No subject
Wed May 9 12:08:04 EDT 2012
ent than the header files and libraries. By this I mean that it will pick u=
p the python header files and libraries from one version of python and the =
python interpretor will be from a different version. I don't think that's w=
hat's going on but you may want to check on that in CMake.
Andy
On Tue, Sep 11, 2012 at 11:21 AM, Vanmoer, Mark W <mvanmoer at illinois.edu<ma=
ilto:mvanmoer at illinois.edu>> wrote:
Hi Andy,
Sorry, I lost track of where I was in debugging. What I had was an openmpi/=
pgi debug build that passed the ctest -R CoPro tests. But the app I'm worki=
ng on still crashes when trying to create a python interpreter.
I started over from scratch working with the Wiki example, using gcc 4.4.6 =
and mpich2 1.4.1p1.
I have the C++ wiki example working with both the ParaView-3.14.1-Source ta=
rball and with git commit 2537cabbf0cc9b39f17f347105ee18c559d0041a.
I then made a Fortran version of the wiki example. It works with the ParaVi=
ew-3.14.1-Source tarball build, but crashes when built against the git bran=
ch build. Seems to be at the same spot as the pgi build, when it tries to r=
eturn the python interpreter instance. I stepped through with gdb and don't=
see anything obvious. It seems to crash when it tries to create an interpr=
eter to add the python script to the module search path.
Mark
From: Andy Bauer [mailto:andy.bauer at kitware.com]<mailto:[mailto:andy.bauer@=
kitware.com]>
Sent: Thursday, August 30, 2012 10:26 PM
To: Vanmoer, Mark W
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Python interpreter not being created for coprocessi=
ng?
Glad to hear that it's working. As for the parallel test failure, I think y=
ou can ignore that for now. I need to fix it but I just haven't gotten arou=
nd to it yet. I think it's either a parallel rendering/compositing issue or=
a problem with the actors's visibility in the views getting screwed up. Bo=
th of those things are not my area of expertise so I've been reluctant to g=
o and fix it. Now that you've publicly shamed me I'm going to have to bite =
the bullet and fix it :) Hopefully by the end of next week it will be fixe=
d. I created a mantis issue (http://paraview.org/Bug/view.php?id=3D13417) i=
f you want to follow it.
Andy
On Thu, Aug 30, 2012 at 6:19 PM, Vanmoer, Mark W <mvanmoer at illinois.edu<mai=
lto:mvanmoer at illinois.edu>> wrote:
Hi Andy,
Not sure what changed, but I was able to build pgi/openmpi and got to the p=
oint you did below, where the parallel test fails with "CPGrid0 image compa=
re failed."
Can I ignore this error? Anyway, the python interpreter seems to be created=
, so that issue is closed.
Mark
From: Andy Bauer [mailto:andy.bauer at kitware.com<mailto:andy.bauer at kitware.c=
om>]
Sent: Wednesday, August 29, 2012 12:15 PM
To: Vanmoer, Mark W
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Python interpreter not being created for coprocessi=
ng?
Ok, glad to hear that coprocessing is working in some fashion. Now to figur=
e out how to get it running properly with your desired configuration. Unfor=
tunately at this point I don't know how to move forward except for trying t=
o piecemeal from having it working with GCC without everything you need to =
working with PGI, CUDA and everything else.
Andy
On Tue, Aug 28, 2012 at 2:51 PM, Vanmoer, Mark W <mvanmoer at illinois.edu<mai=
lto:mvanmoer at illinois.edu>> wrote:
[mvanmoer at forge ParaView]$ git log origin/master | head -1
commit 2537cabbf0cc9b39f17f347105ee18c559d0041a
I should mention I do have a gcc, mvapich2 compiled version of coprocessing=
compiled on Forge and it works great. However any program built with PGI/o=
penmpi code (required because of the CUDA Fortran) crashes with MPI errors.=
That's why I was trying to build ParaView with PGI/openmpi. I guess I coul=
d try gcc/openmpi and see if that linked to pgi/openmpi will run.
