CFD Online Logo CFD Online URL
www.cfd-online.com
[Sponsors]
Home > Forums > ParaView

Building Paraview 4.1.0 with MPI and Python support

Register Blogs Members List Search Today's Posts Mark Forums Read

Like Tree2Likes
  • 2 Post By wyldckat

Reply
 
LinkBack Thread Tools Display Modes
Old   February 3, 2014, 16:45
Default Building Paraview 4.1.0 with MPI and Python support
  #1
New Member
 
Join Date: Jan 2013
Location: Edmonton, AB
Posts: 9
Rep Power: 4
reynoldsStress is on a distinguished road
Hello All,

I was attempting to get Paraview 4.1.0 to compile with MPI plus Python support on ubuntu 12.04 64 bit. I am able to compile Paraview 4.1.0 with only MPI support or with only python support, but it fails when I try to have both. The error that it complains about is an undefined reference to a few dlopen functions right when it is building mpi4py modules. I am currently waiting for it to compile again with the additional
Code:
CMAKE_MODULE_LINKER_FLAGS='-ldl'
but i have little faith this will work.
  • Has anyone else successfully built paraview 4.1.0 with openMPI plus PYTHON support in Ubutnu 12.04? OpenMPI is build with static disabled using the standard build scripts in OpenFOAM.
I'm currently using the makeParaview script that is included in OpenFOAM to get me started....but this is not a requirement.
reynoldsStress is offline   Reply With Quote

Old   February 5, 2014, 11:20
Default
  #2
Senior Member
 
dkxls's Avatar
 
Armin
Join Date: Feb 2011
Location: Helsinki, Finland
Posts: 152
Rep Power: 10
dkxls will become famous soon enough
Hi,
did you find a solution to the problem?

I'm having the same problem right now for openSUSE. The build for 12.2 (openmpi 1.5.4) works, the one for 13.1 (openmpi 1.7.2) fails with the same error. :/
Code:
[  870s] CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o: In function `OPENMPI_dlopen_libmpi':
[  870s] MPI.c:(.text+0x6eb1): undefined reference to `dlopen'
[  870s] MPI.c:(.text+0x6ecd): undefined reference to `dlopen'
[  870s] MPI.c:(.text+0x6ee3): undefined reference to `dlopen'
[  870s] MPI.c:(.text+0x6ef9): undefined reference to `dlopen'
[  870s] CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o: In function `__pyx_pf_6mpi4py_3MPI_16Init':
[  870s] MPI.c:(.text+0x1349b): undefined reference to `dlopen'
[  870s] CMakeFiles/mpi4py.MPI.dir/src/MPI.c.o:MPI.c:(.text+0x135bd): more undefined references to `dlopen' follow
[  870s] collect2: error: ld returned 1 exit status
[  870s] make[2]: *** [lib/site-packages/mpi4py/MPI.so] Error 1
[  870s] make[1]: *** [ThirdParty/mpi4py/vtkmpi4py/CMakeFiles/mpi4py.MPI.dir/all] Error 2
[  870s] make[1]: *** Waiting for unfinished jobs....
dkxls is offline   Reply With Quote

Old   February 6, 2014, 07:20
Default
  #3
Senior Member
 
dkxls's Avatar
 
Armin
Join Date: Feb 2011
Location: Helsinki, Finland
Posts: 152
Rep Power: 10
dkxls will become famous soon enough
I brought up the topic on the paraview mailing-list:
http://www.paraview.org/pipermail/pa...ry/030484.html

A quick-and-dirty workaround is also given there, and hopefully the developers will come up with a proper fix.

-Armin
dkxls is offline   Reply With Quote

Old   March 16, 2014, 12:12
Default
  #4
Super Moderator
 
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 8,258
Blog Entries: 34
Rep Power: 84
wyldckat is just really nicewyldckat is just really nicewyldckat is just really nicewyldckat is just really nice
@Armin: Many thanks for reporting this!

For future readers, here are the steps for quickly patching the source code for fixing this issue:
Code:
cd $WM_THIRD_PARTY_DIR/ParaView-4.1.0
wget http://www.paraview.org/pipermail/paraview/attachments/20140210/464496cc/attachment.bin -O Fix.patch
patch -p1 < Fix.patch
cd ..
then proceed with running makeParaView4 with the same options as used before.
The file downloaded by wget is given here: http://www.paraview.org/pipermail/pa...ry/030517.html
monto and FerdiFuchs like this.
wyldckat is offline   Reply With Quote

Old   September 10, 2014, 09:57
Default
  #5
Senior Member
 
Samuele Z
Join Date: Oct 2009
Location: Mozzate - Co - Italy
Posts: 490
Rep Power: 9
samiam1000 is on a distinguished road
Hi All,

I am trying to compile paraview - along with OpenFOAM - with the Python support. Which is the option I have to use, during the compilation?

