[petsc-users] pc_gamg_type geo broken in 3.3?
Blaise Bourdin
bourdin at lsu.edu
Wed Jul 25 09:19:00 CDT 2012
Sorry, I should have done that with the initial bug report. I
Here is stack trace I get when using the intel 11.1 compilers. The segfault appears to be in triangle. WHen using gcc, everything seems to work fine.
Blaise
Program received signal EXC_BAD_ACCESS, Could not access memory.
Reason: KERN_INVALID_ADDRESS at address: 0x000000001402e000
0x000000010f1e55aa in poolinit (pool=0x10fc31580, bytecount=32, itemcount=4092, wtype=FLOATINGPOINT, alignment=0) at src/triangle.c:3227
3227 *(pool->firstblock) = (VOID *) NULL;
(gdb) where
#0 0x000000010f1e55aa in poolinit (pool=0x10fc31580, bytecount=32, itemcount=4092, wtype=FLOATINGPOINT, alignment=0) at src/triangle.c:3227
#1 0x000000010f1e5da7 in initializepointpool () at src/triangle.c:3547
#2 0x000000010f203462 in transfernodes (pointlist=0x7fb408aa2370, pointattriblist=0x0, pointmarkerlist=0x0, numberofpoints=2307, numberofpointattribs=0) at src/triangle.c:11486
#3 0x000000010f205f69 in triangulate (triswitches=0x7fff6d9429c8 "npczQ", in=0x7fff6d9429d0, out=0x7fff6d942828, vorout=0x0) at src/triangle.c:12965
#4 0x000000010e46c325 in triangulateAndFormProl (selected_2=0x7fb408a9ad70, data_stride=12100, coords=0x113b0c770, nselected_1=2307, clid_lid_1=0x7fb408ac8f70, agg_lists_1=0x7fb408ab9b70, crsGID=0x7fb408b00770, bs=1, a_Prol=0x7fb408abb370, a_worst_best=0x7fff6d942dd0) at geo.c:253
#5 0x000000010e47420d in PCGAMGProlongator_GEO (pc=0x7fb408a07370, Amat=0x7fb40889cb70, Gmat=0x7fb408b4d770, agg_lists=0x7fb408ab9b70, a_P_out=0x7fff6d944420) at geo.c:848
#6 0x000000010e429526 in PCSetUp_GAMG (pc=0x7fb408a07370) at gamg.c:658
#7 0x000000010ecc05d8 in PCSetUp (pc=0x7fb408a07370) at precon.c:832
#8 0x000000010e5df6ed in KSPSetUp (ksp=0x7fb4089ccf70) at itfunc.c:278
#9 0x000000010e5e12b3 in KSPSolve (ksp=0x7fb4089ccf70, b=0x7fb408968570, x=0x7fb40894cd70) at itfunc.c:402
#10 0x000000010dd4c632 in main ()
On Jul 25, 2012, at 8:56 AM, Mark F. Adams wrote:
> Humm, I did check petsc-3.3 before it was released and petsc-dev works.
>
> Could you attache the debugger and get a line number?
>
> Mark
>
> On Jul 24, 2012, at 10:59 PM, Blaise Bourdin wrote:
>
>> Hi,
>>
>> is pc_gamg_type geo broken in petsc-3.3? I get the following when I make runex54 in src/ksp/ksp/examples/tutorials:
>>
>> iMac:tutorials blaise$ make runex54
>> 1,28c1,128
>> < 0 KSP Residual norm 132.598
>> < 1 KSP Residual norm 39.159
>> < 2 KSP Residual norm 15.7856
>> < 3 KSP Residual norm 8.91321
>> < 4 KSP Residual norm 6.95961
>> < 5 KSP Residual norm 15.1387
>> < 6 KSP Residual norm 12.5547
>> < 7 KSP Residual norm 3.78056
>> < 8 KSP Residual norm 2.38412
>> < 9 KSP Residual norm 3.91952
>> < 10 KSP Residual norm 1.3192
>> < 11 KSP Residual norm 1.70681
>> < 12 KSP Residual norm 1.74052
>> < 13 KSP Residual norm 0.482779
>> < 14 KSP Residual norm 0.634571
>> < 15 KSP Residual norm 0.264686
>> < 16 KSP Residual norm 0.240607
>> < 17 KSP Residual norm 0.10998
>> < 18 KSP Residual norm 0.0853072
>> < 19 KSP Residual norm 0.0551939
>> < 20 KSP Residual norm 0.0231032
>> < 21 KSP Residual norm 0.0286234
>> < 22 KSP Residual norm 0.0110345
>> < 23 KSP Residual norm 0.00582651
>> < 24 KSP Residual norm 0.00256534
>> < 25 KSP Residual norm 0.00176112
>> < 26 KSP Residual norm 0.000730267
>> < Linear solve converged due to CONVERGED_RTOL iterations 26
>> ---
>>> [2]PETSC ERROR: ------------------------------------------------------------------------
>>> [2]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
>>> [2]PETSC ERROR: [0]PETSC ERROR: ------------------------------------------------------------------------
>>> [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
>>> [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>> [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>> [0]PETSC ERROR: [1]PETSC ERROR: ------------------------------------------------------------------------
>>> [1]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
>>> [1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>> [1]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>> [1]PETSC ERROR: likely location of problem given in stack below
>>> [1]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>> [1]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>> [1]PETSC ERROR: INSTEAD the line number of the start of the function
>>> [1]PETSC ERROR: is given.