Mark
From: Andy Bauer [mailto:andy.bauer at kitware.com<mailto:andy.bauer at kitware.c=
om>]
Sent: Tuesday, August 28, 2012 12:19 PM
To: Vanmoer, Mark W
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Python interpreter not being created for coprocessi=
ng?
Hmm, ParaView has been undergoing a lot of changes lately so it's been a bi=
t unstable. I just checked out a clean version and built it without any pro=
blems. The SHA from that was 2537cabbf0cc9b39f17f347105ee18c559d0041a. What=
version are you on?
Have you tried building with GCC instead of PGI? I'm thinking of ways to si=
mplify the build since I haven't tried building with PGI+CUDA+MPI+Python my=
self.
Andy
On Mon, Aug 27, 2012 at 3:31 PM, Vanmoer, Mark W <mvanmoer at illinois.edu<mai=
lto:mvanmoer at illinois.edu>> wrote:
Hi Andy, I just did a fresh git clone and ccmake gives me
Make Error at VTK/CMake/vtkModuleTop.cmake:29 (message):
No such module "vtkWrappingTools" needed by "vtkUtilitiesWrapClientServe=
r"
Call Stack (most recent call first):
VTK/CMake/vtkModuleTop.cmake:45 (vtk_module_check)
VTK/CMake/vtkModuleTop.cmake:52 (vtk_module_check)
VTK/CMakeLists.txt:334 (include)
Mark
From: Andy Bauer [mailto:andy.bauer at kitware.com<mailto:andy.bauer at kitware.c=
om>]
Sent: Monday, August 27, 2012 11:59 AM
To: Vanmoer, Mark W
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Python interpreter not being created for coprocessi=
ng?
Hi Mark,
With the modularization of VTK and ParaView the coprocessing tests were tem=
porarily in a bad state. The serial ones are fixed now (the parallel runs b=
ut gives incorrect results for the screenshot). Is it possible for you to u=
pdate your version of ParaView and retry this?
Thanks,
Andy
On Fri, Aug 24, 2012 at 4:03 PM, Vanmoer, Mark W <mvanmoer at illinois.edu<mai=
lto:mvanmoer at illinois.edu>> wrote:
Hi, I rebuilt with ParaViewData directory set and it's only finding 1 out 3=
of the CoProcessing tests. Did I forget a step?
$ ctest --verbose --output-on-failure --output-log ctest.out -R CoProcess
UpdateCTestConfiguration from :/usr/apps/vis/ParaView/repo/withTesting/Dar=
tConfiguration.tcl
Parse Config file:/usr/apps/vis/ParaView/repo/withTesting/DartConfiguration=
.tcl
UpdateCTestConfiguration from :/usr/apps/vis/ParaView/repo/withTesting/Dar=
tConfiguration.tcl
Parse Config file:/usr/apps/vis/ParaView/repo/withTesting/DartConfiguration=
.tcl
Test project /usr/apps/vis/ParaView/repo/withTesting
Constructing a list of tests
Done constructing a list of tests
Checking test dependency graph...
