[Paraview] problems building superbuild

Brock Palen brockp at umich.edu
Thu May 8 00:27:16 EDT 2014 

Ok this all worked.

Few notes though, the 

make install

Using the super build breaks PDB file reading.  Paraview tries to open an elements.xml file from the source tree, and bombs out.

Just FYI.  Thanks, we have a limited paraview working for VTK files for OpenFoam which was the request, with our local OpenMPI install, with a subset of other readers.  We always try to install the kitchen sink to support as many user bases as possible.

Thanks for the tool!

Brock Palen
www.umich.edu/~brockp
CAEN Advanced Computing
XSEDE Campus Champion
brockp at umich.edu
(734)936-1985



On May 5, 2014, at 4:57 PM, Sebastien Jourdain <sebastien.jourdain at kitware.com> wrote:

> Yes you can...
> 
> 
> On Mon, May 5, 2014 at 1:50 PM, Brock Palen <brockp at umich.edu> wrote:
> Adding the -pthread or -lpthread to CMAKE_CXX_FLAGS CMAKE_C_FLAGS, in the top level superbuild config breaks building python,
> 
> Using USE_SYSTEM_python yes
> 
> Breaks buidling numpy because it tries todo it by egg, egg-info is missing. even if you leave ENABLE_numpy on or if you have numpy installed in your python (we do) so I have now just ripped out all the python and trying again.
> 
> Is paraview the last build in super build?  Thus can I do
> 
> ccmake  (spuer build)
> make (until paraview fails)
> 
> cd paraview/src/paraview-build/
> ccmake .
> (add pthread to compiler flags)
> 
> make
> 
> At that point can I go back to the top level and make my package that support our install of OpenMPI?  That is all I want, as we have IB and MXM/FCA, I am building full GUI to support users who use our VNC and future Virtual GL for lack of using paraview in client server relationship.
> 
> Brock Palen
> www.umich.edu/~brockp
> CAEN Advanced Computing
> XSEDE Campus Champion
> brockp at umich.edu
> (734)936-1985
> 
> 
> 
> On May 5, 2014, at 2:14 PM, Brock Palen <brockp at umich.edu> wrote:
> 
> > Ok those last two changes fixed it, so the configuration checks for some reason are not catching that pthread needs to be explicitly passed for some of the libraries.
> >
> > Then because I was not using System Python, to get paraview to build I had to do:
> >
> > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/tmp/brockp/paraview-sb/python/src/python-build/ make -j 10
> >
> > It then built fine.
> >
> > I am going to back up and see if I can make the full super build to work as expected.
> >
> > Brock Palen
> > www.umich.edu/~brockp
> > CAEN Advanced Computing
> > XSEDE Campus Champion
> > brockp at umich.edu
> > (734)936-1985
> >
> >
> >
> > On May 5, 2014, at 1:44 PM, Brock Palen <brockp at umich.edu> wrote:
> >
> >> Right ok it is actually grabbing everything, I thought it wasn't due to the way the compile acted, but if I did:
> >>
> >> make -j 4  it failed right away,  make (serial) takes a long time to fail, so I thought it was touching everything over again.  I should have used better language.  It does appear to grab everything.
> >>
> >> As for the pthread error,  it still fails even though I added  -lpthread  to
> >> CMAKE_EXE_LINKER_FLAGS
> >>
> >> I am now running a new configure/gen adding it to CMAKE_CXX_FLAGS CMAKE_C_FLAGS   and will see if that works,
> >>
> >> Brock Palen
> >> www.umich.edu/~brockp
> >> CAEN Advanced Computing
> >> XSEDE Campus Champion
> >> brockp at umich.edu
> >> (734)936-1985
> >>
> >>
> >>
> >> On May 5, 2014, at 11:46 AM, Sebastien Jourdain <sebastien.jourdain at kitware.com> wrote:
> >>
> >>> Also is there anyway to run ccmake in the paraview-build directory and have it use all the options from the superbuild ccmake? Just so I can see what was set?
> >>>
> >>> => That's exactly the case... So which option is missing?
> >>>
> >>>
> >>> On Mon, May 5, 2014 at 9:25 AM, Brock Palen <brockp at umich.edu> wrote:
> >>> Ok here is the error about pthread_cancel:
> >>>
> >>> Any thoughts why this isn't getting picked up?
> >>>
