[Paraview] problems building superbuild

Sebastien Jourdain sebastien.jourdain at kitware.com
Mon May 5 16:57:53 EDT 2014 

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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