[Users] New MPI config designation, specifying libs?
Alexander Beck-Ratzka
alexander.beck-ratzka at aei.mpg.de
Thu Aug 9 01:53:04 CDT 2012
Hi Scott,
can you please post your sim build command, and the concerning optionlist?
Best wishes
Alexander
On Monday 06 August 2012 22:15:34 Scott Hawley 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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