December 2011 - petsc-users - mailman3.cels.anl.gov

How to use class function in SNESSetFunction
by behzad baghapour 20 Mar '17

20 Mar '17

Dear developers, In my code, the function "residual" used in SNESSetFunction() for calculating Nonlinear function is a member of a class called "solver". When compiling with Petsc, I received the error: error: argument of type ‘PetscErrorCode (solver::)(_p_SNES*, _p_Vec*, _p_Vec*, void*)’ does not match ‘PetscErrorCode (*)(_p_SNES*, _p_Vec*, _p_Vec*, void*)’ How can I access that class member function is SNESSetFunction()? I need to keep my code structure as before. Thanks, BB.

3 4

Petsc compilation with -MDd using visual studio c++ 2008
by Mengda Wu 11 Aug '14

11 Aug '14

Hi all, I am trying to compile with a debug version of Petsc with -MDd options using visual studio c++ 2008. The following options are used. ./config/configure.py --with-cc='cl' --with-fc=0 --with-cxx='cl' --with-mpi=0 --with-debugging=1 --download-f2cblaslapack=/path/to/f2cblaslapack-3.1.1.q.tar.gz -CFLAGS='-MDd -wd4996' -CXXFLAGS='-MDd -wd4996' But it seems that f2cblaslapack does not recognize "-MDd" completely. Some files are still compiled with '-MD' instead of "-MDd". This will lead to a problem that not all libraries are linked with the same MS C library. I think it may be caused by the variable "CNOOPT" is not set properly in config/BuildSystem/config/packages/f2cblaslapack.py and config/BuildSystem/config/packages/BlasLapack.py. Only '-MD' is present there. See def getWindowsNonOptFlags(self,cflags): for flag in ['-MT','-MTd','-MD','-threads']: if cflags.find(flag) >=0: return flag return '' If I substitute '-MD' with '-MDd', then it works. But this will lead to problem when '-MD' is preferred. I am wondering if anyone can fix this problem. Thanks, Mengda

2 3

ML - zero pivot error
by Stijn A. M. Vantieghem 17 Jul '12

17 Jul '12

Dear all, I am using PETSc (Fortran interface) to solve a Poisson equation with Neumann boundary conditions. Up till now, I managed to do this with Hypre's BoomerAMG. Now, I am investigating whether I can improve the performance of my code by using ML. However, at execution I receive a zero pivot error; I tried to remove the (constant) null space with KSPSetNullSpace, but this didn't solve my problem. Do you have an idea of what I'm doing wrong? Thanks. The relevant portions of my code are as follows: !**************************************************** call KSPCreate(PETSC_COMM_WORLD,ksp,ierr) call KSPSetOperators(ksp,M,M,DIFFERENT_NONZERO_PATTERN,ierr) call MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,PETSC_NULL,sp,ierr) call KSPSetNullSpace(ksp,sp,ierr) call KSPGetPC(ksp,pc,ierr) call PCSetType(pc,PCML,ierr) call KSPSetFromOptions(ksp,ierr) ... call KSPSetInitialGuessNonzero(ksp,PETSC_TRUE,ierr) call KSPSolve(ksp,petsc_rhs,petsc_pressure,ierr) !**************************************************** and the error message is: [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Detected zero pivot in LU factorization see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Ze…! [0]PETSC ERROR: Zero pivot row 0 value 3.57045e-20 tolerance 1e-12! [0]PETSC ERROR: ------------------------------------------------------------------------ ... [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: MatLUFactorNumeric_SeqAIJ() line 574 in src/mat/impls/aij/seq/aijfact.c [0]PETSC ERROR: MatLUFactorNumeric() line 2587 in src/mat/interface/matrix.c [0]PETSC ERROR: PCSetUp_LU() line 158 in src/ksp/pc/impls/factor/lu/lu.c [0]PETSC ERROR: PCSetUp() line 795 in src/ksp/pc/interface/precon.c [0]PETSC ERROR: KSPSetUp() line 237 in src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: PCSetUp_MG() line 602 in src/ksp/pc/impls/mg/mg.c [0]PETSC ERROR: PCSetUp_ML() line 668 in src/ksp/pc/impls/ml/ml.c [0]PETSC ERROR: PCSetUp() line 795 in src/ksp/pc/interface/precon.c [0]PETSC ERROR: KSPSetUp() line 237 in src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: KSPSolve() line 353 in src/ksp/ksp/interface/itfunc.c Regards Stijn Stijn A.M. Vantieghem Earth and Planetary Magnetism Institute for Geophysics ETH Zürich Sonneggstrasse 5 - CH 8092 Zürich tel: +41 44 632 39 90 e-mail: stijn.vantieghem(a)erdw.ethz.ch

