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nektar++ 4.4.1 make (verbose) NekMesh

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Sep 13th, 2018
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  1. [ 66%] Linking CXX executable NekMesh
  2. cd /home/mikkel/nektar/nektar++-4.4.1/build/utilities/NekMesh && /usr/bin/cmake -E cmake_link_script CMakeFiles/NekMesh.dir/link.txt --verbose=1
  3. /usr/bin/c++  -O3 -DNDEBUG -Wall -Wno-deprecated -Wno-sign-compare -DNEKTAR_RELEASE  -rdynamic CMakeFiles/NekMesh.dir/InputModules/InputGmsh.cpp.o CMakeFiles/NekMesh.dir/InputModules/InputNek.cpp.o CMakeFiles/NekMesh.dir/InputModules/InputNek5000.cpp.o CMakeFiles/NekMesh.dir/InputModules/InputNekpp.cpp.o CMakeFiles/NekMesh.dir/InputModules/InputPly.cpp.o CMakeFiles/NekMesh.dir/InputModules/InputSem.cpp.o CMakeFiles/NekMesh.dir/InputModules/InputSwan.cpp.o CMakeFiles/NekMesh.dir/InputModules/InputStarTec.cpp.o CMakeFiles/NekMesh.dir/NekMesh.cpp.o CMakeFiles/NekMesh.dir/OutputModules/OutputGmsh.cpp.o CMakeFiles/NekMesh.dir/OutputModules/OutputNekpp.cpp.o CMakeFiles/NekMesh.dir/OutputModules/OutputSTL.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessBL.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessCurve.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessCurvedEdges.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessCyl.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessDetectSurf.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessExtractSurf.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessExtractTetPrismInterface.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessJac.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessLinkCheck.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessLinear.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessPerAlign.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessScalar.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessSpherigon.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessTetSplit.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessOptiExtract.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessInsertSurface.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessExtrude.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessVarOpti/ProcessVarOpti.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessVarOpti/PreProcessing.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessVarOpti/NodeOpti.cpp.o CMakeFiles/NekMesh.dir/ProcessModules/ProcessVarOpti/ElUtil.cpp.o  -o NekMesh  -L/home/mikkel/nektar/nektar++-4.4.1/build/ThirdParty/dist/lib  -L/home/mikkel/nektar/nektar++-4.4.1/build/library/NekMeshUtils  -L/home/mikkel/nektar/nektar++-4.4.1/build/library/FieldUtils  -L/home/mikkel/nektar/nektar++-4.4.1/build/library/GlobalMapping  -L/home/mikkel/nektar/nektar++-4.4.1/build/library/MultiRegions  -L/home/mikkel/nektar/nektar++-4.4.1/build/library/Collections  -L/home/mikkel/nektar/nektar++-4.4.1/build/library/LocalRegions  -L/home/mikkel/nektar/nektar++-4.4.1/build/library/SpatialDomains  -L/home/mikkel/nektar/nektar++-4.4.1/build/library/StdRegions  -L/home/mikkel/nektar/nektar++-4.4.1/build/library/LibUtilities -Wl,-rpath,/home/mikkel/nektar/nektar++-4.4.1/build/ThirdParty/dist/lib:/home/mikkel/nektar/nektar++-4.4.1/build/library/NekMeshUtils:/home/mikkel/nektar/nektar++-4.4.1/build/library/FieldUtils:/home/mikkel/nektar/nektar++-4.4.1/build/library/GlobalMapping:/home/mikkel/nektar/nektar++-4.4.1/build/library/MultiRegions:/home/mikkel/nektar/nektar++-4.4.1/build/library/Collections:/home/mikkel/nektar/nektar++-4.4.1/build/library/LocalRegions:/home/mikkel/nektar/nektar++-4.4.1/build/library/SpatialDomains:/home/mikkel/nektar/nektar++-4.4.1/build/library/StdRegions:/home/mikkel/nektar/nektar++-4.4.1/build/library/LibUtilities: ../../library/NekMeshUtils/libNekMeshUtils.so.4.4.1 ../../library/FieldUtils/libFieldUtils.so.4.4.1 ../../library/GlobalMapping/libGlobalMapping.so.4.4.1 ../../library/MultiRegions/libMultiRegions.so.4.4.1 ../../library/Collections/libCollections.so.4.4.1 ../../library/LocalRegions/libLocalRegions.so.4.4.1 ../../library/SpatialDomains/libSpatialDomains.so.4.4.1 ../../library/StdRegions/libStdRegions.so.4.4.1 ../../library/LibUtilities/libLibUtilities.so.4.4.1 -lboost_thread -lboost_iostreams -lboost_date_time -lboost_program_options -lboost_filesystem -lboost_system -lboost_timer -lboost_chrono -lz -ltinyxml -lrt -llapack -lblas
  4. /usr/bin/ld: CMakeFiles/NekMesh.dir/ProcessModules/ProcessVarOpti/NodeOpti.cpp.o: undefined reference to symbol 'pthread_condattr_setclock@@GLIBC_2.3.3'
  5. /usr/bin/ld: /usr/lib/libpthread.so.0: error adding symbols: DSO missing from command line
  6. collect2: error: ld returned 1 exit status
  7. make[2]: *** [utilities/NekMesh/CMakeFiles/NekMesh.dir/build.make:585: utilities/NekMesh/NekMesh] Error 1
  8. make[2]: Leaving directory '/home/mikkel/nektar/nektar++-4.4.1/build'
  9. make[1]: *** [CMakeFiles/Makefile2:4573: utilities/NekMesh/CMakeFiles/NekMesh.dir/all] Error 2
  10. make[1]: *** Waiting for unfinished jobs....
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