Hello All:
I am new to deal.II and am trying to migrate some of my old code to
use deal.II. I have been going through the tutorial/examples and have
run into a virtual brick wall with the examples that use PETSc. I am
going to describe my installation procedure and the errors I get using
the debug and optimized compilations. I did find some helpful past
posts, but I think that I have a different error...
1) Install PETSc using Ubuntu's package manager: "aptitude install
petsc3.0.0-dbg petsc3.0.0-dev"
2) Download and build deal.II:
"./configure --with-petsc=/usr/lib/petscdir/3.0.0
--with-petsc-arch=linux-gnu-c-opt"
"make -j 2 debug optimized"
I am using a dual-core machine, and no additional machines through an
interconnect.
3) Using, for instance, example 17, I compile and then run via (a)
without MPI in debug mode (''./step-17") and with MPI using a single
processor ("mpiexec -np 1 ./step-17") and (b) with MPI in debug mode
("mpiexec -np 2 ./step-17"), here is my output:
METHOD A
expected output (so not included)
---BEGIN---METHOD B---
nas...@nasser-laptop:~/deal.II/examples/step-17$ mpiexec -np 2 ./step-17
Cycle 0:
Number of active cells: 64
Cycle 0:
Number of active cells: 64
--------------------------------------------------------
An error occurred in line <163> of file
<source/petsc_parallel_vector.cc> in function
virtual void
dealii::PETScWrappers::MPI::Vector::create_vector(unsigned int, unsigned
int)
The violated condition was:
size() == n
The name and call sequence of the exception was:
ExcInternalError()
Additional Information:
(none)
Stacktrace:
-----------
#0 /home/nasser/deal.II/lib/liblac.g.so.6.2.1:
dealii::PETScWrappers::MPI::Vector::create_vector(unsigned int, unsigned
int)
#1 /home/nasser/deal.II/lib/liblac.g.so.6.2.1:
dealii::PETScWrappers::MPI::Vector::reinit(ompi_communicator_t* const&,
unsigned int, unsigned int, bool)
#2 ./step-17: ElasticProblem<2>::setup_system()
#3 ./step-17: ElasticProblem<2>::run()
#4 ./step-17: main
--------------------------------------------------------
nasser-laptop:03239] *** Process received signal ***
[nasser-laptop:03239] Signal: Aborted (6)
[nasser-laptop:03239] Signal code: (-6)
[nasser-laptop:03239] [ 0] [0xbc3410]
[nasser-laptop:03239] [ 1] [0xbc3422]
[nasser-laptop:03239] [ 2] /lib/tls/i686/cmov/libc.so.6(gsignal+0x51)
[0x4544d1]
[nasser-laptop:03239] [ 3] /lib/tls/i686/cmov/libc.so.6(abort+0x182)
[0x457932]
[nasser-laptop:03239] [ 4]
/home/nasser/deal.II/lib/libbase.g.so.6.2.1(_ZN6dealii18deal_II_exceptions9internals18issue_error_assertEPKciS3_S3_S3_RNS_13ExceptionBaseE+0x1d7)
[0x91bb7f]
[nasser-laptop:03239] [ 5]
/home/nasser/deal.II/lib/libdeal_II_2d.g.so.6.2.1(_ZN6dealii18deal_II_exceptions9internals20issue_error_assert_1INS_18StandardExceptions16ExcInternalErrorEEEvPKciS6_S6_S6_T_+0x40)
[0x11b0069]
[nasser-laptop:03239] [ 6]
/home/nasser/deal.II/lib/liblac.g.so.6.2.1(_ZN6dealii13PETScWrappers3MPI6Vector13create_vectorEjj+0x1e2)
[0x52db092]
[nasser-laptop:03239] [ 7]
