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

Fri Oct 26 17:06:21 EDT 2012

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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