>>> [1]PETSC ERROR: [1] triangulateAndFormProl line 180 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/geo.c
>>> [1]PETSC ERROR: [1] PCGAMGProlongator_GEO line 756 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/geo.c
>>> [1]PETSC ERROR: [1] PCSetUp_GTry option -start_in_debugger or -on_error_attach_debugger
>>> [2]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[2]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>> [2]PETSC ERROR: likely location of problem given in stack below
>>> [2]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>> [2]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>> [2]PETSC ERROR: INSTEAD the line number of the start of the function
>>> [2]PETSC ERROR: is given.
>>> [2]PETSC ERROR: [2] triangulateAndFormProl line 180 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/geo.c
>>> [2]PETSC ERROR: [2] PCGAMGProlongator_GEO line 756 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/geo.c
>>> [2]PETSC ERROR: [2] PCSetUp_GAMG line 560 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/gamg.c
>>> [2]PETSC ERROR: [2] PCSetUp line 810 /opt/HPC/petsc-3.3/src/ksp/pc/interface/precon.c
>>> [2]PETSC ERROR: [2] KSPSetUp line 182 /opt/HPC/petsc-3.3/src/ksp[3]PETSC ERROR: ------------------------------------------------------------------------
>>> [3]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range
>>> [3]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
>>> [3]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[3]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors
>>> [3]PETSC ERROR: likely location of problem given in stack below
>>> [3]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>> [3]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>> [3]PETSC ERROR: INSTEAD the line number of the start of the function
>>> [3]PETSC ERROR: is given.
>>> [3]PETSC ERROR: [3] triangulateAndFormProl line 180 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/geo.c
>>> [3]PETSC ERROR: [3] PCGAMGProlongator_GEO line 756 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/geo.c
>>> [3]PETSC ERROR: [3] PCSetUp_Glikely location of problem given in stack below
>>> [0]PETSC ERROR: --------------------- Stack Frames ------------------------------------
>>> [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not available,
>>> [0]PETSC ERROR: INSTEAD the line number of the start of the function
>>> [0]PETSC ERROR: is given.
>>> [0]PETSC ERROR: [0] triangulateAndFormProl line 180 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/geo.c
>>> [0]PETSC ERROR: [0] PCGAMGProlongator_GEO line 756 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/geo.c
>>> [0]PETSC ERROR: [0] PCSetUp_GAMG line 560 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/gamg.c
>>> [0]PETSC ERROR: [0] PCSetUp line 810 /opt/HPC/petsc-3.3/src/ksp/pc/interface/precon.c
>>> [0]PETSC ERROR: [0] KSPSetUp line 182 /opt/HPC/petsc-3.3/src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: [0] KSPSolve line 351 /opt/HPC/petsc-3.3/src/ksp/ksp/interface/itfunc.c
>>> [0]PETSC ERROR: --------------------- Error Message ------------------------------------
>>> [0]PETSC ERROR: Signal received!