Checking test dependency graph end
test 29
Start 29: vtkCoProcessor-HeaderTest
29: Test command: /usr/bin/python "/usr/apps/vis/ParaView/repo/ParaView/VTK=
/Testing/Core/HeaderTesting.py" "/usr/apps/vis/ParaView/repo/ParaView/CoPro=
cessing/Core" "VTKCOPROCESSOR_EXPORT"
29: Test timeout computed to be: 1500
29: Use export macro: VTKCOPROCESSOR_EXPORT
1/3 Test #29: vtkCoProcessor-HeaderTest ........ Passed 0.37 sec
test 100
Start 100: CoProcessingTestPythonScript
100: Test command: /usr/apps/vis/CMake/2.8.9/bin/cmake "-Dcfg=3DRelease" "-=
P" "/usr/apps/vis/ParaView/repo/withTesting/CoProcessing/CoProcessingTestPy=
thonScript.cmake"
100: Test timeout computed to be: 1500
100: CMake Error at /usr/apps/vis/ParaView/repo/withTesting/CoProcessing/Co=
ProcessingTestPythonScript.cmake:6 (message):
100:
100: '/usr/apps/vis/ParaView/repo/withTesting/ThirdParty/protobuf/vtkprot=
obuf/bin/Release/CoProcessingPythonScriptExample.exe'
100: does not exist
100:
100:
2/3 Test #100: CoProcessingTestPythonScript .....***Failed 0.79 sec
CMake Error at /usr/apps/vis/ParaView/repo/withTesting/CoProcessing/CoProce=
ssingTestPythonScript.cmake:6 (message):
'/usr/apps/vis/ParaView/repo/withTesting/ThirdParty/protobuf/vtkprotobuf/=
bin/Release/CoProcessingPythonScriptExample.exe'
does not exist
test 101
Start 101: PCoProcessingTestPythonScript
101: Test command: /usr/apps/vis/CMake/2.8.9/bin/cmake "-Dcfg=3DRelease" "-=
P" "/usr/apps/vis/ParaView/repo/withTesting/CoProcessing/PCoProcessingTestP=
ythonScript.cmake"
101: Test timeout computed to be: 1500
101: CMake Error at /usr/apps/vis/ParaView/repo/withTesting/CoProcessing/PC=
oProcessingTestPythonScript.cmake:6 (message):
101:
101: '/usr/apps/vis/ParaView/repo/withTesting/ThirdParty/protobuf/vtkprot=
obuf/bin/Release/CoProcessingPythonScriptExample.exe'
101: does not exist
101:
101:
3/3 Test #101: PCoProcessingTestPythonScript ....***Failed 0.01 sec
CMake Error at /usr/apps/vis/ParaView/repo/withTesting/CoProcessing/PCoProc=
essingTestPythonScript.cmake:6 (message):
'/usr/apps/vis/ParaView/repo/withTesting/ThirdParty/protobuf/vtkprotobuf/=
bin/Release/CoProcessingPythonScriptExample.exe'
does not exist
The following tests passed:
vtkCoProcessor-HeaderTest
33% tests passed, 2 tests failed out of 3
Total Test time (real) =3D 8.14 sec
The following tests FAILED:
100 - CoProcessingTestPythonScript (Failed)
101 - PCoProcessingTestPythonScript (Failed)
Errors while running CTest
Mark
From: Andy Bauer [mailto:andy.bauer at kitware.com<mailto:andy.bauer at kitware.c=
om>]
Sent: Thursday, August 23, 2012 3:06 PM
To: Vanmoer, Mark W
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Python interpreter not being created for coprocessi=
ng?
On Thu, Aug 23, 2012 at 4:00 PM, Vanmoer, Mark W <mvanmoer at illinois.edu<mai=
lto:mvanmoer at illinois.edu>> wrote:
Two questions - is there a way to tell ctest where the ParaViewData is with=
out having to go back into cmake and rebuilding?
Not possible for most, if not all, tests. The reason is that the test doesn=
't get added unless ParaViewData is available.
And 2, is there a way to tell ctest to not use MPIEXEC_MAX_NUMPROCS when ru=
nning tests?
Many parallel tests, including the parallel coprocessing test, usually just=
have it hard coded to use 2 or 4 processes for testing.
Mark
From: Andy Bauer [mailto:andy.bauer at kitware.com<mailto:andy.bauer at kitware.c=
om>]
Sent: Thursday, August 23, 2012 1:32 PM
To: Vanmoer, Mark W
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Python interpreter not being created for coprocessi=
ng?
It looks like you've built it properly. At least I don't see anything that =
looks wrong. I think the reason you didn't get any coprocessing tests is th=
at they depend on ParaViewDAta. Maybe the next step is to download ParaView=
Data (git://paraview.org/ParaViewData.git<http://paraview.org/ParaViewData.=
git>) and then set the location ParaViewData in cmake. After that, run the =
coprocessing tests (ctest -R CoProcess) and show me the output from that.
Andy
On Wed, Aug 22, 2012 at 12:26 PM, Vanmoer, Mark W <mvanmoer at illinois.edu<ma=
ilto:mvanmoer at illinois.edu>> wrote:
Hi Andy,
I set PARAVIEW_ENABLE_PYTHON to ON, is more needed? It did build pvpython, =
I don't know if that's separate thing entirely, though.
