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=
=92t see anything obvious. It seems to crash when it tries to create an int=
erpreter 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 =93CPGrid0 image com=
pare failed.=94
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=92s why I was trying to build ParaView with PGI/openmpi. I guess I co=
uld 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=92s 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 =96 is there a way to tell ctest where the ParaViewData is wi=
thout 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=92t know if that=92s separate thing entirely, though.
$ pvserver =96version
paraview version 3.14.1-1549-g5f34f40
$ python =96version
Python 2.6.6
$ cmake =96version
cmake version 2.8.9
CMakeCache.txt is attached.
I also just noticed that ctest =96R CoProcessing returns No tests were foun=
d!!!, 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>
<div style=3D"font-family:Calibri,sans-serif; font-size:11pt">Hi Andy, that=
sounds like some deep debugging, thanks for your effort. I'll test this an=
d 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<br>
</div>
</div>
<hr>
<span style=3D"font-family:Tahoma,sans-serif; font-size:10pt; font-weight:b=
old">From:
</span><span style=3D"font-family:Tahoma,sans-serif; font-size:10pt">Andy B=
auer</span><br>
<span style=3D"font-family:Tahoma,sans-serif; font-size:10pt; font-weight:b=
old">Sent:
</span><span style=3D"font-family:Tahoma,sans-serif; font-size:10pt">9/19/2=
012 1:12 PM</span><br>
<span style=3D"font-family:Tahoma,sans-serif; font-size:10pt; font-weight:b=
old">To:
</span><span style=3D"font-family:Tahoma,sans-serif; font-size:10pt">Vanmoe=
r, Mark W</span><br>
<span style=3D"font-family:Tahoma,sans-serif; font-size:10pt; font-weight:b=
old">Cc:
</span><span style=3D"font-family:Tahoma,sans-serif; font-size:10pt">paravi=
ew at paraview.org</span><br>
<span style=3D"font-family:Tahoma,sans-serif; font-size:10pt; font-weight:b=
old">Subject:
</span><span style=3D"font-family:Tahoma,sans-serif; font-size:10pt">Re: [P=
araview] Python interpreter not being created for coprocessing?</span><br>
<br>
<div>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">http://gcc.gnu.o=
rg/wiki/Visibility</a>) the FortranAdaptor API methods weren'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<br>
<br>
<div class=3D"gmail_quote">On Wed, Sep 12, 2012 at 4:42 PM, Vanmoer, Mark W=
<span dir=3D"ltr">
<<a href=3D"mailto:mvanmoer at illinois.edu" target=3D"_blank">mvanmoer at ill=
inois.edu</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex; border-left:1=
px #ccc solid; padding-left:1ex">
<div lang=3D"EN-US">
<div>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt; font-family:"C=
alibri","sans-serif"; color:#1f497d">Tarball attached, it=92=
s not exactly the wiki example because I didn=92t want to bother with passi=
ng a DataGenerator object back and forth from C++ to Fortran,
so I just make a sphere. The pipeline script is a shrink filter generated =
by pvclient.<u></u><u></u></span></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt; font-family:"C=
alibri","sans-serif"; color:#1f497d"><u></u> <u></u></s=
pan></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt; font-family:"C=
alibri","sans-serif"; color:#1f497d">I checked CMake and it =
looks like it=92s finding the same version of python.<u></u><u></u></span><=
/p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt; font-family:"C=
alibri","sans-serif"; color:#1f497d">Mark<u></u><u></u></spa=
n></p>
<p class=3D"MsoNormal"><span style=3D"font-size:11.0pt; font-family:"C=
alibri","sans-serif"; color:#1f497d"><u></u> <u></u></s=
pan></p>
<p class=3D"MsoNormal"><b><span style=3D"font-size:10.0pt; font-family:&quo=
t;Tahoma","sans-serif"">From:</span></b><span style=3D"font-=
size:10.0pt; font-family:"Tahoma","sans-serif""> Andy B=
auer [mailto:<a href=3D"mailto:andy.bauer at kitware.com" target=3D"_blank">an=
dy.bauer at kitware.com</a>]
<br>
<b>Sent:</b> Wednesday, September 12, 2012 1:02 PM</span></p>
<div>
<div class=3D"h5"><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?<u></u><u></u></div>
</div>
<p></p>
<div>
<div class=3D"h5">
<p class=3D"MsoNormal"><u></u> <u></u></p>
<p class=3D"MsoNormal" style=3D"margin-bottom:12.0pt">Can you send me your =
Fortran version of the wiki example?<br>
<br>
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