> >>> Also is there anyway to run ccmake in the paraview-build directory and have it use all the options from the superbuild ccmake? Just so I can see what was set?
> >>>
> >>> Linking CXX shared library ../../../lib/libvtkPVClientServerCoreCore-pv4.1.so
> >>> cd /tmp/brockp/paraview-sb/paraview/src/paraview-build/ParaViewCore/ClientServerCore/Core && /usr/cac/rhel6/cmake/2.8.8/bin/cmake -E cmake_link_script CMakeFiles/vtkPVClientServerCoreCore.dir/link.txt --verbose=1
> >>> /home/software/rhel6/gcc/4.7.0/bin/c++  -fPIC -fPIC  -Wno-deprecated -g -Wl,--fatal-warnings -Wl,--no-undefined -lc -L/tmp/brockp/paraview-sb/install/lib  -shared -Wl,-soname,libvtkPVClientServerCoreCore-pv4.1.so.1 -o ../../../lib/libvtkPVClientServerCoreCore-pv4.1.so.1 CMakeFiles/vtkPVClientServerCoreCore.dir/vtkCompleteArrays.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkExtractsDeliveryHelper.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkMPIMToNSocketConnection.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkMPIMToNSocketConnectionPortInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkNetworkAccessManager.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPConvertSelection.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkProcessModuleAutoMPI.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkProcessModule.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVAlgorithmPortsInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVArrayInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVClassNameInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVCompositeDataInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVCompositeDataInformationIterator.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVDataInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVDataInformationHelper.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVDataSetAttributesInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVDataSizeInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVDisableStackTraceSignalHandler.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVEnableStackTraceSignalHandler.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVExtractSelection.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVExtractArraysOverTime.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVGenericAttributeInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVMemoryUseInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVMultiClientsInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVOptions.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVOptionsXMLParser.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVPlugin.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVPluginLoader.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVPluginsInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVPluginTracker.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVProgressHandler.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVPythonModule.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVPythonOptions.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVPythonPluginInterface.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVServerInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVServerManagerPluginInterface.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVServerOptions.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVSession.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVSILInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVSystemConfigInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVSystemInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVTempo
> >>> ralDataInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVTimerInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkSession.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkSessionIterator.cxx.o CMakeFiles/vtkPVClientServerCoreCore.d
> >>> ir/vtkTCPNetworkAccessManager.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPythonAnimationCue.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPythonExtractSelection.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPythonProgrammableFilter.cxx.o CMa
