Hi there,
Thanks a lot for the help.
Yes now I can compile deal.II with Petsc and Metis.
However there is a run-time error for example 17. (attached below)
I was running the program on a parallel computer with 16 cpus.
But the DOFs are only partitioned into a section.
Do you have any idea what could go wrong?
Thanks,
Huan
============================ Running step-17
Cycle 0:
Number of active cells: 64
Number of degrees of freedom: 162 (by partition: 162)
Solver converged in 9 iterations.
Cycle 1:
Number of active cells: 124
Number of degrees of freedom: 302 (by partition: 302)
Solver converged in 17 iterations.
Cycle 2:
Number of active cells: 238
Number of degrees of freedom: 570 (by partition: 570)
Solver converged in 26 iterations.
Cycle 3:
Number of active cells: 454
Number of degrees of freedom: 1046 (by partition: 1046)
[0]PETSC ERROR: --------------------- Error
Message ------------------------------------
[0]PETSC ERROR: Invalid argument!
[0]PETSC ERROR: Invalid object cookie 1211234
This often happens if you compile with PETSC_USE_DYNAMIC_LIBRARIES, but link
with static libraries.!
[0]PETSC
ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 9, Fri Oct 23 13:37:28
CDT 2009
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC
ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: ./step-17 on a linux-gnu named titanium by hsun Sun Nov 29
01:27:01 2009
[0]PETSC ERROR: Libraries linked from
/ima/home/hsun/petsc/linux-gnu-cxx-debug/lib
[0]PETSC ERROR: Configure run at Fri Nov 27 23:13:43 2009
[0]PETSC ERROR: Configure
options --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --download-f-blas-lapack=1
--download-mpich=1 --with-shared=1 --with-dynamic=1 --with-clanguage=C++ --with-x=0
[0]PETSC
ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: ClassRegLogGetClass() line 281 in
src/sys/plog/utils/classLog.c
[0]PETSC ERROR: PetscLogObjCreateDefault() line 309 in
src/sys/plog/utils/classLog.c
[0]PETSC ERROR: KSPCreate() line 476 in src/ksp/ksp/interface/itcreate.c
[0]PETSC ERROR: --------------------- Error
Message ------------------------------------
[0]PETSC ERROR: Null argument, when expecting valid pointer!
[0]PETSC ERROR: Null Object: Parameter # 1!
[0]PETSC
ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: Petsc Release Version 3.0.0, Patch 9, Fri Oct 23 13:37:28
CDT 2009
[0]PETSC ERROR: See docs/changes/index.html for recent updates.
[0]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
[0]PETSC ERROR: See docs/index.html for manual pages.
[0]PETSC
ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: ./step-17 on a linux-gnu named titanium by hsun Sun Nov 29
01:27:01 2009
[0]PETSC ERROR: Libraries linked from
/ima/home/hsun/petsc/linux-gnu-cxx-debug/lib
[0]PETSC ERROR: Configure run at Fri Nov 27 23:13:43 2009
[0]PETSC ERROR: Configure
options --with-cc=gcc --with-fc=gfortran --with-cxx=g++ --download-f-blas-lapack=1
--download-mpich=1 --with-shared=1 --with-dynamic=1 --with-clanguage=C++ --with-x=0
[0]PETSC
ERROR: ------------------------------------------------------------------------
[0]PETSC ERROR: KSPDestroy() line 633 in src/ksp/ksp/interface/itfunc.c
terminate called after throwing an instance of
'dealii::PETScWrappers::SolverBase::ExcPETScError'
what(): --------------------------------------------------------
An error occurred in line <38> of file <source/petsc_solver.cc> in function
dealii::PETScWrappers::SolverBase::SolverData::~SolverData()
The violated condition was:
ierr == 0
The name and call sequence of the exception was:
ExcPETScError(ierr)
Additional Information:
An error with error number 85 occured while calling a PETSc function
--------------------------------------------------------
make: *** [run] Aborted (core dumped)
--------------------------------------------------
From: <[email protected]>
Sent: Saturday, November 28, 2009 8:15 AM
To: "Huan Sun" <[email protected]>
Cc: <[email protected]>
Subject: Re: [deal.II] problem with METIS
I think you must compile metis in dynamic version with option -fPIC.
You'd better to try to recompile with this option.
On Sat, November 28, 2009 7:21 am, Huan Sun wrote:
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 â?~void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)â?T:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable â?~ierrâ?T
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function â?~void dealii::FullMatrix<number>::gauss_jordan() [with
number = double]â?T:
source/full_matrix.inst:1: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable â?~typical_diagonal_elementâ?T
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function â?~void dealii::FullMatrix<number>::gauss_jordan() [with
number = float]â?T:
source/full_matrix.inst:29: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable â?~typical_diagonal_elementâ?T
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function â?~void dealii::FullMatrix<number>::gauss_jordan() [with
number = long double]â?T:
source/full_matrix.inst:57: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable â?~typical_diagonal_elementâ?T
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function â?~void dealii::FullMatrix<number>::gauss_jordan() [with
number = std::complex<double>]â?T:
source/full_matrix.inst:994: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable â?~typical_diagonal_elementâ?T
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function â?~void dealii::FullMatrix<number>::gauss_jordan() [with
number = std::complex<float>]â?T:
source/full_matrix.inst:1001: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable â?~typical_diagonal_elementâ?T
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h: In
member function â?~void dealii::FullMatrix<number>::gauss_jordan() [with
number = std::complex<long double>]â?T:
source/full_matrix.inst:1008: instantiated from here
/ima/home/hsun/deal.II/lac/include/lac/full_matrix.templates.h:1840:
warning: unused variable â?~typical_diagonal_elementâ?T
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 â?~void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)â?T:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable â?~ierrâ?T
=====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 â?~void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)â?T:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable â?~ierrâ?T
=====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 â?~void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)â?T:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable â?~ierrâ?T
=====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 â?~void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)â?T:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable â?~ierrâ?T
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 â?~void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)â?T:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable â?~ierrâ?T
In file included from source/petsc_precondition.cc:15:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function â?~void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)â?T:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable â?~ierrâ?T
In file included from source/petsc_solver.cc:16:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h: In member
function â?~void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)â?T:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable â?~ierrâ?T
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 â?~void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)â?T:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable â?~ierrâ?T
=====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 â?~void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)â?T:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable â?~ierrâ?T
=====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 â?~void dealii::PETScWrappers::MatrixBase::add(unsigned int,
unsigned int, const unsigned int*, const PetscScalar*, bool, bool)â?T:
/ima/home/hsun/deal.II/lac/include/lac/petsc_matrix_base.h:1682:
warning: unused variable â?~ierrâ?T
=====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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