[petsc-users] pc_gamg_type geo broken in 3.3?
Mark F. Adams
mark.adams at columbia.edu
Wed Jul 25 09:46:43 CDT 2012
Note, the geo solver is really not useful. It is there as an experiment.
But if you want to pursue this I'd blow away exernalpackages/Triangle and even you $PETSC_ARCH directory and reconfigure and build.
Mark
On Jul 25, 2012, at 10:19 AM, Blaise Bourdin wrote:
> 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
>
>
>
>
>
>
>
>
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