Hi all,
I was trying to install deal.II 6.2.1 together with Petsc and Metis on a
parallel computer but I have the following error message when compiling
'make all':
/usr/bin/ld: /ima/home/hsun/metis/libmetis.a(pmetis.o): relocation
R_X86_64_32 against `a local symbol' can not be used when making a
shared object; recompile with -fPIC
/ima/home/hsun/metis/libmetis.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[1]: *** [/ima/home/hsun/deal.II/lib/liblac.so] Error 1
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/lac'
make: *** [laco] Error 2
Any suggestions how I can fix this problem?
Thanks a lot!
Huan
The whole compiling info is attached below:
cd /ima/home/hsun/deal.II/common/scripts && /usr/bin/make
make_dependencies
cd /ima/home/hsun/deal.II/common/scripts && /usr/bin/make
expand_instantiations
make[1]: Entering directory `/ima/imavisitor/hsun/deal.II/contrib'
make[1]: Entering directory
`/ima/imavisitor/hsun/deal.II/common/scripts'
make[1]: `make_dependencies' is up to date.
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/common/scripts'
make[1]: Entering directory
`/ima/imavisitor/hsun/deal.II/common/scripts'
make[1]: `expand_instantiations' is up to date.
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/common/scripts'
cd /ima/home/hsun/deal.II/base && /usr/bin/make Makefile.dep
make[2]: Entering directory
`/ima/imavisitor/hsun/deal.II/contrib/functionparser'
make[2]: `/ima/home/hsun/deal.II/lib/contrib/functionparser/fparser.o'
is up to date.
make[2]: Leaving directory
`/ima/imavisitor/hsun/deal.II/contrib/functionparser'
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/contrib'
make[1]: Entering directory `/ima/imavisitor/hsun/deal.II/base'
make[1]: `Makefile.dep' is up to date.
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/base'
cd /ima/home/hsun/deal.II/lac && /usr/bin/make Makefile.dep
make[1]: Entering directory `/ima/imavisitor/hsun/deal.II/lac'
make[1]: `Makefile.dep' is up to date.
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/lac'
cd /ima/home/hsun/deal.II/deal.II && /usr/bin/make Makefile.dep
make[1]: Entering directory `/ima/imavisitor/hsun/deal.II/deal.II'
make[1]: `Makefile.dep' is up to date.
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/deal.II'
cd /ima/home/hsun/deal.II/lib && /usr/bin/make external-links
make[1]: Entering directory `/ima/imavisitor/hsun/deal.II/lib'
make[1]: Nothing to be done for `external-links'.
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/lib'
cd /ima/home/hsun/deal.II/contrib && /usr/bin/make
make[1]: Entering directory `/ima/imavisitor/hsun/deal.II/contrib'
make[2]: Entering directory
`/ima/imavisitor/hsun/deal.II/contrib/functionparser'
make[2]: `/ima/home/hsun/deal.II/lib/contrib/functionparser/fparser.o'
is up to date.
make[2]: Leaving directory
`/ima/imavisitor/hsun/deal.II/contrib/functionparser'
make[2]: Entering directory `/ima/imavisitor/hsun/deal.II/contrib/tbb'
make[3]: Entering directory
`/ima/imavisitor/hsun/deal.II/contrib/tbb/tbb22_20090809oss'
make[4]: Entering directory
`/ima/imavisitor/hsun/deal.II/lib/contrib/tbb/linux_intel64_gcc_cc4.2.4_libc2.7_kernel2.6.24_debug'
sh
/ima/imavisitor/hsun/deal.II/contrib/tbb/tbb22_20090809oss/./build/generate_tbbvars.sh
=====tbb=========================MT== debug/libtbb_debug.so.2
make[4]: Leaving directory
`/ima/imavisitor/hsun/deal.II/lib/contrib/tbb/linux_intel64_gcc_cc4.2.4_libc2.7_kernel2.6.24_debug'
make[4]: Entering directory
`/ima/imavisitor/hsun/deal.II/lib/contrib/tbb/linux_intel64_gcc_cc4.2.4_libc2.7_kernel2.6.24_release'
sh
/ima/imavisitor/hsun/deal.II/contrib/tbb/tbb22_20090809oss/./build/generate_tbbvars.sh
=====tbb=========================MT== release/libtbb.so.2
make[4]: Leaving directory
`/ima/imavisitor/hsun/deal.II/lib/contrib/tbb/linux_intel64_gcc_cc4.2.4_libc2.7_kernel2.6.24_release'
make[3]: Leaving directory
`/ima/imavisitor/hsun/deal.II/contrib/tbb/tbb22_20090809oss'
make[2]: Leaving directory `/ima/imavisitor/hsun/deal.II/contrib/tbb'
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/contrib'
cd /ima/home/hsun/deal.II/base && /usr/bin/make libg
cd /ima/home/hsun/deal.II/base && /usr/bin/make libo
make[1]: Entering directory `/ima/imavisitor/hsun/deal.II/base'
make[1]: Nothing to be done for `libo'.
