Did you specify "make *-rebuild" after changing these options? This may not be picked up automatically (although it should).
-erik
On Mon, Aug 6, 2012 at 6:15 PM, Scott Hawley scott.hawley@belmont.edu wrote:
Hi. Apparently the build system is looking for -lmpi_cxx, which does not exist on Nautilus. instead it is -lmpi++. I tried setting MPI_LIBS directly in my options file, but it didn't remove the reference. See error at bottom of this message.
% cat ~/options.nautilus.gnu | grep -i MPI CPPFLAGS = -LMPICH_IGNORE_CXX_SEEK MPI_DIR = /opt/sgi/mpt/mpt-2.04/ MPI_LIBS = mpi mpi++
The only place this reference seems to be is.. % grep -r mpi_cxx configs/etk/ configs/etk/bindings/Configuration/Capabilities/make.MPI.defn:MPI_LIBS = mpi mpi_cxx
(it's not in my environment... % env | /bin/grep mpi % )
How to fix this? Thanks, Scott
make etk SILENT=no ... ________________________________________________________________________ Creating cactus_etk in /nics/c/home/hawleys/Cactus/exe from CactusArchive/ADM EinsteinAnalysis/ADMAnalysis EinsteinBase/ADMBase EinsteinAnalysis/ADMConstraints EinsteinBase/ADMCoupling EinsteinBase/ADMMacros AEIThorns/ADMMass AEIThorns/AEILocalInterp EinsteinAnalysis/AHFinder EinsteinAnalysis/AHFinderDirect ExternalLibraries/BLAS CactusBase/Boundary EinsteinAnalysis/CalcK Carpet/Carpet Carpet/CarpetEvolutionMask Carpet/CarpetIOASCII Carpet/CarpetIOBasic Carpet/CarpetIOHDF5 Carpet/CarpetIOScalar Carpet/CarpetInterp Carpet/CarpetInterp2 Carpet/CarpetLib Carpet/CarpetMask Carpet/CarpetReduce Carpet/CarpetRegrid Carpet/CarpetRegrid2 Carpet/CarpetSlab Carpet/CarpetTracker CactusBase/CartGrid3D CactusNumerical/Cartoon2D EinsteinBase/Constants CactusBase/CoordBase EinsteinBase/CoordGauge CactusNumerical/Dissipation EinsteinInitialData/DistortedBHIVP EinsteinAnalysis/EHFinder EinsteinBase/EOS_Base EinsteinEOS/EOS_Hybrid EinsteinEOS/EOS_IdealFluid EinsteinEOS/EOS_Omni EinsteinEOS/EOS_Polytrope EinsteinExact/EinsteinExact_Test CactusElliptic/EllBase CactusElliptic/EllSOR EinsteinInitialData/Exact EinsteinAnalysis/Extract ExternalLibraries/FFTW3 CactusUtils/Formaline CactusBase/Fortran EinsteinEvolve/GRHydro EinsteinInitialData/GRHydro_InitData ExternalLibraries/GSL EinsteinExact/GaugeWave KrancNumericalTools/GenericFD ExternalLibraries/HDF5 CactusConnect/HTTPD CactusConnect/HTTPDExtra EinsteinBase/HydroBase EinsteinAnalysis/Hydro_Analysis EinsteinInitialData/Hydro_InitExcision EinsteinInitialData/IDAnalyticBH EinsteinInitialData/IDAxiBrillBH EinsteinInitialData/IDAxiOddBrillBH EinsteinInitialData/IDBrillData EinsteinInitialData/IDConstraintViolate EinsteinInitialData/IDFileADM EinsteinInitialData/IDLinearWaves CactusWave/IDScalarWave CactusWave/IDScalarWaveC CactusWave/IDScalarWaveCXX CactusWave/IDScalarWaveElliptic CactusBase/IOASCII CactusBase/IOBasic CactusPUGHIO/IOHDF5 CactusPUGHIO/IOHDF5Util CactusIO/IOJpeg CactusBase/IOUtil CactusBase/InitBase CactusNumerical/InterpToArray EinsteinExact/KerrSchild ExternalLibraries/LAPACK ExternalLibraries/LORENE EinsteinEvolve/LegoExcision