[Users] New MPI config designation, specifying libs?

Scott Hawley scott.hawley at belmont.edu
Mon Aug 6 17:34:17 CDT 2012 

Thanks Erik,

I had done a "make *-config" and then another make.
I guess I'm out of the loop.  "make *-rebuild" seems to have fixed it...
ish:

...
Formaline: Created git tag
build-etk-conseil.nics.utk.edu-hawleys-2012.08.06-22.30.20-2719
Formaline: Updated git branch
config-etk-conseil.nics.utk.edu-nics-c-home-hawleys-Cactus
sh: /nics/c/home/hawleys/Cactus/bin/sim: No such file or directory
Formaline: Pushing source tree to master git repository...
Formaline: Done.
Formaline: (Formaline has finished updating the git repositories.
Formaline:  If the build process seems to hang, some other command
Formaline:  is still running, e.g. the final link stage.)
All done !




What does the "sim: No such file or directory" mean?   (This was a serial
make, not a parallel one)


-Scott






On 8/6/12 5:25 PM, "Erik Schnetter" <schnetter at cct.lsu.edu> wrote:

>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 at 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/LOREN
>>E/
>> 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
>>
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>> Users mailing list
>> Users at einsteintoolkit.org
>> http://lists.einsteintoolkit.org/mailman/listinfo/users
>
>
>
>-- 
>Erik Schnetter <schnetter at cct.lsu.edu>
>http://www.perimeterinstitute.ca/personal/eschnetter/
>

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