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/base'
cd /ima/home/hsun/deal.II/lac && /usr/bin/make libo
make[1]: Entering directory `/ima/imavisitor/hsun/deal.II/base'
make[1]: Nothing to be done for `libg'.
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/base'
cd /ima/home/hsun/deal.II/lac && /usr/bin/make libg
make[1]: Entering directory `/ima/imavisitor/hsun/deal.II/lac'
=====lac==============optimized==MT== block_matrix_array.cc
=====lac==============optimized==MT== block_sparse_matrix.cc
=====lac==============optimized==MT== block_sparse_matrix_ez.cc
=====lac==============optimized==MT== block_sparsity_pattern.cc
make[1]: Entering directory `/ima/imavisitor/hsun/deal.II/lac'
=====lac==============optimized==MT== block_vector.cc
=====lac==============debug======MT== Linking library: liblac.g.so
=====lac==============optimized==MT== chunk_sparse_matrix.cc
=====lac==============optimized==MT== chunk_sparsity_pattern.cc
=====lac==============optimized==MT== compressed_set_sparsity_pattern.cc
=====lac==============optimized==MT==
compressed_simple_sparsity_pattern.cc
=====lac==============optimized==MT== compressed_sparsity_pattern.cc
=====lac==============optimized==MT== constraint_matrix.cc
=====lac==============optimized==MT== full_matrix.cc
=====lac==============optimized==MT== lapack_full_matrix.cc
/usr/bin/ld: /ima/home/hsun/metis/libmetis.a(pmetis.o): relocation
R_X86_64_32 against `a local symbol' can not be used when making a
shared object; recompile with -fPIC
/ima/home/hsun/metis/libmetis.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[1]: *** [/ima/home/hsun/deal.II/lib/liblac.g.so] Error 1
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/lac'
make: *** [lacg] Error 2
make: *** Waiting for unfinished jobs....
=====lac==============optimized==MT== matrix_lib.cc
=====lac==============optimized==MT== matrix_out.cc
=====lac==============optimized==MT== petsc_block_sparse_matrix.cc
=====lac==============optimized==MT== petsc_full_matrix.cc
=====lac==============optimized==MT== petsc_matrix_base.cc
In file included
from /ima/home/hsun/deal.II/lac/include/lac/petsc_sparse_matrix.h:19,
from /ima/home/hsun/deal.II/lac/include/lac/petsc_block_sparse_matrix.h:20,
from /ima/home/hsun/deal.II/lac/include/lac/constraint_matrix.templates.h:25,
from source/constraint_matrix.cc:16:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function ‘void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)’:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable ‘ierr’
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function ‘void dealii::FullMatrix<number>::gauss_jordan() [with
number = double]’:
source/full_matrix.inst:1: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable ‘typical_diagonal_element’
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function ‘void dealii::FullMatrix<number>::gauss_jordan() [with
number = float]’:
source/full_matrix.inst:29: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable ‘typical_diagonal_element’
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function ‘void dealii::FullMatrix<number>::gauss_jordan() [with
number = long double]’:
source/full_matrix.inst:57: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable ‘typical_diagonal_element’
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function ‘void dealii::FullMatrix<number>::gauss_jordan() [with
number = std::complex<double>]’:
source/full_matrix.inst:994: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable ‘typical_diagonal_element’
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function ‘void dealii::FullMatrix<number>::gauss_jordan() [with
number = std::complex<float>]’:
source/full_matrix.inst:1001: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable ‘typical_diagonal_element’
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function ‘void dealii::FullMatrix<number>::gauss_jordan() [with
number = std::complex<long double>]’:
source/full_matrix.inst:1008: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable ‘typical_diagonal_element’
In file included
from /ima/home/hsun/deal.II/lac/include/lac/petsc_sparse_matrix.h:19,
from /ima/home/hsun/deal.II/lac/include/lac/petsc_block_sparse_matrix.h:20,
from source/petsc_block_sparse_matrix.cc:14:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function ‘void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)’:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable ‘ierr’
=====lac==============optimized==MT==
petsc_parallel_block_sparse_matrix.cc
In file included
from /ima/home/hsun/deal.II/lac/include/lac/petsc_full_matrix.h:19,
from source/petsc_full_matrix.cc:15:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function ‘void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)’:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable ‘ierr’
=====lac==============optimized==MT== petsc_parallel_block_vector.cc