CactusNumerical/LocalInterp CactusNumerical/LocalReduce Carpet/LoopControl McLachlan/ML_ADMConstraints McLachlan/ML_ADMQuantities McLachlan/ML_BSSN McLachlan/ML_BSSN_Helper McLachlan/ML_BSSN_Test McLachlan/ML_CCZ4 McLachlan/ML_CCZ4_Helper McLachlan/ML_CCZ4_Test McLachlan/ML_WaveToy ExternalLibraries/MPI EinsteinInitialData/Meudon_Bin_BH EinsteinInitialData/Meudon_Bin_NS EinsteinInitialData/Meudon_Mag_NS EinsteinExact/Minkowski CactusNumerical/MoL EinsteinExact/ModifiedSchwarzschildBL EinsteinAnalysis/Multipole CactusUtils/NaNChecker EinsteinEvolve/NewRad CactusUtils/Nice EinsteinInitialData/NoExcision CactusUtils/NoMPI CactusNumerical/Noise CactusNumerical/Norms PITTNullCode/NullConstr PITTNullCode/NullDecomp PITTNullCode/NullEvolve PITTNullCode/NullExact PITTNullCode/NullGrid PITTNullCode/NullInterp PITTNullCode/NullNews PITTNullCode/NullPsiInt PITTNullCode/NullSHRExtract PITTNullCode/NullVars ExternalLibraries/OpenSSL CactusPUGH/PUGH CactusPUGH/PUGHInterp CactusPUGH/PUGHReduce CactusPUGH/PUGHSlab CactusNumerical/Periodic AEIThorns/PunctureTracker LSUThorns/QuasiLocalMeasures CactusNumerical/ReflectionSymmetry EinsteinInitialData/RotatingDBHIVP CactusNumerical/RotatingSymmetry180 CactusNumerical/RotatingSymmetry90 EinsteinUtils/SetMask_SphericalSurface EinsteinExact/ShiftedGaugeWave CactusNumerical/Slab CactusNumerical/SlabTest CactusConnect/Socket CactusNumerical/SpaceMask PITTNullCode/SphericalHarmonicDecomp PITTNullCode/SphericalHarmonicRecon CactusNumerical/SphericalSurface EinsteinBase/StaticConformal LSUThorns/SummationByParts CactusBase/SymBase AEIThorns/SystemStatistics TAT/TATelliptic EinsteinUtils/TGRtensor EinsteinInitialData/TOVSolver CactusUtils/TerminationTrigger CactusTest/TestArrays CactusTest/TestComplex CactusTest/TestCoordinates CactusTest/TestFortranDependencies1 CactusTest/TestFortranDependencies2 CactusTest/TestFpointerNULL CactusTest/TestFreeF90 CactusTest/TestGlobalReduce CactusTest/TestInclude1 CactusTest/TestInclude2 CactusTest/TestLocalReduce CactusTest/TestLoop CactusTest/TestPar CactusTest/TestReduce CactusTest/TestSchedule CactusTest/TestStrings CactusTest/TestTable CactusTest/TestTimers CactusTest/TestTypes CactusBase/Time CactusUtils/TimerReport EinsteinBase/TmunuBase EinsteinInitialData/TwoPunctures EinsteinExact/Vaidya2 LSUThorns/Vectors CactusWave/WaveBinarySource CactusWave/WaveToyC CactusWave/WaveToyCXX CactusWave/WaveToyExtra CactusWave/WaveToyF77 CactusWave/WaveToyF90 CactusWave/WaveToyFreeF90 EinsteinAnalysis/WeylScal4 ExternalLibraries/hwloc ExternalLibraries/libjpeg ExternalLibraries/zlib datetime=`/bin/date +'%Y-%m-%dT%H:%M:%S%z' 2>&1` ; \ if [ $? != 0 ]; then datetime=`/bin/date` ; fi ; \ gcc -std=gnu99 -m64 -g -O0 -O3 -fopenmp -DCCTK_COMPILE_DATETIME="$datetime" -c -o "/nics/c/home/hawleys/Cactus/configs/etk/datestamp.o" -I"/nics/c/home/hawleys/Cactus/src/include" -I"/nics/c/home/hawleys/Cactus/configs/etk/config-data" "/nics/c/home/hawleys/Cactus/src/datestamp.c" if [ ! -d /nics/c/home/hawleys/Cactus/exe ]; then mkdir -p /nics/c/home/hawleys/Cactus/exe ; fi g++ -o "/nics/c/home/hawleys/Cactus/exe/cactus_etk" -LMPICH_IGNORE_CXX_SEEK -g -DCARPET_DEBUG -fopenmp -O2 -m64 -std=gnu++0x -D__builtin_isinf=std::isinf -D__builtin_isnan=std::isnan -g -O0 -O3 -fopenmp "/nics/c/home/hawleys/Cactus/configs/etk/datestamp.o" -L/nics/c/home/hawleys/Cactus/configs/etk/lib -lthorn_Cactus -lthorn_CactusBindings -lthorn_CarpetEvolutionMask -lthorn_IOHDF5 -lthorn_IOHDF5Util -lthorn_CarpetIOScalar -lthorn_ML_WaveToy -lthorn_Meudon_Mag_NS -lthorn_HTTPDExtra -lthorn_HTTPD -lthorn_RotatingSymmetry90 -lthorn_NoExcision -lthorn_Hydro_InitExcision -lthorn_ML_BSSN_Helper -lthorn_GaugeWave -lthorn_NullPsiInt -lthorn_PUGHInterp -lthorn_Cartoon2D -lthorn_SetMask_SphericalSurface -lthorn_EHFinder -lthorn_EOS_IdealFluid -lthorn_ModifiedSchwarzschildBL -lthorn_Multipole -lthorn_CarpetTracker -lthorn_SphericalHarmonicRecon -lthorn_QuasiLocalMeasures -lthorn_TGRtensor -lthorn_Exact -lthorn_Periodic -lthorn_IOJpeg -lthorn_CarpetRegrid -lthorn_TestGlobalReduce -lthorn_CarpetInterp2 -lthorn_Vaidya2 -lthorn_GRHydro_InitData -lthorn_TestLoop -lthorn_LegoExcision -lthorn_ADMMass -lthorn_ADM -lthorn_CarpetSlab -lthorn_NoMPI -lthorn_PunctureTracker -lthorn_CarpetRegrid2 -lthorn_IDScalarWaveElliptic -lthorn_IDScalarWaveCXX -lthorn_IDScalarWaveC -lthorn_IDScalarWave -lthorn_ML_ADMQuantities -lthorn_ML_BSSN -lthorn_WaveToyExtra -lthorn_CarpetMask -lthorn_ML_CCZ4_Helper -lthorn_ML_CCZ4 -lthorn_AHFinderDirect -lthorn_Meudon_Bin_BH -lthorn_ADMConstraints -lthorn_ML_ADMConstraints -lthorn_PUGHSlab -lthorn_TestFortranDependencies1 -lthorn_TwoPunctures -lthorn_CalcK -lthorn_IOBasic -lthorn_NullExact -lthorn_NullConstr -lthorn_NullNews -lthorn_CarpetInterp -lthorn_IDBrillData -lthorn_Extract -lthorn_WaveBinarySource -lthorn_WaveToyFreeF90 -lthorn_WaveToyF90 -lthorn_WaveToyF77 -lthorn_WaveToyCXX -lthorn_WaveToyC -lthorn_IDAxiOddBrillBH -lthorn_CarpetIOBasic -lthorn_CarpetIOASCII -lthorn_Minkowski -lthorn_SlabTest -lthorn_Dissipation -lthorn_SphericalSurface -lthorn_EOS_Hybrid -lthorn_EOS_Polytrope -lthorn_DistortedBHIVP -lthorn_Meudon_Bin_NS -lthorn_LORENE -lthorn_LAPACK -lthorn_IDAxiBrillBH -lthorn_EllSOR -lthorn_NewRad -lthorn_IOASCII -lthorn_NullSHRExtract -lthorn_NullEvolve -lthorn_NullInterp -lthorn_NullDecomp -lthorn_NullGrid -lthorn_AHFinder -lthorn_RotatingDBHIVP -lthorn_SphericalHarmonicDecomp -lthorn_WeylScal4 -lthorn_IDConstraintViolate -lthorn_TOVSolver -lthorn_GRHydro -lthorn_TmunuBase -lthorn_SpaceMask -lthorn_EOS_Omni -lthorn_IDAnalyticBH -lthorn_ShiftedGaugeWave -lthorn_CarpetIOHDF5 -lthorn_HDF5 -lthorn_NaNChecker -lthorn_PUGHReduce -lthorn_PUGH -lthorn_CarpetReduce -lthorn_Carpet -lthorn_CarpetLib -lthorn_ADMAnalysis -lthorn_zlib -lthorn_libjpeg -lthorn_hwloc -lthorn_Time -lthorn_TestTypes -lthorn_TestTimers -lthorn_TestTable -lthorn_TestStrings -lthorn_TestSchedule -lthorn_TestReduce -lthorn_TestPar -lthorn_TestLocalReduce -lthorn_TestInclude2 -lthorn_TestInclude1 -lthorn_TestFreeF90 -lthorn_TestFpointerNULL -lthorn_TestFortranDependencies2 -lthorn_TestCoordinates -lthorn_TestComplex -lthorn_TestArrays -lthorn_TerminationTrigger -lthorn_TATelliptic -lthorn_SystemStatistics -lthorn_SymBase -lthorn_SummationByParts -lthorn_Socket -lthorn_ReflectionSymmetry -lthorn_OpenSSL -lthorn_NullVars -lthorn_Norms -lthorn_Nice -lthorn_MoL -lthorn_ML_CCZ4_Test -lthorn_ML_BSSN_Test -lthorn_LocalReduce -lthorn_LocalInterp -lthorn_InterpToArray -lthorn_Fortran -lthorn_FFTW3 -lthorn_EllBase -lthorn_EinsteinExact_Test -lthorn_EOS_Base -lthorn_CoordGauge -lthorn_Constants -lthorn_BLAS -lthorn_AEILocalInterp -lthorn_ADMMacros -lthorn_ADMCoupling -lthorn_Formaline -lthorn_RotatingSymmetry180 -lthorn_Slab -lthorn_Hydro_Analysis -lthorn_HydroBase -lthorn_InitBase -lthorn_KerrSchild -lthorn_LoopControl -lthorn_Vectors -lthorn_GSL -lthorn_GenericFD -lthorn_IDLinearWaves -lthorn_IDFileADM -lthorn_IOUtil -lthorn_StaticConformal -lthorn_ADMBase -lthorn_Boundary -lthorn_TimerReport -lthorn_MPI -lthorn_Noise -lthorn_CartGrid3D -lthorn_CoordBase -lthorn_Cactus -lthorn_CactusBindings -lthorn_Formaline-cactus-source -L/usr/lib/ -L/nics/c/home/hawleys/Cactus/configs/etk/scratch/external/hwloc/lib -L/opt/sgi/mpt/mpt-2.04//lib -L/nics/c/home/hawleys/Cactus/configs/etk/scratch/external/LORENE/Lib -L/usr/lib/ -L/nics/c/home/hawleys/Cactus/configs/etk/scratch/external/HDF5/lib -L/sw/analysis/gsl/1.14/sles11.1_gnu4.3.4/lib -L/sw/analysis/fftw/3.3/sles11.1_gnu4.3.4/lib -L/sw/analysis/gotoblas2/2.1.13/sles11.1_gnu4.3.4/ -L/usr/lib64/gcc/x86_64-suse-linux/4.3 -Wl,-rpath,/usr/lib/ -Wl,-rpath,/nics/c/home/hawleys/Cactus/configs/etk/scratch/external/hwloc/l ib -Wl,-rpath,/opt/sgi/mpt/mpt-2.04//lib -Wl,-rpath,/nics/c/home/hawleys/Cactus/configs/etk/scratch/external/LORENE/ Lib -Wl,-rpath,/usr/lib/ -Wl,-rpath,/nics/c/home/hawleys/Cactus/configs/etk/scratch/external/HDF5/li b -Wl,-rpath,/sw/analysis/gsl/1.14/sles11.1_gnu4.3.4/lib -Wl,-rpath,/sw/analysis/fftw/3.3/sles11.1_gnu4.3.4/lib -Wl,-rpath,/sw/analysis/gotoblas2/2.1.13/sles11.1_gnu4.3.4/ -Wl,-rpath,/usr/lib64/gcc/x86_64-suse-linux/4.3 -llapack -lpthread -lz -ljpeg -lhwloc -lmpi -lmpi_cxx -llorene_export -llorene -llorenef77 -llapack -lhdf5_hl_cpp -lhdf5_cpp -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -lz -lm -lgsl -lgslcblas -lm -lfftw3 -lblas -lcrypt -ldl -lgfortran /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib//libpthread.so when searching for -lpthread /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib//libpthread.a when searching for -lpthread /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib//libpthread.so when searching for -lpthread /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: skipping incompatible /usr/lib//libpthread.a when searching for -lpthread /usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../x86_64-suse-linux/bin/ld: cannot find -lmpi_cxx collect2: ld returned 1 exit status make[1]: *** [/nics/c/home/hawleys/Cactus/exe/cactus_etk] Error 1 make[1]: Leaving directory `/nics/c/home/hawleys/Cactus' make: *** [etk] Error 2
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