[petsc-users] Hypre 2.10 lapack undefined symbols (OS-X)

Sun Jul 12 03:54:23 CDT 2015

On Sun, Jul 12, 2015 at 3:12 AM, Denis Davydov <davydden at gmail.com> wrote:

> Dear all,
>
> I have Lapack-related undefined symbols errors when trying to run tests on
> Hypre, configured and compiled by PETSc
> (./configure --download-superlu_dist --download-metis --download-parmetis
> --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --with-debugging=0
> --download-hypre).
> Any ideas what’s happening?
>

We need configure.log. This certainly sounds like a problem from mixing
builds. Had you had unsuccessful
builds in this directory before? I would recommend wiping out the
$PETSC_ARCH directory completely in
these cases.

  Thanks,

    Matt

> During the build also some "has no symbols” shows up, which does not look
> good either. There are no compiler errors though...
>
>
> Regards,
> Denis.
>
> p.s. Hypre configure resulting from PETSc is:
> ./configure
> --prefix=/Users/davydden/Downloads/petsc-3.6.0/arch-darwin-c-opt
> MAKE=/usr/bin/make
> --libdir=/Users/davydden/Downloads/petsc-3.6.0/arch-darwin-c-opt/lib
> CC=mpicc CFLAGS=-fPIC -O CXX=mpicxx CXXFLAGS=-O -fPIC F90=mpif90
> F90FLAGS=-fPIC -ffree-line-length-0 -O F77=mpif90 FFLAGS=-fPIC
> -ffree-line-length-0 -O FC=mpif90 FCFLAGS=-fPIC -ffree-line-length-0 -O
> --with-MPI-include=/usr/local/Cellar/open-mpi/1.8.6/include
> --with-MPI-lib-dirs= --with-MPI-libs= --with-blas-libs=
> --with-blas-lib-dir= --with-lapack-libs= --with-lapack-lib-dir=
> --with-blas=yes --with-lapack=yes --with-fmangle-blas=one-underscore
> --with-fmangle-lapack=one-underscore --without-babel --without-mli
> --without-fei --without-superlu AR=/usr/bin/ar cr
>
>
> === check ===
> $ make check
> Checking the library ...
> mpicc -fPIC -O -DHAVE_CONFIG_H -I. -I./..
> -I/Users/davydden/Downloads/petsc-3.6.0/arch-darwin-c-opt/externalpackages/hypre-2.10.0b-p1/src/hypre/include
> -I/usr/local/Cellar/open-mpi/1.8.6/include -DHYPRE_TIMING -DHYPRE_FORTRAN
> -c ij.c
> Building ij ...
> mpicc -o ij ij.o
> -L/Users/davydden/Downloads/petsc-3.6.0/arch-darwin-c-opt/externalpackages/hypre-2.10.0b-p1/src/hypre/lib
> -lHYPRE          -lm
> Undefined symbols for architecture x86_64:
>   "_dgels_", referenced from:
>       _ComputeValuesNonsym in libHYPRE.a(ParaSails.o)
>       _hypre_BoomerAMGFitVectors in libHYPRE.a(par_gsmg.o)
>   "_dgetrf_", referenced from:
>       _hypre_BoomerAMGRelax in libHYPRE.a(par_relax.o)
>       _hypre_GaussElimSolve in libHYPRE.a(par_relax.o)
>       _hypre_AMGCreateDomainDof in libHYPRE.a(schwarz.o)
>       _hypre_ParAMGCreateDomainDof in libHYPRE.a(schwarz.o)
>   "_dgetrs_", referenced from:
>       _hypre_BoomerAMGRelax in libHYPRE.a(par_relax.o)
>       _hypre_GaussElimSolve in libHYPRE.a(par_relax.o)
>       _hypre_ParMPSchwarzSolve in libHYPRE.a(schwarz.o)
>       _hypre_MPSchwarzSolve in libHYPRE.a(schwarz.o)
>       _hypre_MPSchwarzCFSolve in libHYPRE.a(schwarz.o)
>       _hypre_MPSchwarzFWSolve in libHYPRE.a(schwarz.o)
>       _hypre_MPSchwarzCFFWSolve in libHYPRE.a(schwarz.o)
>       ...
>   "_dpotrf_", referenced from:
>       _dpotrf_interface in libHYPRE.a(HYPRE_lobpcg.o)
>       _ComputeValuesSym in libHYPRE.a(ParaSails.o)
>       _hypre_AMGNodalSchwarzSmoother in libHYPRE.a(schwarz.o)
>       _hypre_AMGCreateDomainDof in libHYPRE.a(schwarz.o)
>       _hypre_ParAMGCreateDomainDof in libHYPRE.a(schwarz.o)
>   "_dpotrs_", referenced from:
>       _ComputeValuesSym in libHYPRE.a(ParaSails.o)
>       _hypre_ParMPSchwarzSolve in libHYPRE.a(schwarz.o)
>       _hypre_MPSchwarzSolve in libHYPRE.a(schwarz.o)
>       _hypre_MPSchwarzCFSolve in libHYPRE.a(schwarz.o)
>       _hypre_MPSchwarzFWSolve in libHYPRE.a(schwarz.o)
>       _hypre_MPSchwarzCFFWSolve in libHYPRE.a(schwarz.o)
>       _hypre_AdSchwarzSolve in libHYPRE.a(schwarz.o)
>       ...
>   "_dsygv_", referenced from:
>       _dsygv_interface in libHYPRE.a(HYPRE_lobpcg.o)
>
>
> === has no symbols: ===
>
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE_utilities.a(hypre_complex.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE_utilities.a(hypre_mpi_comm_f2c.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE_utilities.a(threading.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE_utilities.a(hypre_complex.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE_utilities.a(hypre_mpi_comm_f2c.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE_utilities.a(threading.o) has no symbols
>
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file:
> libHYPRE_MatrixMatrix.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has
> no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file:
> libHYPRE_MatrixMatrix.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has
> no symbols
>
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(hypre_complex.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(hypre_mpi_comm_f2c.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(threading.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(HYPRE_ConvertPETScMatrixToDistributedMatrix.o) has no
> symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(hypre_complex.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(hypre_mpi_comm_f2c.o) has no symbols
> /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib:
> file: libHYPRE.a(threading.o) has no symbols
>
>
>
>

-- 
What most experimenters take for granted before they begin their
experiments is infinitely more interesting than any results to which their
experiments lead.
-- Norbert Wiener
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