[Paraview] ParaView thinks that it does not have a wind blade reader
Sohail Shafii
ssshafii at ucdavis.edu
Sat Nov 3 16:15:51 EDT 2012
At this point the changes will have to wait, unfortunately. For the past
two weeks I've been involved with a TopoInVis submission so I couldn't get
around to it. I'll look at it this weekend. No need to wait for me.
On Thu, Nov 1, 2012 at 10:29 AM, Andy Bauer <andy.bauer at kitware.com> wrote:
> 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 for newer data sets but fails for the outdated one that you guys use for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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