<div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px">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?</span><br>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px">=> That's exactly the case... So which option is missing?</span></div></div>
<div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, May 5, 2014 at 9:25 AM, Brock Palen <span dir="ltr"><<a href="mailto:brockp@umich.edu" target="_blank">brockp@umich.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Ok here is the error about pthread_cancel:<br>
<br>
Any thoughts why this isn't getting picked up?<br>
<br>
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?<br>
<br>
Linking CXX shared library ../../../lib/<a href="http://libvtkPVClientServerCoreCore-pv4.1.so" target="_blank">libvtkPVClientServerCoreCore-pv4.1.so</a><br>
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<br>

/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<br>

ralDataInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVTimerInformation.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkSession.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkSessionIterator.cxx.o CMakeFiles/vtkPVClientServerCoreCore.d<br>

ir/vtkTCPNetworkAccessManager.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPythonAnimationCue.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPythonExtractSelection.cxx.o CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPythonProgrammableFilter.cxx.o CMa<br>

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 ../<br>

../../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<br>

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<br>

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<br>

ath /usr/local/torque/lib/libtorque.so -ldl -lm -lnuma -lrt -lnsl -lutil -lm ../../../lib/libvtkFiltersModeling-pv4.1.so.1 ../..<br>
/../lib/libvtkRenderingCore-pv4.1.so.1 ../../../lib/libvtkFiltersExtraction-pv4.1.so.1 ../../../lib/libvtkFiltersStatistics-pv4.<br>
1.so.1 ../../../lib/libvtkImagingFourier-pv4.1.so.1 ../../../lib/libvtkImagingCore-pv4.1.so.1 ../../../lib/<a href="http://libvtkalglib-pv4.1.so" target="_blank">libvtkalglib-pv4.1.so</a><br>
.1 ../../../lib/libvtkFiltersGeometry-pv4.1.so.1 ../../../lib/libvtkFiltersSources-pv4.1.so.1 ../../../lib/libvtkFiltersGeneral-<br>
pv4.1.so.1 ../../../lib/libvtkCommonComputationalGeometry-pv4.1.so.1 ../../../lib/libvtkPVCommon-pv4.1.so.1 ../../../lib/libvtkC<br>
lientServer-pv4.1.so.1 ../../../lib/libvtkPythonInterpreter-pv4.1.so.1 ../../../lib/libvtkWrappingPython27Core-pv4.1.so.1 /tmp/b<br>
rockp/paraview-sb/install/lib/<a href="http://libpython2.7.so" target="_blank">libpython2.7.so</a> ../../../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<br>

CMakeFiles/vtkPVClientServerCoreCore.dir/vtkExtractsDeliveryHelper.cxx.o:(.data.rel.ro.local+0x0): undefined reference to `pthread_cancel'<br>
CMakeFiles/vtkPVClientServerCoreCore.dir/vtkMPIMToNSocketConnection.cxx.o:(.data.rel.ro.local+0x0): undefined reference to `pthread_cancel'<br>
CMakeFiles/vtkPVClientServerCoreCore.dir/vtkMPIMToNSocketConnectionPortInformation.cxx.o:(.data.rel.ro.local+0x0): undefined reference to `pthread_cancel'<br>
CMakeFiles/vtkPVClientServerCoreCore.dir/vtkProcessModuleAutoMPI.cxx.o:(.data.rel.ro.local+0x0): undefined reference to `pthread_cancel'<br>
CMakeFiles/vtkPVClientServerCoreCore.dir/vtkProcessModule.cxx.o:(.data.rel.ro.local+0x0): undefined reference to `pthread_cancel'<br>
CMakeFiles/vtkPVClientServerCoreCore.dir/vtkPVArrayInformation.cxx.o:(.data.rel.ro.local+0x0): more undefined references to `pthread_cancel' follow<br>
collect2: error: ld returned 1 exit status<br>
make[2]: *** [lib/libvtkPVClientServerCoreCore-pv4.1.so.1] Error 1<br>
make[2]: Leaving directory `/tmp/brockp/paraview-sb/paraview/src/paraview-build'<br>
make[1]: *** [ParaViewCore/ClientServerCore/Core/CMakeFiles/vtkPVClientServerCoreCore.dir/all] Error 2<br>
make[1]: Leaving directory `/tmp/brockp/paraview-sb/paraview/src/paraview-build'<br>
<div class="im HOEnZb"><br>
Brock Palen<br>
<a href="http://www.umich.edu/~brockp" target="_blank">www.umich.edu/~brockp</a><br>
CAEN Advanced Computing<br>
XSEDE Campus Champion<br>
<a href="mailto:brockp@umich.edu">brockp@umich.edu</a><br>
<a href="tel:%28734%29936-1985" value="+17349361985">(734)936-1985</a><br>
<br>
<br>
<br>
</div><div class="HOEnZb"><div class="h5">On May 2, 2014, at 4:19 PM, Sebastien Jourdain <<a href="mailto:sebastien.jourdain@kitware.com">sebastien.jourdain@kitware.com</a>> wrote:<br>
<br>
> Broke, you can still go and run CMake to each sub-project independently and all make as well.<br>
><br>
> For example:<br>
> cd paraview/src/paraview-build<br>
> ccmake .<br>
> make<br>
><br>
> Seb<br>
><br>
><br>
> On Fri, May 2, 2014 at 1:42 PM, Brock Palen <<a href="mailto:brockp@umich.edu">brockp@umich.edu</a>> wrote:<br>
> Sebastien,<br>
> 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.<br>

