>>>>> vtkWindBladeReader
>>>>> >> proxy) is multiple processes, which causes a return of "false" from
>>>>> that
>>>>> >> function.  This makes ParaView think that the wind blade reader
>>>>> can't read
>>>>> >> a
>>>>> >> .wind file in serial.  According to Andy, the reader works find in
>>>>> >> parallel.
>>>>> >>
>>>>> >> I assume that a fix for this is pretty trivial? It never did this
>>>>> before
>>>>> >> in
>>>>> >> previous versions of ParaView and I think that the wind blade
>>>>> reader code
>>>>> >> has remained mostly the same. Andy mentioned some details in person
>>>>> when
>>>>> >> he
>>>>> >> was talking with Jon but at that time I didn't know as much as I do
>>>>> now.
>>>>> >> There is a mention below about enabling the filter in serial and
>>>>> parallel
>>>>> >> --
>>>>> >> is this done in a xml file?
>>>>> >>
>>>>> >> Sohail
>>>>> >>
>>>>> >> ________________________________
>>>>> >> From: David E DeMarle <dave.demarle at kitware.com>
>>>>> >> To: Sohail Shafii <sohailshafii at yahoo.com>
>>>>> >> Cc: Andy Bauer <andy.bauer at kitware.com>; "migichen at gmail.com"
>>>>> >> <migichen at gmail.com>; "paraview at paraview.org" <
>>>>> paraview at paraview.org>;
>>>>> >> "Woodring, Jonathan L" <woodring at lanl.gov>
>>>>> >> Sent: Tuesday, July 17, 2012 7:00 PM
>>>>> >>
>>>>> >> Subject: Re: [Paraview] ParaView thinks that it does not have a
>>>>> wind blade
>>>>> >> reader
>>>>> >>
>>>>> >> Each file that has an association with that file extension, made
>>>>> via the
>>>>> >> XML, has its CanReadFile method called. Put a breakpoint there to
>>>>> >> determine
>>>>> >> if ParaView even knows about that reader.
>>>>> >>
>>>>> >> On Tuesday, July 17, 2012, Sohail Shafii wrote:
>>>>> >>
>>>>> >> Sorry, but I meant to ask a different question.  Here's what Andy
>>>>> said
>>>>> >> before, which relates to my concern:
>>>>> >> ">
>>>>> >>> I went through the code and it jogged my memory about previous
>>>>> problems
>>>>> >>> with
>>>>> >>> it. It had an explicit MPI call in the constructor that would cause
>>>>> >>> problems
>>>>> >>> when paraview wasn't getting built with MPI. Any time a user tried
>>>>> to
>>>>> >>> open
>>>>> >>> an unknown file it would try to create a windblade reader to see
>>>>> if the
>>>>> >>> reader could handle the file and this would cause a crash. If you
>>>>> launch
>>>>> >>> a
>>>>> >>> separate pvserver the wind blade reader will be available in the
>>>>> gui."
>>>>> >>
>>>>> >> What I meant was; which ParaView class "creates" or "tests" a
>>>>> reader to
>>>>> >> see
>>>>> >> if it can handle a file? The test code you specified has a
>>>>> predefined data
>>>>> >> set that is loaded in, and I think is more of an example to your
>>>>> average
>>>>> >> user. Correct me if I'm wrong.
>>>>> >>
>>>>> >> So basically ParaView will recognize the file extension, tries to
>>>>> load it,
>>>>> >> crashes somewhere, then asks you specify the data format from a
>>>>> dialog.
>>>>> >> I'm
>>>>> >> trying to figure out where it crashes so that I can see how that
>>>>> relates
>>>>> >> to
>>>>> >> the wind blade reader class and any MPI calls that are in there.
>>>>> >>
>>>>> >> Sohail
>>>>> >>
>>>>> >> Subject: Re: [Paraview] ParaView thinks that it does not have a
>>>>> wind blade
>>>>> >> reader
>>>>> >>
>>>>> >> kargad:ParaView demarle$ find . -name "*WindBlade*" -print
>>>>> >> ---> ./VTK/IO/Parallel/Testing/Cxx/TestWindBladeReader.cxx
>>>>> >> ./VTK/IO/Parallel/vtkWindBladeReader.cxx
>>>>> >> ./VTK/IO/Parallel/vtkWindBladeReader.h
>>>>> >>
>>>>> >> David E DeMarle
>>>>> >> Kitware, Inc.
