[Paraview] Problems with Paraview 3.6.1 on cluster (client - server mode)
Jonathan Vincent
jonathan.k.vincent at gmail.com
Sun Nov 1 04:00:41 EST 2009
I have to agree with that. We were getting an error similar to this one, i.e.
1/ Load file, showing the wireframe only.
2/ attempt to use openGL to plot a surface
3/ crash very much like the one you describe, with the same traceback.
When using client/server mode and OSMesa with off screen rendering.
The way I fixed it was by rebuilding the Mesa library as the one that
came with CentOS 5 (on x86_64) did not work. Rebuilding the library
from source (Including a couple of dependencies, which might have been
related to the problem, as the latest package for one of the
dependencies is too old) fixed everything and now it works perfectly.
Building Mesa was relatively easy, some of the dependencies were a bit
more difficult, but did not take that long.
Jon
On Fri, Oct 30, 2009 at 7:18 PM, Moreland, Kenneth <kmorel at sandia.gov> wrote:
> (Responding back to ParaView list.)
>
> No clue. This still looks like a problem with library linking mismatch to
> me (although I could be wrong). Even though the error does not specify the
> OpenGL library, I would still check that. That is the library that I find
> is most likely to cause trouble.
>
> -Ken
>
>
> On 10/28/09 3:39 AM, "myaccountmail9 myaccountmail9"
> <myaccountmail9 at gmail.com> wrote:
>
> Hi Kein
> I apologize again.
>
> We recompiled ParaView this time using BUILD_SHARED_LIBS = OFF (not ON), and
> the error on the library /usr/lib/libGL.so is gone.
> Now it remains the error on the library /lib/libpthread.so.0:
>
> Client connected.
> [hpc:15607] *** Process received signal ***
> [hpc:15607] Signal: Segmentation fault (11)
> [hpc:15607] Signal code: Address not mapped (1)
> [hpc:15607] Failing at address: (nil)
> [hpc:15607] [ 0] /lib/libpthread.so.0 [0x7f51e4573a80]
> [hpc:15607] *** End of error message ***
> Segmentation fault
>
> Have you any idea?
>
> Thank you very much.
> Luis
>
>
>
> 2009/10/28 myaccountmail9 myaccountmail9 <myaccountmail9 at gmail.com>
>
> It sounds like you are still linking to the system OpenGL libraries somehow.
> Those symbols should be defined in the libGL.so that is built with Mesa
> (whereas the /usr/lib/libGL.so on your system probably does not have them).
>
>
> Hi Ken,
> thanks again.
>
> Looking the errors such as:
>
>
> "home/myuser/TempOSMesa/Mesa-7.6/lib/libOSMesa.so: undefined reference to
> `_mesa_free_context_data'"
>
> I believe those symbols must be defined in libOSMesa.so library and not in
> /usr/lib/libGL.so library.
>
> In fact, if we install OSMessa using Debian packages we can compile
> ParaView, but we can't connect client and server; the error always is
> similar to:
>
>
> ParaView3/Servers/Common/vtkServerConnection.cxx, line 67
> vtkServerConnection (0x3182220): Server Connection Closed!
>
> Executing with: 0
> *** Process received signal ***
> Signal: Segmentation fault (11)
> Signal code: (128)
> Failing at address: (nil)
> [ 0] /lib/libpthread.so.0 [0x7f4fc6536a80]
> [ 1] /usr/lib/libGL.so.1(glBlendFuncSeparateEXT+0x16) [0x7f4fc7bc12e6]
> *** End of error message ***
> Segmentation fault
>
>
> If instead we compile OSMesa ourselves we can't compile ParaView: I believe
> that something went wrong compiling OSMesa (some simbols aren't present in
> libOSMesa.so created), but I don't know if compiling OSMesa ourselves can
> help us to resolve our problem.
>
> We also tried to install on our cluster ParaView 3.6.1already compiled
> (downloaded from http://www.paraview.org/paraview/resources/software.html)
> and it works: we can establish client-server connection.
>
> But if we try to run more 2 or more pvserver instances on the same node
> (mpirun -np 2 pvserver), we have this error:
>
> "vtkProcessModuleConnectionManager (0x23d6da0): Failed to set up server
> socket"
>
>
>
> Did you do a clean build of ParaView (that is, delete the binary directory
> and start over from scratch)? If you just tried to change some CMake
> variables in an existing build, you may have some stale libraries built.