> >>> keFiles/vtkPVClientServerCoreCore.dir/vtkPythonAnnotationFilter.cxx.o ../../../lib/libvtkFiltersExtraction-pv4.1.so.1 ../../../lib/libvtkFiltersParallel-pv4.1.so.1 ../../../lib/libvtkFiltersProgrammable-pv4.1.so.1 ../../../lib/libvtkPVCommon-pv4.1.so.1 ../
> >>> ../../lib/libvtkPVCommon-pv4.1.so.1 ../../../lib/libvtkPVVTKExtensionsCore-pv4.1.so.1 ../../../lib/libvtkParallelMPI-pv4.1.so.1 ../../../lib/libvtkPythonInterpreter-pv4.1.so.1 ../../../lib/libvtksys-pv4.1.so.1 /home/software/rhel6/openmpi-1.6.5/gcc-4.7.0/l
> >>> ib/libmpi.so -losmcomp -lrdmacm -libverbs /home/software/rhel6/fca/2.5/lib/libfca.so -lrt -lnsl -lutil -lm /home/software/rhel6/mxm/2.0/lib/libmxm.so -lpsm_infinipath /usr/local/torque/lib/libtorque.so -ldl -lm -lnuma -lrt -lnsl -lutil -lm /home/software/r
> >>> hel6/openmpi-1.6.5/gcc-4.7.0/lib/libmpi_cxx.so /home/software/rhel6/openmpi-1.6.5/gcc-4.7.0/lib/libmpi.so -losmcomp -lrdmacm -libverbs /home/software/rhel6/fca/2.5/lib/libfca.so -lrt -lnsl -lutil -lm /home/software/rhel6/mxm/2.0/lib/libmxm.so -lpsm_infinip
> >>> ath /usr/local/torque/lib/libtorque.so -ldl -lm -lnuma -lrt -lnsl -lutil -lm ../../../lib/libvtkFiltersModeling-pv4.1.so.1 ../..
> >>> /../lib/libvtkRenderingCore-pv4.1.so.1 ../../../lib/libvtkFiltersExtraction-pv4.1.so.1 ../../../lib/libvtkFiltersStatistics-pv4.
> >>> 1.so.1 ../../../lib/libvtkImagingFourier-pv4.1.so.1 ../../../lib/libvtkImagingCore-pv4.1.so.1 ../../../lib/libvtkalglib-pv4.1.so
> >>> .1 ../../../lib/libvtkFiltersGeometry-pv4.1.so.1 ../../../lib/libvtkFiltersSources-pv4.1.so.1 ../../../lib/libvtkFiltersGeneral-
> >>> pv4.1.so.1 ../../../lib/libvtkCommonComputationalGeometry-pv4.1.so.1 ../../../lib/libvtkPVCommon-pv4.1.so.1 ../../../lib/libvtkC
> >>> lientServer-pv4.1.so.1 ../../../lib/libvtkPythonInterpreter-pv4.1.so.1 ../../../lib/libvtkWrappingPython27Core-pv4.1.so.1 /tmp/b
> >>> rockp/paraview-sb/install/lib/libpython2.7.so ../../../lib/libvtkIOXMLParser-pv4.1.so.1 ../../../lib/libvtkFiltersCore-pv4.1.so.1 ../../../lib/libvtkParallelCore-pv4.1.so.1 ../../../lib/libvtkIOLegacy-pv4.1.so.1 ../../../lib/libvtkIOCore-pv4.1.so.1 ../../../lib/libvtkCommonExecutionModel-pv4.1.so.1 ../../../lib/libvtkCommonDataModel-pv4.1.so.1 ../../../lib/libvtkCommonSystem-pv4.1.so.1 ../../../lib/libvtkCommonTransforms-pv4.1.so.1 ../../../lib/libvtkCommonMisc-pv4.1.so.1 ../../../lib/libvtkCommonMath-pv4.1.so.1 ../../../lib/libvtkCommonCore-pv4.1.so.1 ../../../lib/libvtksys-pv4.1.so.1 -ldl /home/software/rhel6/openmpi-1.6.5/gcc-4.7.0/lib/libmpi_cxx.so -Wl,-rpath,/tmp/brockp/paraview-sb/paraview/src/paraview-build/lib:/home/software/rhel6/openmpi-1.6.5/gcc-4.7.0/lib:/home/software/rhel6/fca/2.5/lib:/home/software/rhel6/mxm/2.0/lib:/usr/local/torque/lib:/tmp/brockp/paraview-sb/install/lib: -Wl,-rpath-link,/tmp/brockp/paraview-sb/paraview/src/paraview-build/lib
> >>> CMakeFiles/vtkPVClientServerCoreCore.dir/vtkExtractsDeliveryHelper.cxx.o:(.data.rel.ro.local+0x0): undefined reference to `pthread_cancel'
> >>> CMakeFiles/vtkPVClientServerCoreCore.dir/vtkMPIMToNSocketConnection.cxx.o:(.data.rel.ro.local+0x0): undefined reference to `pthread_cancel'
> >>> CMakeFiles/vtkPVClientServerCoreCore.dir/vtkMPIMToNSocketConnectionPortInformation.cxx.o:(.data.rel.ro.local+0x0): undefined reference to `pthread_cancel'
> >>> CMakeFiles/vtkPVClientServerCoreCore.dir/vtkProcessModuleAutoMPI.cxx.o:(.data.rel.ro.local+0x0): undefined reference to `pthread_cancel'
> >>> CMakeFiles/vtkPVClientServerCoreCore.dir/vtkProcessModule.cxx.o:(.data.rel.ro.local+0x0): undefined reference to `pthread_cancel'
> >>> CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVArrayInformation.cxx.o:(.data.rel.ro.local+0x0): more undefined references to `pthread_cancel' follow
> >>> collect2: error: ld returned 1 exit status
> >>> make[2]: *** [lib/libvtkPVClientServerCoreCore-pv4.1.so.1] Error 1
> >>> make[2]: Leaving directory `/tmp/brockp/paraview-sb/paraview/src/paraview-build'