>>>>> >> R&D Engineer
>>>>> >> 21 Corporate Drive
>>>>> >> Clifton Park, NY 12065-8662
>>>>> >> Phone: 518-881-4909
>>>>> >>
>>>>> >>
>>>>> >> On Tue, Jul 17, 2012 at 2:09 PM, Sohail Shafii <
>>>>> sohailshafii at yahoo.com>
>>>>> >> wrote:
>>>>> >>> What is the class that is responsible for testing to reader to see
>>>>> if it
>>>>> >>> can
>>>>> >>> open the .wind file?
>>>>> >>>
>>>>> >>> Sohail
>>>>> >>>
>>>>> >>> ________________________________
>>>>> >>> From: Andy Bauer <andy.bauer at kitware.com>
>>>>> >>> To: Sohail Shafii <sohailshafii at yahoo.com>
>>>>> >>> Cc: "Woodring, Jonathan L" <woodring at lanl.gov>; Sebastien Jourdain
>>>>> >>> <sebastien.jourdain at kitware.com>; "migichen at gmail.com"
>>>>> >>> <migichen at gmail.com>;
>>>>> >>> "paraview at paraview.org" <paraview at paraview.org>
>>>>> >>> Sent: Wednesday, July 11, 2012 10:53 AM
>>>>> >>>
>>>>> >>> Subject: Re: [Paraview] ParaView thinks that it does not have a
>>>>> wind
>>>>> >>> blade
>>>>> >>> reader
>>>>> >>>
>>>>> >>> I was reluctant to enable the reader in serial (i.e. not using MPI
>>>>> IO
>>>>> >>> which
>>>>> >>> I think is getting done by default with the parallel build)
>>>>> because of
>>>>> >>> the
>>>>> >>> following warnings that I got:
>>>>> >>>
>>>>> >>> Warning: In /home/acbauer/CODE/ParaView/
>>>>> >>> ParaView/VTK/IO/Parallel/vtkWindBladeReader.cxx, line 942
>>>>> >>> vtkWindBladeReader (0x3a0c800): WindBladeReader error reading file:
>>>>> >>>
>>>>> /home/acbauer/DATA/VTKLargeData/Data/WindBladeReader/test1_topo.wind
>>>>> >>> Premature EOF while reading block of data. Expected 896000 but got
>>>>> 0
>>>>> >>>
>>>>> >>> I just assumed that it was getting bad results so I didn't check
>>>>> the
>>>>> >>> serial
>>>>> >>> output with the parallel output. In either case the code should be
>>>>> >>> changed
>>>>> >>> before enabling it in serial so that it reads the files correctly
>>>>> and
>>>>> >>> doesn't produce any warning messages.
>>>>> >>>
>>>>> >>> Andy
>>>>> >>>
>>>>> >>> On Wed, Jul 11, 2012 at 12:04 PM, Sohail Shafii <
>>>>> sohailshafii at yahoo.com>
>>>>> >>> wrote:
>>>>> >>>
>>>>> >>> I'm not aware of any option to build/link against mpi-io.  This is
>>>>> just a
>>>>> >>> standard build with mpi support that suffers from this issue.
>>>>> >>>
>>>>> >>> The ParaView website's builds also have the same bug.
>>>>> >>>
>>>>> >>> ________________________________
>>>>> >>> From: "Woodring, Jonathan L" <woodring at lanl.gov>
>>>>> >>> To: Sohail Shafii <sohailshafii at yahoo.com>; Andy Bauer
>>>>> >>> <andy.bauer at kitware.com>; Sebastien Jourdain
>>>>> >>> <sebastien.jourdain at kitware.com>
>>>>> >>> Cc: "migichen at gmail.com" <migichen at gmail.com>; "
>>>>> paraview at paraview.org"
>>>>> >>> <paraview at paraview.org>
>>>>> >>> Sent: Tuesday, July 10, 2012 10:06 AM
>>>>> >>>
>>>>> >>> Subject: Re: [Paraview] ParaView thinks that it does not have a
>>>>> wind
>>>>> >>> blade
>>>>> >>> reader
>>>>> >>>
>>>>> >>> I added the MPI calls to be in sync with what was being added in
>>>>> the
>>>>> >>> simulation.
>>>>> >>>
>>>>> >>> In the SuperComputing demo last year, we updated both the HiGrad
>>>>> FireTec
>>>>> >>> to
>>>>> >>> use MPI-IO and likewise ParaView to do the same thing.
>>>>> >>>
>>>>> >>> It w
>>>>> >>
>>>>> >>
>>>>> >>
>>>>> >> --
>>>>> >> David E DeMarle
>>>>> >> Kitware, Inc.
>>>>> >> R&D Engineer
>>>>> >> 21 Corporate Drive
>>>>> >> Clifton Park, NY 12065-8662
>>>>> >> Phone: 518-881-4909
>>>>> >>
>>>>> >>
>>>>> >
>>>>> >
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
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