$ pvserver -version
paraview version 3.14.1-1549-g5f34f40
$ python -version
Python 2.6.6
$ cmake -version
cmake version 2.8.9
CMakeCache.txt is attached.
I also just noticed that ctest -R CoProcessing returns No tests were found!=
!!, yet it does have other tests.
Let me know what else you need.
Mark
From: Andy Bauer [mailto:andy.bauer at kitware.com<mailto:andy.bauer at kitware.c=
om>]
Sent: Wednesday, August 22, 2012 10:49 AM
To: Vanmoer, Mark W
Cc: paraview at paraview.org<mailto:paraview at paraview.org>
Subject: Re: [Paraview] Python interpreter not being created for coprocessi=
ng?
Hi Mark,
I think I can guess what the problem is but can't be certain without some m=
ore information. My guess is that you're using ParaView 3.14.1 for this and=
you're trying to use the fortran interface but haven't built ParaView with=
Python enabled. There were some dependency issues there that have been iro=
ned out since then though. If that's not the case though I'll need more inf=
ormation on versions and maybe sending your CMakeCache.txt in your ParaView=
build directory.
Andy
On Wed, Aug 22, 2012 at 11:12 AM, Vanmoer, Mark W <mvanmoer at illinois.edu<ma=
ilto:mvanmoer at illinois.edu>> wrote:
Hello,
I'm setting up someone's code to use coprocessing with OSMesa and openmpi/p=
gi/cuda fortran on NCSA's Forge using ParaView from the git repo. I'm getti=
ng segfaults and pgdbg gives me this error when coprocessorinitialize is ca=
lled:
[0] Signalled SIGSEGV at 0x2B62188CFD9A, function vtkCPPythonHelper::GetPyt=
honInterpretor(), file /usr/apps/vis/ParaView/repo/ParaView/CoProcessing/Co=
Processor/vtkCPPythonHelper.cxx, line 136
0x2B62188CFD9A: 48 8B 41 38 movq 56(%rcx),%rax
which is:
vtkPVPythonInterpretor* vtkCPPythonHelper::GetPythonInterpretor()
{
return Instance->PythonInterpretor;
}
The call stack is
vtkCPPythonHelper::GetPythonInterpretor() line 136 in vtkCPPythonHelper.cxx
vtkCPPythonScriptPipeline::Initialize(const char *) line 69 in vtkCPPythonS=
criptPipeline.cxx
coprocessorinitialize_ line 88 in FortranAdaptorAPI.cxx
So is an Instance not getting created? I have the system python in my path.
Thanks,
Mark
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<div class=3D"WordSection1">
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D">Hi Andy,<o:p></o:p></span=
></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"><o:p> </o:p></span><=
/p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D">Thanks for asking. Had to=
put this aside for a while, but where I am now is I decided I wanted to al=
ter the C++ wiki example to work with a partitioned vtkImageData
set, similar to the Python example. Then translate that to Fortran, so I w=
ould have a better idea of what I needed to do for the actual application.<=
o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"><o:p> </o:p></span><=
/p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D">C++ works fine, b=
ut in the Fortran version, with mpirun –np 2 I’m getting the fo=
llowing error:<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D">ERROR: In /home/mvanmoer/=
builds/ParaView/repo/ParaView/VTK/Common/ExecutionModel/vtkExecutive.cxx, l=
ine 753<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D">vtkCompositeDataPipeline =
(0x3cf5130): Algorithm vtkXMLImageDataWriter(0x3cf4d20) returned failure fo=
r request: vtkInformation (0x3cf70c0)<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"> Debug: Off<o:p></o=
:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"> Modified Time: 114=
245<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"> Reference Count: 1=
<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"> Registered Events:=
(none)<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"> Request: REQUEST_D=
ATA<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"> FROM_OUTPUT_PORT: =
-1<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"> FORWARD_DIRECTION:=
0<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"> ALGORITHM_AFTER_FO=
RWARD: 1<o:p></o:p></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"><o:p> </o:p></span><=
/p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D">I don’t get that er=
ror for any other np, 1, 3, 4, 5, 6, 8, 16, etc. Wrong values in the output=
.vtis though (except for np 1). My guess is I’m not sending the