>
> We did "make clean".
>
> You should also check to make sure that the executables being built are
> linking to your compiled Mesa libraries instead of the system libraries.
> You can check this with the ldd command. You may have to set your
> LD_LIBRARY_PATH environment variable to point to
> /home/myuser/TempOSMesa/Mesa-7.6.
>
> We also tried to set LD_LIBRARY_PATH.
>
> Can you help us?
> Luis
>
>
>
> -Ken
>
>
>
> On 10/23/09 3:27 AM, "myaccountmail9 myaccountmail9"
> <myaccountmail9 at gmail.com <http://myaccountmail9@gmail.com> > wrote:
>
> Hi Ken,
> thank you.
> We compiled Mesa with:
>
> ./configure --enable-gl-osmesa --disable-gallium
> make
> make install
>
> and we configured Paraview with:
>
> OPENGL_INCLUDE_DIR=/home/myuser/TempOSMesa/Mesa-.6/include
> OPENGL_gl_LIBRARY=/home/myuser/TempOSMesa/Mesa-7.6/lib/libGL.so
> OPENGL_glu_LIBRARY=/home/myuser/TempOSMesa/Mesa-7.6/lib/libGLU.so
> OPENGL_xmesa_INCLUDE_DIR=/home/myuser/TempOSMesa/Mesa-7.6/include
> OSMESA_INCLUDE_DIR=/home/myuser/TempOSMesa/Mesa-7.6/include
> OSMESA_LIBRARY=/home/myuser/TempOSMesa/Mesa-7.6/lib/libOSMesa.so
>
> but we have many error compiling Paraview; for example:
>
> /home/myuser/TempOSMesa/Mesa-7.6/lib/libOSMesa.so: undefined reference to
> `_mesa_free_context_data'
> /home/myuser/TempOSMesa/Mesa-7.6/lib/libOSMesa.so: undefined reference to
> `_mesa_get_current_context'
> /home/myuser/TempOSMesa/Mesa-7.6/lib/libOSMesa.so: undefined reference to
> `_mesa_enable_2_1_extensions'
>
> Do you think there is something went wrong installing Mesa?
> Can you help us?
>
> Thank you again.
> Luis
>
>
>
>
> 2009/10/21 Moreland, Kenneth <kmorel at sandia.gov <http://kmorel@sandia.gov> >
>
> Not really, but I would consider trying downloading the Mesa source and
> compiling it myself. Since the error is happening somewhere in the OpenGL
> libraries (and is not really being replicated on other user’s platforms),
> the only cause I can come up with is a problem with the libraries (and
> mismatched libraries is the most common problem). Compiling Mesa is
> actually pretty easy, so it is worth taking the effort to check.
>
> -Ken
>
>
>
> On 10/21/09 12:54 AM, "myaccountmail9 myaccountmail9"
> <myaccountmail9 at gmail.com <http://myaccountmail9@gmail.com>
> <http://myaccountmail9@gmail.com> > wrote:
>
> Hi Ken,
> thank you for your reply.
> No, we didn't compile OSMesa ourselves, but we installed OSMesa library on
> each node downloading the .deb packages with:
>
> apt-get install libosmesa6
> apt-get install libosmesa6-dev
>
> Have you got any other idea?
> Thank you again.
> Luis
>
>
> 2009/10/20 Moreland, Kenneth <kmorel at sandia.gov <http://kmorel@sandia.gov>
> <http://kmorel@sandia.gov> >
>
> Could it be a problem with mismatched libraries? I notice in the error
> below that it occurs in /usr/lib/libGL.so.1. This is a system library. Did
> you compile OSMesa yourself? If so, then you should not be using the system
> GL libraries; you should be using the libraries that you compiled when you
> also generated the OSMesa library.
>
> -Ken
>
>
>
> On 10/20/09 1:56 AM, "myaccountmail9 myaccountmail9"
> <myaccountmail9 at gmail.com <http://myaccountmail9@gmail.com>
> <http://myaccountmail9@gmail.com> <http://myaccountmail9@gmail.com> >
> wrote:
>
> Hi,
> we have a Linux (Debian) cluster without gpu and we have a big problem using
> Paraview 3.6.1in client - server mode.