>>> [0]PETSC ERROR: ----------------AMG line 560 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/gamg.c
>>> [1]PETSC ERROR: [1] PCSetUp line 810 /opt/HPC/petsc-3.3/src/ksp/pc/interface/precon.c
>>> [1]PETSC ERROR: [1] KSPSetUp line 182 /opt/HPC/petsc-3.3/src/ksp/ksp/interface/itfunc.c
>>> [1]PETSC ERROR: [1] KSPSolve line 351 /opt/HPC/petsc-3.3/src/ksp/ksp/interface/itfunc.c
>>> [1]PETSC ERROR: --------------------- Error Message ------------------------------------
>>> [1]PETSC ERROR: Signal received!
>>> [1]PETSC ERROR: ------------------------------------------------------------------------
>>> [1]PETSC ERROR: Petsc Release Version 3.3.0, Patch 2, unknown
>>> [1]PETSC ERROR: See docs/changes/index.html for recent updates.
>>> [1]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>> [1]PETSC ERROR: See docs/index.html for manual pages.
>>> [1]PETSC ERROR: ------------------------------------------------------------------------
>>> [1]PETSC ERROR: ./ex54 on a Darwin-in named iMac.local by blaise Tue Jul 24 21:51:38 2012
>>> [1]PETSC ERROR: Libraries linked from /opt/HPC/petsc-3.3/Darwi/ksp/interface/itfunc.c
>>> [2]PETSC ERROR: [2] KSPSolve line 351 /opt/HPC/petsc-3.3/src/ksp/ksp/interface/itfunc.c
>>> [2]PETSC ERROR: --------------------- Error Message ------------------------------------
>>> [2]PETSC ERROR: Signal received!
>>> [2]PETSC ERROR: ------------------------------------------------------------------------
>>> [2]PETSC ERROR: Petsc Release Version 3.3.0, Patch 2, unknown
>>> [2]PETSC ERROR: See docs/changes/index.html for recent updates.
>>> [2]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>> [2]PETSC ERROR: See docs/index.html for manual pages.
>>> [2]PETSC ERROR: ------------------------------------------------------------------------
>>> [2]PETSC ERROR: ./ex54 on a Darwin-in named iMac.local by blaise Tue Jul 24 21:51:38 2012
>>> [2]PETSC ERROR: Libraries linked from /opt/HPC/petsc-3.3/Darwin-intel11.1-g/lib
>>> [2]PETSC ERROR: Configure run at Mon Jul 23 20:49:44 2012
>>> [2]PETSC ERROR: Configure options --download-hdf5=1 --download-metis=1 --download-parmetis=1 --download-sowing=1 --download-triangle=1 AMG line 560 /opt/HPC/petsc-3.3/src/ksp/pc/impls/gamg/gamg.c
>>> [3]PETSC ERROR: [3] PCSetUp line 810 /opt/HPC/petsc-3.3/src/ksp/pc/interface/precon.c
>>> [3]PETSC ERROR: [3] KSPSetUp line 182 /opt/HPC/petsc-3.3/src/ksp/ksp/interface/itfunc.c
>>> [3]PETSC ERROR: [3] KSPSolve line 351 /opt/HPC/petsc-3.3/src/ksp/ksp/interface/itfunc.c
>>> [3]PETSC ERROR: --------------------- Error Message ------------------------------------
>>> [3]PETSC ERROR: Signal received!
>>> [3]PETSC ERROR: ------------------------------------------------------------------------
>>> [3]PETSC ERROR: Petsc Release Version 3.3.0, Patch 2, unknown
>>> [3]PETSC ERROR: See docs/changes/index.html for recent updates.
>>> [3]PETSC ERROR: See docs/faq.html for hints about trouble shooting.
>>> [3]PETSC ERROR: See docs/index.html for manual pages.