Fortran array to the coprocessor correctly. I’m trying to use a 3D f=
ortran array and I think I might need to switch to a 1D.<o:p></o:p></span><=
/p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"><o:p> </o:p></span><=
/p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D">Mark<o:p></o:p></span></p=
>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"><o:p> </o:p></span><=
/p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt;font-family:"Ca=
libri","sans-serif";color:#1F497D"><o:p> </o:p></span><=
/p>
<p class=3D"MsoNormal"><b><span style=3D"font-size:10.0pt;font-family:"=
;Tahoma","sans-serif"">From:</span></b><span style=3D"font-s=
ize:10.0pt;font-family:"Tahoma","sans-serif""> Andy Bau=
er [mailto:andy.bauer at kitware.com]
<br>
<b>Sent:</b> Friday, October 12, 2012 4:23 PM<br>
<b>To:</b> Vanmoer, Mark W<br>
<b>Cc:</b> paraview at paraview.org<br>
<b>Subject:</b> Re: [Paraview] Python interpreter not being created for cop=
rocessing?<o:p></o:p></span></p>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<p class=3D"MsoNormal" style=3D"margin-bottom:12.0pt">Hi Mark,<br>
<br>
I just wanted to check in with you to see how far you got. I'm interested i=
n seeing if you got it to build with all of the options you were looking fo=
r.<br>
<br>
Andy<o:p></o:p></p>
<div>
<p class=3D"MsoNormal">On Thu, Sep 27, 2012 at 10:40 AM, Andy Bauer <<a =
href=3D"mailto:andy.bauer at kitware.com" target=3D"_blank">andy.bauer at kitware=
.com</a>> wrote:<o:p></o:p></p>
<p class=3D"MsoNormal">Yeah, for structured grids you'll need to set the ex=
tent on each process as well as use
<span style=3D"font-size:11.0pt;font-family:"Calibri","sans-=
serif";color:#1F497D">vtkCPInputDataDescription::SetWholeExtent() to s=
pecify the global grid extent. The partitioned arrays in addfields() for si=
ngle component tuples needs to be the same length as the
number of points/cells on the local, partitioned grid. <br>
<br>
The extent support for coprocessing is a git dodgy as we're trying to do th=
ings in a way that the pipeline doesn't like. One solution to that is to us=
e a vtkMultiPieceDataSet but I haven't tried that enough yet to see how wel=
l it works.</span><span style=3D"font-size:11.0pt;font-family:"Calibri=
","sans-serif";color:#888888"><br>
<br>
<span class=3D"hoenzb">Andy</span></span><o:p></o:p></p>
<div>
<div>
<p class=3D"MsoNormal"><o:p> </o:p></p>
<div>
<p class=3D"MsoNormal">On Tue, Sep 25, 2012 at 6:12 PM, Vanmoer, Mark W <=
;<a href=3D"mailto:mvanmoer at illinois.edu" target=3D"_blank">mvanmoer at illino=
is.edu</a>> wrote:<o:p></o:p></p>
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">Ah, apparently I’m not setting th=
e extents with SetExtent(), vtkCPInputDataDescription::SetWholeExtent()
as mentioned on slide 79 of the SC12 slides.</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">I’ve been working off of the Phas=
ta example. So if I understand the general idea right, I need to
be sending the extent information from the application to the coprocessor =
call, then</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">I need to make sure that those also get=
passed to the image data set creator, and I need to also
send the partitioned arrays to the addfields_() call?</span><o:p></o:p></p=
>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">Mark</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<div>
<div style=3D"border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in =
0in 0in">
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><b><span style=3D"font-size:10.0pt;font-family:"Tahoma",=
"sans-serif"">From:</span></b><span style=3D"font-size:10.0pt;fon=
t-family:"Tahoma","sans-serif""> Vanmoer, Mark W
<br>
<b>Sent:</b> Tuesday, September 25, 2012 3:28 PM</span><o:p></o:p></p>
<div>
<p class=3D"MsoNormal"><br>
<b>To:</b> 'Andy Bauer'<br>
<b>Cc:</b> <a href=3D"mailto:paraview at paraview.org" target=3D"_blank">parav=
iew at paraview.org</a><br>
<b>Subject:</b> RE: [Paraview] Python interpreter not being created for cop=
rocessing?<o:p></o:p></p>
</div>
</div>
</div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"> <o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">Right, single process. I’m workin=
g with one code that’s all CPU and another that’s mixed CPU/GPU=
.