> The server has been compiled with OSMesa library and following the
> instructions reported here (in particular the section "OSMesa support"):
>
> http://www.itk.org/Wiki/Setting_up_a_ParaView_Server
>
> If we try to connect the client started with the command:
>
> paraview
>
> and the server, started with the command:
>
> pvserver --use-offscreen-rendering
>
> we must disable the checkbox "Remote rendering threshold" (but this causes
> bad performances) in the client settings (Edit -> Settings -> Render view ->
> Server), othervise Paraview crashes after loading a big input or performing
> some operation such us changing "outline" to "wireframe"...
>
> The error always is (similar to):
>
> ParaView3/Servers/Common/vtkServerConnection.cxx, line 67
> vtkServerConnection (0x3182220): Server Connection Closed!
>
> Executing with: 0
> *** Process received signal ***
> Signal: Segmentation fault (11)
> Signal code: (128)
> Failing at address: (nil)
> [ 0] /lib/libpthread.so.0 [0x7f4fc6536a80]
> [ 1] /usr/lib/libGL.so.1(glBlendFuncSeparateEXT+0x16) [0x7f4fc7bc12e6]
> *** End of error message ***
> Segmentation fault
>
>
> This error also occurs if we start client and server logging directly
> (without any ssh connection) on the master node; on master node X is running
> and we can execute the test:
>
> mpirun -np 4 /usr/X11R6/bin/glxgears
>
> So, it doen't seem a problem regarding X connection and permission...
>
> Moreover, executing the test:
>
> /ParaView/ParaView-bin$ ctest -I ,,10
>
> we obtain some segmentation fault, but the log file can't give any useful
> information.
>
> 111/475 Testing TestGradientBackground ***Exception: SegFault
> 121/475 Testing TestOSConeCxx ***Exception: SegFault
> 131/475 Testing TestTranslucentLUTDepthPeeling***Exception: SegFault
> 141/475 Testing BoxWidget ***Exception: SegFault
> 151/475 Testing TestParallelopipedWidget ***Exception: SegFault
>
> ..
>
> On our local machine with gpu 100% test passed, and we haven't any problem
> to connect client and server on that machine.
>
>
> MPI version is: mpirun (Open MPI) 1.2.7rc2
> OSMesa version is: 7.0.3-7
>
>
> We searched on google, on Paraview wiki... without any succes: can you help
> us please?
>
> If you need more information let us now
>
> Thank you very much
>
> Luis
>
>
>
>
>
>
>
>
> **** Kenneth Moreland
> *** Sandia National Laboratories
> ***********
> *** *** *** email: kmorel at sandia.gov <http://kmorel@sandia.gov>
> <http://kmorel@sandia.gov> <http://kmorel@sandia.gov>
> ** *** ** phone: (505) 844-8919
> *** web: http://www.cs.unm.edu/~kmorel
> <http://www.cs.unm.edu/%7Ekmorel> <http://www.cs.unm.edu/%7Ekmorel>
> <http://www.cs.unm.edu/%7Ekmorel>
>
>
>
>
>
> **** Kenneth Moreland
> *** Sandia National Laboratories
> ***********
> *** *** *** email: kmorel at sandia.gov <http://kmorel@sandia.gov>
> <http://kmorel@sandia.gov>
> ** *** ** phone: (505) 844-8919
> *** web: http://www.cs.unm.edu/~kmorel
> <http://www.cs.unm.edu/%7Ekmorel> <http://www.cs.unm.edu/%7Ekmorel>
>
>
>
>
>
> **** Kenneth Moreland
> *** Sandia National Laboratories
> ***********
> *** *** *** email: kmorel at sandia.gov <http://kmorel@sandia.gov>
> ** *** ** phone: (505) 844-8919
> *** web: http://www.cs.unm.edu/~kmorel
> <http://www.cs.unm.edu/%7Ekmorel>
>
>
>
>
>
>
> **** Kenneth Moreland
> *** Sandia National Laboratories
> ***********
> *** *** *** email: kmorel at sandia.gov
> ** *** ** phone: (505) 844-8919
> *** web: http://www.cs.unm.edu/~kmorel
>
>
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