[Paraview] problems building superbuild

Mon May 5 15:50:13 EDT 2014

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:
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>>>>> 
>>>>> 
>>>> 
>>>> 
>>> 
>>> 
>> 
> 

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