Coprocessing works well for both. There’s also MPI versions of the c=
odes that I’m trying to instrument.
</span><o:p></o:p></p>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">The computational mesh is completely re=
gular so I’ve been using vtkImageData. The MPI versions split
the mesh over the ranks. When I run an MPI version with –np &g=
t; 1, then I get the following for each process:</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">ERROR: In /home/mvanmoer/builds/ParaVie=
w/ParaView-3.14.1-Source/ParaViewCore/VTKExtensions/vtkKdTreeGenerator.cxx,
line 168</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">vtkKdTreeGenerator (0x5ac6430): RegionI=
Ds cannot be 0.</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">It doesn’t crash, but it gives an=
incorrect image. I’ll look through your updated tutorials, I’d
been looking through the SC10 slides.</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
</div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">Mark</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><b><span style=3D"font-size:10.0pt;font-family:"Tahoma",=
"sans-serif"">From:</span></b><span style=3D"font-size:10.0pt;fon=
t-family:"Tahoma","sans-serif""> Andy Bauer
<a href=3D"mailto:[mailto:andy.bauer at kitware.com]" target=3D"_blank">[mailt=
o:andy.bauer at kitware.com]</a>
<br>
<b>Sent:</b> Tuesday, September 25, 2012 2:15 PM</span><o:p></o:p></p>
<div>
<div>
<p class=3D"MsoNormal"><br>
<b>To:</b> Vanmoer, Mark W<br>
<b>Cc:</b> <a href=3D"mailto:paraview at paraview.org" target=3D"_blank">parav=
iew at paraview.org</a><br>
<b>Subject:</b> Re: [Paraview] Python interpreter not being created for cop=
rocessing?<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"> <o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;margin-bottom:12.0p=
t"> <o:p></o:p></p>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto">On Tue, Sep 25, 2012 at 12:21 PM, Vanmoer, Mark W <<a href=3D"m=
ailto:mvanmoer at illinois.edu" target=3D"_blank">mvanmoer at illinois.edu</a>>=
; wrote:<o:p></o:p></p>
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">I pulled it directly from stage/13460_C=
P_FortranAdaptor. </span><o:p></o:p></p>
</div>
</div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><br>
Great, then it was me after all that fixed it!<br>
<o:p></o:p></p>
</div>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;padding:0i=
n 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-=
bottom:5.0pt">
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">I’m now at the point where it run=
s great on a single node with GPUs, I’m trying to extend it to multip=
le
nodes, which I think involves setting up vtkMultiBlockDataSets? I was goin=
g to look through the NPICAdaptor for hints on that.</span><o:p></o:p></p>
</div>
</div>
</blockquote>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><br>
By single node I'm assuming that you mean a single process, correct? What's=
the type of grid that you're planning on using? The PhastaAdaptor is an ex=
ample of dealing with an unstructured grid. I also just updated the coproce=
ssing tutorials page (now at
<a href=3D"http://paraview.org/Wiki/Coprocessing_Tutorials" target=3D"_blan=
k">http://paraview.org/Wiki/Coprocessing_Tutorials</a>) to include the tuto=
rial I'll be doing at SC12. It should have some useful information for doin=