> I find a little more if I run:  make VERBOSE=1  but still the errors are mixed in with good compiles.<br>
><br>
> So two quesions, how can I force serial make when debugging where the error is.<br>
><br>
> 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?<br>
><br>
> Brock Palen<br>
> <a href="http://www.umich.edu/~brockp" target="_blank">www.umich.edu/~brockp</a><br>
> CAEN Advanced Computing<br>
> XSEDE Campus Champion<br>
> <a href="mailto:brockp@umich.edu">brockp@umich.edu</a><br>
> <a href="tel:%28734%29936-1985" value="+17349361985">(734)936-1985</a><br>
><br>
><br>
><br>
> On Apr 30, 2014, at 4:42 PM, Sebastien Jourdain <<a href="mailto:sebastien.jourdain@kitware.com">sebastien.jourdain@kitware.com</a>> wrote:<br>
><br>
> > Hi Brock,<br>
> ><br>
> > make sure that ENABLE_cosmotools is OFF.<br>
> ><br>
> > That is the only thing that depends on generic_io.<br>
> > If you turned it ON once, you may need to delete your build tree and start again from scratch.<br>
> ><br>
> > If that is not the solution, we will need to digg more and figure out why generic_io was pulled in.<br>
> > But I couldn't find any reference in the super build.<br>
> ><br>
> > Seb<br>
> ><br>
> ><br>
> > On Wed, Apr 30, 2014 at 2:16 PM, Brock Palen <<a href="mailto:brockp@umich.edu">brockp@umich.edu</a>> wrote:<br>
> > 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).<br>
> ><br>
> >     module load gcc/4.7.0<br>
> >     module load openmpi/1.6.5/gcc/4.7.0<br>
> >     module load cmake/2.8.8<br>
> ><br>
> >     git clone git://<a href="http://paraview.org/ParaViewSuperbuild.git" target="_blank">paraview.org/ParaViewSuperbuild.git</a><br>
> >     git checkout -b 4.1.0 v4.1.0<br>
> ><br>
> >     mkdir paraview-bin<br>
> >     cd paraview-bin<br>
> ><br>
> >     ccmake ../ParaViewSuperbuild<br>
> ><br>
> ><br>
> > 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:<br>
> ><br>
> >   Failed to clone repository:<br>
> >   'git://<a href="http://kwsource.kitwarein.com/genericio/genericio.git" target="_blank">kwsource.kitwarein.com/genericio/genericio.git</a>'<br>
> ><br>
> > 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).<br>
> ><br>
> > Is there any way to get more information about why genericio is being pulled in?   <a href="http://kwsource.kitwarein.com" target="_blank">kwsource.kitwarein.com</a> doesn't even resolve.<br>
> ><br>
> > Thanks!<br>
> ><br>
> > Brock Palen<br>
> > <a href="http://www.umich.edu/~brockp" target="_blank">www.umich.edu/~brockp</a><br>
> > CAEN Advanced Computing<br>
> > XSEDE Campus Champion<br>
> > <a href="mailto:brockp@umich.edu">brockp@umich.edu</a><br>
> > <a href="tel:%28734%29936-1985" value="+17349361985">(734)936-1985</a><br>
> ><br>
> ><br>
> ><br>
> ><br>
> > _______________________________________________<br>
> > Powered by <a href="http://www.kitware.com" target="_blank">www.kitware.com</a><br>
> ><br>
> > Visit other Kitware open-source projects at <a href="http://www.kitware.com/opensource/opensource.html" target="_blank">http://www.kitware.com/opensource/opensource.html</a><br>
> ><br>
> > Please keep messages on-topic and check the ParaView Wiki at: <a href="http://paraview.org/Wiki/ParaView" target="_blank">http://paraview.org/Wiki/ParaView</a><br>
> ><br>
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> ><br>
> ><br>
><br>
><br>
<br>
</div></div></blockquote></div><br></div>