Thanks a lot,
Samuele.
samiam1000 is offline   Reply With Quote

Old   September 10, 2014, 10:08
Default
  #6
Senior Member
 
dkxls's Avatar
 
Armin
Join Date: Feb 2011
Location: Helsinki, Finland
Posts: 152
Rep Power: 10
dkxls will become famous soon enough
Here are the options I use to build the openSUSE packages with MPI and python support:
https://build.opensuse.org/package/v...araview41.spec

On openSUSE these are "1 click install" packages:
http://software.opensuse.org/package/paraview41
dkxls is offline   Reply With Quote

Old   September 10, 2014, 10:41
Default
  #7
Senior Member
 
Samuele Z
Join Date: Oct 2009
Location: Mozzate - Co - Italy
Posts: 490
Rep Power: 9
samiam1000 is on a distinguished road
This is my makeParaview4 file:

Code:
# USER OPTIONS:
# ~~~~~~~~~~~~~

# MPI support:
withMPI=false
MPI_MAX_PROCS=4

# Python support:
# note: script will try to determine the appropriate python library.
#       If it fails, specify the path using the PYTHON_LIBRARY variable
withPYTHON=true
# PYTHON_LIBRARY=""
PYTHON_LIBRARY="/usr/lib/libpython2.7.so.1.0"

# MESA graphics support:
withMESA=false
MESA_INCLUDE="/usr/include/GL"
MESA_LIBRARY="/usr/lib64/libOSMesa.so"

# extra QT gui support (useful for some third party apps)
withQT=true

# Set the path to the Qt-4.5 (or later) qmake if the system Qt is older
QMAKE_PATH=""

# Set the path to cmake
CMAKE_PATH=""
and this is the error I get:

Code:
.
.
.

-- Check if system supports 64 bit streams
-- Check if system supports 64 bit streams - yes
CMake Error at VTK/CMake/FindPythonLibs.cmake:112 (FILE):
  file STRINGS file "/usr/include/python2.7/patchlevel.h" cannot be read.
Call Stack (most recent call first):
  VTK/CMake/vtkPythonWrapping.cmake:1 (find_package)
  VTK/Wrapping/Python/CMakeLists.txt:2 (include)


CMake Error at VTK/CMake/FindPythonLibs.cmake:112 (FILE):
  file STRINGS file "/usr/include/python2.7/patchlevel.h" cannot be read.
Call Stack (most recent call first):
  VTK/CMake/vtkPythonWrapping.cmake:1 (find_package)
  Utilities/PythonInitializer/CMakeLists.txt:16 (include)


-- Plugin: VaporPlugin - Plugin to read NCAR VDR files : Disabled
-- Plugin: VRPlugin - Virtual Reality Devices and Interactor styles : Disabled
-- Plugin: InSituExodus - Experimental memory-conserving Exodus II file reader. : Disabled
-- Plugin: StreamingParticles - Render Particles with Streaming : Enabled
-- Plugin: AdiosReader - Reader for *.bp files based on Adios : Disabled
-- Plugin: SciberQuestToolKit - SciberQuestToolKit - Domain specific visualization tools for magnetospheric sciences. : Enabled
CMake Error at VTK/CMake/FindPythonLibs.cmake:112 (FILE):
  file STRINGS file "/usr/include/python2.7/patchlevel.h" cannot be read.
Call Stack (most recent call first):
  CMake/ParaViewPlugins.cmake:1241 (find_package)
  Plugins/SciberQuestToolKit/CMakeLists.txt:26 (pv_process_modules)


-- Plugin: H5PartReader - Reader for h5part files : Enabled
-- Plugin: SLACTools - SLAC Tools : Enabled
-- Plugin: EyeDomeLighting - Add 3D View with eye-dome Lighting support : Enabled
CMake Error at VTK/CMake/FindPythonLibs.cmake:112 (FILE):
  file STRINGS file "/usr/include/python2.7/patchlevel.h" cannot be read.
Call Stack (most recent call first):
  CMake/ParaViewPlugins.cmake:1241 (find_package)
  Plugins/EyeDomeLighting/CMakeLists.txt:17 (pv_process_modules)