g this. You could just do a polydata
input, just set the center of the sphere source in your example based on t=
he process rank (e.g. Sphere->SetCenter(10*rank, 0, 0); ) so that it's e=
asy to tell the difference between each processes input part/domain partiti=
on.<br>
<br>
Andy<br>
<o:p></o:p></p>
</div>
<blockquote style=3D"border:none;border-left:solid #CCCCCC 1.0pt;padding:0i=
n 0in 0in 6.0pt;margin-left:4.8pt;margin-top:5.0pt;margin-right:0in;margin-=
bottom:5.0pt">
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">Mark</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><b><span style=3D"font-size:10.0pt;font-family:"Tahoma",=
"sans-serif"">From:</span></b><span style=3D"font-size:10.0pt;fon=
t-family:"Tahoma","sans-serif""> Andy Bauer [mailto:<a =
href=3D"mailto:andy.bauer at kitware.com" target=3D"_blank">andy.bauer at kitware=
.com</a>]
<br>
<b>Sent:</b> Tuesday, September 25, 2012 10:13 AM</span><o:p></o:p></p>
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><br>
<b>To:</b> Vanmoer, Mark W<br>
<b>Cc:</b> <a href=3D"mailto:paraview at paraview.org" target=3D"_blank">parav=
iew at paraview.org</a><br>
<b>Subject:</b> Re: [Paraview] Python interpreter not being created for cop=
rocessing?<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"> <o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;margin-bottom:12.0p=
t">Did you get my changes from ParaView's stage branch? My changes didn't m=
ake it into ParaView master yet so I'm not sure what changed that caused th=
ings to work now. Well, if it's working
I'm glad -- I'm not sure I can personally take credit for it though :)<br>
<br>
Let me know how it goes with the GPU stuff.<br>
<br>
Andy<o:p></o:p></p>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto">On Mon, Sep 24, 2012 at 5:48 PM, Vanmoer, Mark W <<a href=3D"ma=
ilto:mvanmoer at illinois.edu" target=3D"_blank">mvanmoer at illinois.edu</a>>=
wrote:<o:p></o:p></p>
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">Hi Andy,</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">I’ve tested this and it works wit=
h both gcc/mpich2 and pgi/openmpi.
</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">Thanks again!</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">Mark</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<div>
<div style=3D"border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in =
0in 0in">
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><b><span style=3D"font-size:10.0pt;font-family:"Tahoma",=
"sans-serif"">From:</span></b><span style=3D"font-size:10.0pt;fon=
t-family:"Tahoma","sans-serif""> Vanmoer, Mark W
<br>
<b>Sent:</b> Wednesday, September 19, 2012 1:30 PM<br>
<b>To:</b> Andy Bauer<br>
<b>Cc:</b> <a href=3D"mailto:paraview at paraview.org" target=3D"_blank">parav=
iew at paraview.org</a><br>
<b>Subject:</b> RE: [Paraview] Python interpreter not being created for cop=
rocessing?</span><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"> <o:p></o:p></p>
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif"">Hi Andy, that sounds like some deep debugging, thanks=
for your effort. I'll test this and let you know. It's on
my to do list to learn CMake, I've had the book on my desk for a month now=
.<br>
<br>
Also, I made another Fortran example that's closer in spirit to the wiki ex=
ample, which uses the DataGenerator class as the C++ does, if you'r=
e interested.
