[Paraview] problems building superbuild

Sebastien Jourdain sebastien.jourdain at kitware.com
Mon May 5 11:46:45 EDT 2014 

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
> > >
> > >
> > >
> > >
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> >
> >
>
>
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