=====lac==============optimized==MT== petsc_parallel_sparse_matrix.cc
=====lac==============optimized==MT== petsc_parallel_vector.cc
In file included from source/petsc_matrix_base.cc:15:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function ‘void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)’:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable ‘ierr’
=====lac==============optimized==MT== petsc_precondition.cc
=====lac==============optimized==MT== petsc_solver.cc
=====lac==============optimized==MT== petsc_sparse_matrix.cc
=====lac==============optimized==MT== petsc_vector.cc
=====lac==============optimized==MT== petsc_vector_base.cc
=====lac==============optimized==MT== precondition_block.cc
=====lac==============optimized==MT== precondition_block_ez.cc
In file included
from /ima/home/hsun/deal.II/lac/include/lac/petsc_parallel_sparse_matrix.h:20,
from
/ima/home/hsun/deal.II/lac/include/lac/petsc_parallel_block_sparse_matrix.h:20,
from source/petsc_parallel_block_sparse_matrix.cc:14:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function ‘void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)’:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable ‘ierr’
In file included
from /ima/home/hsun/deal.II/lac/include/lac/petsc_parallel_sparse_matrix.h:20,
from source/petsc_parallel_sparse_matrix.cc:15:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function ‘void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)’:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable ‘ierr’
In file included from source/petsc_precondition.cc:15:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function ‘void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)’:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable ‘ierr’
In file included from source/petsc_solver.cc:16:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function ‘void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)’:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable ‘ierr’
In file included
from /ima/home/hsun/deal.II/lac/include/lac/petsc_sparse_matrix.h:19,
from source/petsc_sparse_matrix.cc:15:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function ‘void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)’:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable ‘ierr’
=====lac==============optimized==MT== slepc_solver.cc
=====lac==============optimized==MT== slepc_spectral_transformation.cc
=====lac==============optimized==MT== solver.cc
=====lac==============optimized==MT== solver_control.cc
=====lac==============optimized==MT== sparse_decomposition.cc
=====lac==============optimized==MT== sparse_direct.cc
=====lac==============optimized==MT== sparse_ilu.cc
=====lac==============optimized==MT== sparse_matrix.cc
=====lac==============optimized==MT== sparse_matrix_ez.cc
In file included from source/slepc_solver.cc:15:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function ‘void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)’:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable ‘ierr’
=====lac==============optimized==MT== sparse_mic.cc
In file included from source/slepc_spectral_transformation.cc:15:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function ‘void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)’:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable ‘ierr’
=====lac==============optimized==MT== sparse_vanka.cc
=====lac==============optimized==MT== sparsity_pattern.cc
=====lac==============optimized==MT== sparsity_tools.cc
=====lac==============optimized==MT== swappable_vector.cc
=====lac==============optimized==MT== tridiagonal_matrix.cc
=====lac==============optimized==MT== trilinos_block_sparse_matrix.cc
=====lac==============optimized==MT== trilinos_block_vector.cc
=====lac==============optimized==MT== trilinos_precondition.cc
=====lac==============optimized==MT== trilinos_precondition_block.cc
=====lac==============optimized==MT== trilinos_solver.cc
=====lac==============optimized==MT== trilinos_solver_block.cc
=====lac==============optimized==MT== trilinos_sparse_matrix.cc
=====lac==============optimized==MT== trilinos_sparsity_pattern.cc
=====lac==============optimized==MT== trilinos_vector.cc
=====lac==============optimized==MT== trilinos_vector_base.cc
=====lac==============optimized==MT== vector.cc
=====lac==============optimized==MT== vector_memory.cc
=====lac==============optimized==MT== vector_view.cc
=====lac==============optimized==MT== Linking library: liblac.so
/usr/bin/ld: /ima/home/hsun/metis/libmetis.a(pmetis.o): relocation
R_X86_64_32 against `a local symbol' can not be used when making a
shared object; recompile with -fPIC
/ima/home/hsun/metis/libmetis.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make[1]: *** [/ima/home/hsun/deal.II/lib/liblac.so] Error 1
make[1]: Leaving directory `/ima/imavisitor/hsun/deal.II/lac'
make: *** [laco] Error 2
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