>>> [3]PETSC ERROR: ------------------------------------------------------------------------
>>> [3]PETSC ERROR: ./ex54 on a Darwin-in named iMac.local by blaise Tue Jul 24 21:51:38 2012
>>> [3]PETSC ERROR: Libraries linked from /opt/HPC/petsc-3.3/Darwi--------------------------------------------------------
>>> [0]PETSC ERROR: Petsc Release Version 3.3.0, Patch 2, unknown
>>> [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: ./ex54 on a Darwin-in named iMac.local by blaise Tue Jul 24 21:51:38 2012
>>> [0]PETSC ERROR: Libraries linked from /opt/HPC/petsc-3.3/Darwin-intel11.1-g/lib
>>> [0]PETSC ERROR: Configure run at Mon Jul 23 20:49:44 2012
>>> [0]PETSC ERROR: Configure options --download-hdf5=1 --download-metis=1 --download-parmetis=1 --download-sowing=1 --download-triangle=1 --download-yaml=1 --with-blas-lapack-dir=/opt/intel/Compiler/11.1/091/Frameworks/mkl --with-cmake=cmake --with-debugging=1 --with-mpi-dir=/opt/HPC/mpich2-1.4.1p1-intel11.1 --with-pic --with-shared-libraries=1 --with-vendor-compilers=intel --with-x11=1 CFLAGS= CXXFLAn-intel11.1-g/lib
>>> [1]PETSC ERROR: Configure run at Mon Jul 23 20:49:44 2012
>>> [1]PETSC ERROR: Configure options --download-hdf5=1 --download-metis=1 --download-parmetis=1 --download-sowing=1 --download-triangle=1 --download-yaml=1 --with-blas-lapack-dir=/opt/intel/Compiler/11.1/091/Frameworks/mkl --with-cmake=cmake --with-debugging=1 --with-mpi-dir=/opt/HPC/mpich2-1.4.1p1-intel11.1 --with-pic --with-shared-libraries=1 --with-vendor-compilers=intel --with-x11=1 CFLAGS= CXXFLAGS= PETSC_ARCH=Darwin-intel11.1-g
>>> [1]PETSC ERROR: ------------------------------------------------------------------------
>>> [1]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
>>> [cli_1]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 1
>>> --download-yaml=1 --with-blas-lapack-dir=/opt/intel/Compiler/11.1/091/Frameworks/mkl --with-cmake=cmake --with-debugging=1 --with-mpi-dir=/opt/HPC/mpich2-1.4.1p1-intel11.1 --with-pic --with-shared-libraries=1 --with-vendor-compilers=intel --with-x11=1 CFLAGS= CXXFLAGS= PETSC_ARCH=Darwin-intel11.1-g
>>> [2]PETSC ERROR: ------------------------------------------------------------------------
>>> [2]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2
>>> [cli_2]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 2
>>> n-intel11.1-g/lib
>>> [3]PETSC ERROR: Configure run at Mon Jul 23 20:49:44 2012
>>> [3]PETSC ERROR: Configure options --download-hdf5=1 --download-metis=1 --download-parmetis=1 --download-sowing=1 --download-triangle=1 --download-yaml=1 --with-blas-lapack-dir=/opt/intel/Compiler/11.1/091/Frameworks/mkl --with-cmake=cmake --with-debugging=1 --with-mpi-dir=/opt/HPC/mpich2-1.4.1p1-intel11.1 --with-pic --with-shared-libraries=1 --with-vendor-compilers=intel --with-x11=1 CFLAGS= CXXFLAGS= PETSC_ARCH=Darwin-intel11.1-g
>>> [3]PETSC ERROR: ------------------------------------------------------------------------
>>> [3]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3
>>> [cli_3]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 3
>>> GS= PETSC_ARCH=Darwin-intel11.1-g
>>> [0]PETSC ERROR: ------------------------------------------------------------------------
>>> [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file
>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>>> [cli_0]: aborting job:
>>> application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0
>> /opt/HPC/petsc-3.3/src/ksp/ksp/examples/tutorials
>> Possible problem with with ex54_0, diffs above
>> =========================================
>>
>> Also, I though there was a suggestion for the default parameters for GAMG for symmetric elliptic problems in the documentation or the FAQ, but I can't find it. Any suggestion?
>>
>> Regards,
>>
>> Blaise
>>
>> --
>> Department of Mathematics and Center for Computation & Technology
>> Louisiana State University, Baton Rouge, LA 70803, USA
>> Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin
>>
>>
>>
>>
>>
>>
>>
>> --
>> Department of Mathematics and Center for Computation & Technology
>> Louisiana State University, Baton Rouge, LA 70803, USA
>> Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin
>>
>>
>>
>>
>>
>>
>>
>>
>
--
Department of Mathematics and Center for Computation & Technology
Louisiana State University, Baton Rouge, LA 70803, USA
Tel. +1 (225) 578 1612, Fax +1 (225) 578 4276 http://www.math.lsu.edu/~bourdin
More information about the petsc-users
mailing list