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

Thu Nov 1 13:29:00 EDT 2012

We're getting ready for a pre-release of PV 4.0 now so we'll need this
soon. If we need to update to a newer WindBlade file for the test, we can
do that too. You'll have to think though on how to handle backwards
compatibility.

Andy

On Wed, Oct 31, 2012 at 12:37 PM, Sohail Shafii <ssshafii at ucdavis.edu>wrote:

> Well you probably know already, but I won't be able to make the changes
> right now.  I have a submission due this Friday.  The reader still works
> for newer data sets but fails for the outdated one that you guys use for
> testing.  So the fixes will have to come later.
>
>
> On Fri, Oct 26, 2012 at 2:39 PM, Andy Bauer <andy.bauer at kitware.com>wrote:
>
>> This change is only in VTK in gerrit so you need to follow the directions
>> there to check out the code and run the test. The directions are at
>> http://review.source.kitware.com/#/t/1396/
>>
>> I'm not sure why paraview is crashing though. I'll check on that.
>>
>> andy
>>
>>
>> On Fri, Oct 26, 2012 at 5:06 PM, Sohail Shafii <ssshafii at ucdavis.edu>wrote:
>>
>>> Current master version can't launch (MacOS Mountain Lion):
>>>
>>> paraview(575,0x7fff72e33180) malloc: *** error for object 0x111058450:
>>> pointer being freed was not allocated
>>> *** set a breakpoint in malloc_error_break to debug
>>>
>>> Program received signal SIGABRT, Aborted.
>>> 0x00007fff82432212 in __pthread_kill ()
>>> (gdb) bt 14
>>> #0  0x00007fff82432212 in __pthread_kill ()
>>> #1  0x00007fff87964af4 in pthread_kill ()
>>> #2  0x00007fff879a8dce in abort ()
>>> #3  0x00007fff8797c959 in free ()
>>> #4  0x00007fff5fc0762a in
>>> __dyld__ZN4dyldL12registerDOFsERKNSt3__16vectorIN11ImageLoader7DOFInfoENS0_9allocatorIS3_EEEE
>>> ()
>>> #5  0x00007fff5fc0f06b in
>>> __dyld__ZN11ImageLoader4linkERKNS_11LinkContextEbbRKNS_10RPathChainE ()
>>> #6  0x00007fff5fc04ce4 in
>>> __dyld__ZN4dyld4linkEP11ImageLoaderbRKNS0_10RPathChainE ()
>>> #7  0x00007fff5fc0a81a in __dyld_dlopen ()
>>> #8  0x00007fff8ac96dd8 in dlopen ()
>>> #9  0x00007fff83dcfa10 in gfxInitializeLibrary ()
>>> #10 0x000000011e6014fe in gliInitializeLibrary ()
>>> #11 0x00007fff8a4f63e6 in glcPluginCount ()
>>>  #12 0x00007fff8a4f62a8 in glcPluginCount ()
>>> #13 0x00007fff8a4f6091 in glcPluginCount ()
>>> (More stack frames follow...)
>>>
>>>
>>> Which version of the master works, so that I can debug?
>>>
>>> Sohail
>>>
>>>
>>> On Wed, Oct 24, 2012 at 10:04 AM, Andy Bauer <andy.bauer at kitware.com>wrote:
>>>
>>>> A beta version will be released by mid-November. In order for the
>>>> desired changes to make it in to that, the VTK part that's waiting your
>>>> changes needs to go in early next week so that I can make the changes to
>>>> ParaView to enable the WindBlade reader when running in either built-in
>>>> mode or connecting to a serial server.
>>>>
>>>> Andy
>>>>
>>>> On Wed, Oct 24, 2012 at 12:13 PM, Sohail Shafii <sohailshafii at yahoo.com
>>>> > wrote:
>>>>
>>>>>
>>>>> Haven't had a chance yet due to a paper. I'll look at it this week.
>>>>> How soon will it be released?
>>>>>
>>>>> Also please respond to my ssshafii at ucdavis.edu as this address is not
>>>>> on the paraview list anymore.
>>>>>
>>>>> Sohail
>>>>>
>>>>>   ------------------------------
>>>>> *From:* Andy Bauer <andy.bauer at kitware.com>
>>>>> *To:* Sohail Shafii <sohailshafii at yahoo.com>
>>>>> *Cc:* David E DeMarle <dave.demarle 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:* Wednesday, October 24, 2012 8:09 AM
>>>>>
>>>>> *Subject:* Re: [Paraview] ParaView thinks that it does not have a
>>>>> wind blade reader
>>>>>
>>>>> Hi Sohail,
>>>>>
>>>>> Did you get a chance to look at the warnings for the
>>>>> vtkIOGeometryCxx-TestWindBladeReader test for the
>>>>> http://review.source.kitware.com/#/t/1396/ gerrit topic? It's going
>>>>> to need to be fixed pretty soon if it's going to make it into the ParaView
>>>>> 4.0 release.
>>>>>
>>>>> Thanks,
>>>>> Andy
>>>>>
>>>>> On Wed, Oct 3, 2012 at 10:22 PM, Andy Bauer <andy.bauer at kitware.com>wrote:
>>>>>
>>>>> It's available with "git clone git://vtk.org/VTKLargeData.gitVTKLargeData".
>>>>> It's in the Data/WindBladeReader subdirectory there.
>>>>>
>>>>> On Wed, Oct 3, 2012 at 6:27 PM, Sohail Shafii <sohailshafii at yahoo.com>wrote:
>>>>>
>>>>> Which data set are you using for the test?
>>>>>
>>>>> If it's the single turbine data set with the curvy terrain, I don't
>>>>> have it (I use other data sets) so I can't do a similar test.  Let me know
>>>>> where I can download it.
>>>>>
>>>>> Sohail
>>>>>
>>>>>   ------------------------------
>>>>> *From:* Andy Bauer <andy.bauer at kitware.com>
>>>>> *To:* David E DeMarle <dave.demarle at kitware.com>
>>>>> *Cc:* Sohail Shafii <sohailshafii at yahoo.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:* Wednesday, October 3, 2012 3:16 PM
>>>>>
>>>>> *Subject:* Re: [Paraview] ParaView thinks that it does not have a
>>>>> wind blade reader
>>>>>
>>>>> I finally got around to doing the VTK part of the WindBladeReader
>>>>> work. It's on gerrit at http://review.source.kitware.com/#/c/7734/.
>>>>> It still needs some cleanup but at least both the serial test and the
>>>>> parallel test with a single process pass. For the serial test,
>>>>> vtkIOGeometryCxx-TestWindBladeReader, I'm still getting the following
>>>>> warning which needs to be fixed as well:
>>>>> Warning: In
>>>>> /home/acbauer/CODE/VTK/VTK/IO/Geometry/vtkWindBladeReader.cxx, line 568
>>>>> vtkWindBladeReader (0x1373840): 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
>>>>>
>>>>> Sohail, can you check this out and fix it?
>>>>>
>>>>> Thanks,
>>>>> Andy
>>>>>
>>>>> On Fri, Jul 20, 2012 at 12:02 PM, David E DeMarle <
>>>>> dave.demarle at kitware.com> wrote:
>>>>>
>>>>> 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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