<br>
<br>
Thanks, <br>
Mark</span><o:p></o:p></p>
</div>
</div>
<div class=3D"MsoNormal" align=3D"center" style=3D"text-align:center">
<hr size=3D"2" width=3D"100%" align=3D"center">
</div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;margin-bottom:12.0p=
t"><b><span style=3D"font-size:10.0pt;font-family:"Tahoma","=
sans-serif"">From:
</span></b><span style=3D"font-size:10.0pt;font-family:"Tahoma",&=
quot;sans-serif"">Andy Bauer</span><br>
<b><span style=3D"font-size:10.0pt;font-family:"Tahoma","san=
s-serif"">Sent: </span>
</b><span style=3D"font-size:10.0pt;font-family:"Tahoma","sa=
ns-serif"">9/19/2012 1:12 PM</span><br>
<b><span style=3D"font-size:10.0pt;font-family:"Tahoma","san=
s-serif"">To: </span></b><span style=3D"font-size:10.0pt;font-family:&=
quot;Tahoma","sans-serif"">Vanmoer, Mark W</span><br>
<b><span style=3D"font-size:10.0pt;font-family:"Tahoma","san=
s-serif"">Cc: </span></b><span style=3D"font-size:10.0pt;font-family:&=
quot;Tahoma","sans-serif""><a href=3D"mailto:paraview at paravi=
ew.org" target=3D"_blank">paraview at paraview.org</a></span><br>
<b><span style=3D"font-size:10.0pt;font-family:"Tahoma","san=
s-serif"">Subject: </span>
</b><span style=3D"font-size:10.0pt;font-family:"Tahoma","sa=
ns-serif"">Re: [Paraview] Python interpreter not being created for cop=
rocessing?</span><o:p></o:p></p>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;margin-bottom:12.0p=
t">Hi Mark,<br>
<br>
I finally got around to fixing this. It's in the stage branch (remotes/stag=
e/13460_CP_FortranAdaptor) and hopefully will go into the master branch on =
the next gatekeeper review. There were 2 issues fixed in this:<br>
1) for using newer GCC compilers and other compilers that hide symbols in t=
he library (<a href=3D"http://gcc.gnu.org/wiki/Visibility" target=3D"_blank=
">http://gcc.gnu.org/wiki/Visibility</a>) the FortranAdaptor API methods we=
ren't available to other libraries and
executables trying to link to them.<br>
2) Since 3.14.1 I changed around the way ParaView gets initialized through =
the coprocessing library (now through vtkCPProcessor::Initialize() as it sh=
ould be instead of vtkCPPythonScriptPipeline::Initialize()). I forgot to ma=
ke the change in the FortranAdaptorAPI.cxx
which caused the python interpretor to not be initialized properly, as you=
noticed.<br>
<br>
Thanks for the help in finding this problem. Sorry for the slow response on=
it. I created a CMakeLists.txt file to help build as I've been using CMake=
too long and can't remember how to work with Makefiles anymore! I'm attach=
ing it in case you'd like to use
it. I didn't test it with an install of ParaView as I really only work dir=
ectly with ParaView builds.<br>
<br>
Let me know if this solves your problems. I seem to remember there being mo=
re as far as using CUDA and PGI but hopefully this gets you close.<br>
<br>
By the way, I'll probably use what you sent me to create a Fortran test or =
example to help with making sure it doesn't get broken in the future.<br>
<br>
Andy<o:p></o:p></p>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto">On Wed, Sep 12, 2012 at 4:42 PM, Vanmoer, Mark W <<a href=3D"ma=
ilto:mvanmoer at illinois.edu" target=3D"_blank">mvanmoer at illinois.edu</a>>=
wrote:<o:p></o:p></p>
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">Tarball attached, it’s not exactl=
y the wiki example because I didn’t want to bother with passing
a DataGenerator object back and forth from C++ to Fortran, so I ju=
st make a sphere. The pipeline script is a shrink filter generated by pvcli=
ent.</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">I checked CMake and it looks like it=
217;s finding the same version of python.</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D">Mark</span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><span style=3D"font-size:11.0pt;font-family:"Calibri",&q=
uot;sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><b><span style=3D"font-size:10.0pt;font-family:"Tahoma",=
"sans-serif"">From:</span></b><span style=3D"font-size:10.0pt;fon=
t-family:"Tahoma","sans-serif""> Andy Bauer [mailto:<a =
href=3D"mailto:andy.bauer at kitware.com" target=3D"_blank">andy.bauer at kitware=
.com</a>]
<br>
<b>Sent:</b> Wednesday, September 12, 2012 1:02 PM</span><o:p></o:p></p>
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"><br>
<b>To:</b> Vanmoer, Mark W<br>
<b>Cc:</b> <a href=3D"mailto:paraview at paraview.org" target=3D"_blank">parav=
iew at paraview.org</a><br>
<b>Subject:</b> Re: [Paraview] Python interpreter not being created for cop=
rocessing?<o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;mso-margin-bottom-a=
lt:auto"> <o:p></o:p></p>
<p class=3D"MsoNormal" style=3D"mso-margin-top-alt:auto;margin-bottom:12.0p=
t">Can you send me your Fortran version of the wiki example?<br>
<br>
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