/home/nasser/deal.II/lib/liblac.g.so.6.2.1(_ZN6dealii13PETScWrappers3MPI6Vector6reinitERKP19ompi_communicator_tjjb+0x10d)
[0x52daa5d]
[nasser-laptop:03239] [ 8]
./step-17(_ZN14ElasticProblemILi2EE12setup_systemEv+0x140) [0x806d4fe]
[nasser-laptop:03239] [ 9]
./step-17(_ZN14ElasticProblemILi2EE3runEv+0xff) [0x806c547]
[nasser-laptop:03239] [10] ./step-17(main+0x6a) [0x8065c6e]
[nasser-laptop:03239] [11]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6) [0x440b56]
[nasser-laptop:03239] [12] ./step-17 [0x8065b71]
[nasser-laptop:03239] *** End of error message ***
--------------------------------------------------------
An error occurred in line <163> of file
<source/petsc_parallel_vector.cc> in function
virtual void
dealii::PETScWrappers::MPI::Vector::create_vector(unsigned int, unsigned
int)
The violated condition was:
size() == n
The name and call sequence of the exception was:
ExcInternalError()
Additional Information:
(none)
Stacktrace:
-----------
#0 /home/nasser/deal.II/lib/liblac.g.so.6.2.1:
dealii::PETScWrappers::MPI::Vector::create_vector(unsigned int, unsigned
int)
#1 /home/nasser/deal.II/lib/liblac.g.so.6.2.1:
dealii::PETScWrappers::MPI::Vector::reinit(ompi_communicator_t* const&,
unsigned int, unsigned int, bool)
#2 ./step-17: ElasticProblem<2>::setup_system()
#3 ./step-17: ElasticProblem<2>::run()
#4 ./step-17: main
--------------------------------------------------------
[nasser-laptop:03238] *** Process received signal ***
[nasser-laptop:03238] Signal: Aborted (6)
[nasser-laptop:03238] Signal code: (-6)
[nasser-laptop:03238] [ 0] [0x3de410]
[nasser-laptop:03238] [ 1] [0x3de422]
[nasser-laptop:03238] [ 2] /lib/tls/i686/cmov/libc.so.6(gsignal+0x51)
[0x51304d1]
[nasser-laptop:03238] [ 3] /lib/tls/i686/cmov/libc.so.6(abort+0x182)
[0x5133932]
[nasser-laptop:03238] [ 4]
/home/nasser/deal.II/lib/libbase.g.so.6.2.1(_ZN6dealii18deal_II_exceptions9internals18issue_error_assertEPKciS3_S3_S3_RNS_13ExceptionBaseE+0x1d7)
[0x38afb7f]
[nasser-laptop:03238] [ 5]
/home/nasser/deal.II/lib/libdeal_II_2d.g.so.6.2.1(_ZN6dealii18deal_II_exceptions9internals20issue_error_assert_1INS_18StandardExceptions16ExcInternalErrorEEEvPKciS6_S6_S6_T_+0x40)
[0x129b069]
[nasser-laptop:03238] [ 6]
/home/nasser/deal.II/lib/liblac.g.so.6.2.1(_ZN6dealii13PETScWrappers3MPI6Vector13create_vectorEjj+0x1e2)
[0x8a4092]
[nasser-laptop:03238] [ 7]
/home/nasser/deal.II/lib/liblac.g.so.6.2.1(_ZN6dealii13PETScWrappers3MPI6Vector6reinitERKP19ompi_communicator_tjjb+0x10d)
[0x8a3a5d]
[nasser-laptop:03238] [ 8]
./step-17(_ZN14ElasticProblemILi2EE12setup_systemEv+0x140) [0x806d4fe]
[nasser-laptop:03238] [ 9]
./step-17(_ZN14ElasticProblemILi2EE3runEv+0xff) [0x806c547]
[nasser-laptop:03238] [10] ./step-17(main+0x6a) [0x8065c6e]
[nasser-laptop:03238] [11]
/lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe6) [0x511cb56]
[nasser-laptop:03238] [12] ./step-17 [0x8065b71]
[nasser-laptop:03238] *** End of error message ***
--------------------------------------------------------------------------
---END---METHOD B---
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