-- Plugin: ArrowGlyph - Glyph with customizable Arrows : Enabled
-- Plugin: Moments - Filters for Flux and Circulation Fields : Enabled
-- Plugin: GMVReader - Reader for binary or ASCII files stored in General Mesh Viewer file format : Enabled
-- Performing Test Wno-unused-result
-- Performing Test Wno-unused-result - Success
-- Plugin: NonOrthogonalSource - Non Orthogonal Source code sample : Enabled
-- Plugin: QuadView - Add a Quad view to explore data by slicing it along 3 axis. : Enabled
-- Plugin: CoProcessingScriptGenerator - Plugins for creating co-processing Python scripts : Enabled
-- Plugin: PrismPlugin - Filters for Flux and Circulation Fields : Enabled
-- Plugin: TemporalParallelismScriptGenerator - Plugin for creating Python spatio-temporal processing scripts : Disabled
-- Plugin: AnalyzeNIfTIIO - Reader/Writer for Analyze and NifTI files : Enabled
-- Plugin: ForceTime - Override time requests : Disabled
-- Plugin: PacMan - Testing plugin : Enabled
-- Plugin: SierraPlotTools - Sierra Plotting Tools : Enabled
-- Plugin: PointSprite - Point Sprites : Enabled
CMake Error at VTK/CMake/FindPythonLibs.cmake:112 (FILE):
  file STRINGS file "/usr/include/python2.7/patchlevel.h" cannot be read.
Call Stack (most recent call first):
  CMake/ParaViewPlugins.cmake:1241 (find_package)
  Plugins/PointSprite/CMakeLists.txt:30 (pv_process_modules)


-- Plugin: UncertaintyRendering - Add uncertainty visualization support : Enabled
-- Plugin: MantaView - Manta Ray-Cast View : Disabled
-- Plugin: MobileRemoteControl - Use a mobile device to view the ParaView scene and control the camera. : Enabled
-- Plugin: PythonQtPlugin - PythonQt Plugin : Disabled
-- Plugin: SurfaceLIC - Add Surface-LIC vector visualization support : Enabled
-- Configuring incomplete, errors occurred!
    Starting make
make: *** No targets specified and no makefile found.  Stop.
Command exited with non-zero status 2
0.00user 0.00system 0:00.00elapsed 0%CPU (0avgtext+0avgdata 1100maxresident)k
0inputs+0outputs (0major+326minor)pagefaults 0swaps
    Done make
    Installing ParaView to /home/samuele/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc/ParaView-4.1.0
make: *** No rule to make target `install'.  Stop.
    ---
    Installation complete for paraview-4.1.0
    Set environment variables:

        export ParaView_DIR=/home/samuele/OpenFOAM/ThirdParty-2.3.0/platforms/linux64Gcc/ParaView-4.1.0
        export PATH=$ParaView_DIR/bin:$PATH
        export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-4.1
    ---

Done

My OS is Debian Wheezy

Last edited by samiam1000; September 10, 2014 at 12:18. Reason: Missing info
samiam1000 is offline   Reply With Quote

Old   September 21, 2014, 13:40
Default
  #8
Super Moderator
 
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 8,258
Blog Entries: 34
Rep Power: 84
wyldckat is just really nicewyldckat is just really nicewyldckat is just really nicewyldckat is just really nice
Greetings to all!

@Samuele: If I'm not mistaken, on Debian you need to install the package "python-dev":
Code:
sudo apt-get install python-dev
Best regards,
Bruno
wyldckat is offline   Reply With Quote

Old   October 29, 2014, 19:48
Default
  #9
New Member
 
Qi Guan
Join Date: Aug 2011
Posts: 23
Rep Power: 5
entropies is on a distinguished road
Hi Bruno,

I tried to build ParaView on centos 7 and met the same problem in #1. I tried your method in #4. But it still won't work and gives an error like:

CMake Error: The following variables are used in this project, but they are set to NOTFOUND. Please set them or make sure they are set and tested correctly in the CMake files: MPI_EXTRA_LIBRARY (ADVANCED)

Qi
entropies is offline   Reply With Quote

Old   January 24, 2015, 14:32
Default
  #10
Super Moderator
 
Bruno Santos
Join Date: Mar 2009
Location: Lisbon, Portugal
Posts: 8,258
Blog Entries: 34
Rep Power: 84
wyldckat is just really nicewyldckat is just really nicewyldckat is just really nicewyldckat is just really nice
Quote:
Originally Posted by entropies View Post
I tried to build ParaView on centos 7 and met the same problem in #1. I tried your method in #4.
Sorry, I completely forgot about this. And I managed to test things and write detailed instructions here: http://openfoamwiki.net/index.php/In...HEL#CentOS_7.0
wyldckat is offline   Reply With Quote

Reply

Thread Tools
Display Modes

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off
Trackbacks are On
Pingbacks are On
Refbacks are On


Similar Threads
Thread Thread Starter Forum Replies Last Post
help with paraview calim_cfd OpenFOAM Installation 1 December 7, 2012 14:11
How to get Python Shell into ParaView 3.8.1? blaise OpenFOAM Installation 3 July 24, 2012 04:58
critical error during installation of openfoam Fabio88 OpenFOAM Installation 21 June 2, 2010 03:01
Problems in compiling paraview in Suse 10.3 platform chiven OpenFOAM Installation 3 December 1, 2009 08:21
Building Paraview, Redhat PaulK OpenFOAM Installation 6 October 12, 2009 13:01


All times are GMT -4. The time now is 15:39.