> >>> make[1]: *** [ParaViewCore/ClientServerCore/Core/CMakeFiles/vtkPVClientServerCoreCore.dir/all] Error 2
> >>> make[1]: Leaving directory `/tmp/brockp/paraview-sb/paraview/src/paraview-build'
> >>>
> >>> Brock Palen
> >>> www.umich.edu/~brockp
> >>> CAEN Advanced Computing
> >>> XSEDE Campus Champion
> >>> brockp at umich.edu
> >>> (734)936-1985
> >>>
> >>>
> >>>
> >>> On May 2, 2014, at 4:19 PM, Sebastien Jourdain <sebastien.jourdain at kitware.com> wrote:
> >>>
> >>>> Broke, you can still go and run CMake to each sub-project independently and all make as well.
> >>>>
> >>>> For example:
> >>>> cd paraview/src/paraview-build
> >>>> ccmake .
> >>>> make
> >>>>
> >>>> Seb
> >>>>
> >>>>
> >>>> On Fri, May 2, 2014 at 1:42 PM, Brock Palen <brockp at umich.edu> wrote:
> >>>> Sebastien,
> >>>> That helped a lot, and I have sense disabled a few more plugins to get builds to go.  I keep having it error out.  It appears that the top level make in superbuild doesn't respect -j1  so I lose the error message.
> >>>> I find a little more if I run:  make VERBOSE=1  but still the errors are mixed in with good compiles.
> >>>>
> >>>> So two quesions, how can I force serial make when debugging where the error is.
> >>>>
> >>>> Another is one of the errors was not finding a pthread library (linker error pthread_close not defined)  how would I even go about adding -l pthread   to the LDFLAGS for a project like this?
> >>>>
> >>>> Brock Palen
> >>>> www.umich.edu/~brockp
> >>>> CAEN Advanced Computing
> >>>> XSEDE Campus Champion
> >>>> brockp at umich.edu
> >>>> (734)936-1985
> >>>>
> >>>>
> >>>>
> >>>> On Apr 30, 2014, at 4:42 PM, Sebastien Jourdain <sebastien.jourdain at kitware.com> wrote:
> >>>>
> >>>>> Hi Brock,
> >>>>>
> >>>>> make sure that ENABLE_cosmotools is OFF.
> >>>>>
> >>>>> That is the only thing that depends on generic_io.
> >>>>> If you turned it ON once, you may need to delete your build tree and start again from scratch.
> >>>>>
> >>>>> If that is not the solution, we will need to digg more and figure out why generic_io was pulled in.
> >>>>> But I couldn't find any reference in the super build.
> >>>>>
> >>>>> Seb
> >>>>>
> >>>>>
> >>>>> On Wed, Apr 30, 2014 at 2:16 PM, Brock Palen <brockp at umich.edu> wrote:
> >>>>> I am trying to build paraview for our cluster using the superbuild.  I am doing this because I want both the gui and server (we have VNC nodes, and client server users).
> >>>>>
> >>>>>   module load gcc/4.7.0
> >>>>>   module load openmpi/1.6.5/gcc/4.7.0
> >>>>>   module load cmake/2.8.8
> >>>>>
> >>>>>   git clone git://paraview.org/ParaViewSuperbuild.git
> >>>>>   git checkout -b 4.1.0 v4.1.0
> >>>>>
> >>>>>   mkdir paraview-bin
> >>>>>   cd paraview-bin
> >>>>>
> >>>>>   ccmake ../ParaViewSuperbuild
> >>>>>
> >>>>>
> >>>>> at this point I set to use system_mpi a collection of readers etc, but no mater what I do the build always fails with:
> >>>>>
> >>>>> Failed to clone repository:
> >>>>> 'git://kwsource.kitwarein.com/genericio/genericio.git'
> >>>>>
> >>>>> I googled around for this and found reference to private plugins you can't distribute, but I specifically disable genericio (awful name if it is a private plugin, sounds like your standard readers).
> >>>>>
> >>>>> Is there any way to get more information about why genericio is being pulled in?   kwsource.kitwarein.com doesn't even resolve.
> >>>>>
> >>>>> Thanks!
> >>>>>
> >>>>> Brock Palen
> >>>>> www.umich.edu/~brockp
> >>>>> CAEN Advanced Computing
> >>>>> XSEDE Campus Champion
> >>>>> brockp at umich.edu
> >>>>> (734)936-1985
> >>>>>
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Powered by www.kitware.com
> >>>>>
> >>>>> Visit other Kitware open-source projects at http://www.kitware.com/opensource/opensource.html
> >>>>>
> >>>>> Please keep messages on-topic and check the ParaView Wiki at: http://paraview.org/Wiki/ParaView
> >>>>>
> >>>>> Follow this link to subscribe/unsubscribe:
> >>>>> http://www.paraview.org/mailman/listinfo/paraview
> >>>>>
> >>>>>
> >>>>
> >>>>
> >>>
> >>>
> >>
> >
> 
> 

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