5 7

Binary I/O
by Mohamad M. Nasr-Azadani 07 Apr '12

07 Apr '12

Hi everyone, I think I know the answer to my question, but I was double checking. When using PetscViewerBinaryOpen(); It is mentioned that "For writing files it only opens the file on processor 0 in the communicator." Does that mean when writing a parallel vector to file using VecView(), all the data from other processors is first sent to processor zero and then dumped into the file? If so, that would be a very slow processor for big datasets and large number of processor? Any suggestions to speed that process up? Best, Mohamad

3 5

Re: Multiple communicators
by irfan.khan＠gatech.edu 02 Apr '12

02 Apr '12

I use seperete communicators for fluid and solid ranks in a fluid-structure interaction code. I use PETSc tools (KSP) to solve for the solid phase (FEA) which is carried out under a different communicator (FEA_Comm). Unless I am doing something wrong, I have found that the command line options: -ksp_type; -mat_partitioning_type, don't work if there are 2 communicators. But for single communicator they work. Please see the attached files containing output of -log_summary for 2 different codes (scroll down to the end). One with single communicator and the other with two communicators. Both the output have been generated with the same PETSc compilation. Futher -log_summary results are not able to detect all the events that have been registered if they are not in the WORLD communicator. Thank you Irfan ----- Original Message ----- From: "Matthew Knepley" <knepley(a)gmail.com> To: "PETSc users list" <petsc-users(a)mcs.anl.gov> Sent: Tuesday, November 24, 2009 8:03:00 PM GMT -05:00 US/Canada Eastern Subject: Re: Multiple communicators On Tue, Nov 24, 2009 at 6:59 PM, < irfan.khan(a)gatech.edu > wrote: Hello Does the procedure for providing command line options and to obtain profiling data through -log_summary change if there are multiple MPI communicators in a petsc code? There is always WORLD, so it should be fine unless I misunderstand your question. Matt If so, can somebody point me to information, references on how to provide command line options if there are multiple communicators? Thank you Irfan -- PhD Candidate G.W. Woodruff School of Mechanical Engineering Georgia Institute of Technology Atlanta, GA (30332) -- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener -- PhD Candidate G.W. Woodruff School of Mechanical Engineering Georgia Institute of Technology Atlanta, GA (30332)

5 14

Re: [petsc-users] ccgraph.c error
by Rongliang Chen 01 Mar '12

01 Mar '12

Hi Jed, Thank you for your reply. I have no idea if I have passed a invalid graph to Metis. This error just appeared when I run my code with some number of processors. I run my code with the debug version of PETSc and I got the following error message. Best, Rongliang ------------------------------------------------------ ***ASSERTION failed on line 169 of file ccgraph.c: cadjwgtsum[cnvtxs] == idxsum(nedges, cadjwgt) 0 107 106 107 0 [313]PETSC ERROR: ------------------------------------------------------------------------ [313]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [313]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [313]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[313]P…: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [313]PETSC ERROR: likely location of problem given in stack below [313]PETSC ERROR: --------------------- Stack Frames ------------------------------------ ***ASSERTION failed on line 169 of file ccgraph.c: cadjwgtsum[cnvtxs] == idxsum(nedges, cadjwgt) 0 107 106 107 0 [313]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, [313]PETSC ERROR: INSTEAD the line number of the start of the function [313]PETSC ERROR: is given. [313]PETSC ERROR: [313] MatLUFactorNumeric_SuperLU_DIST line 280 src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c [313]PETSC ERROR: [313] MatLUFactorNumeric line 2864 src/mat/interface/matrix.c [313]PETSC ERROR: [313] PCApply line 373 src/ksp/pc/interface/precon.c [313]PETSC ERROR: [313] FGMREScycle line 119 src/ksp/ksp/impls/gmres/fgmres/fgmres.c [313]PETSC ERROR: [313] KSPSolve_FGMRES line 282 src/ksp/ksp/impls/gmres/fgmres/fgmres.c [313]PETSC ERROR: [313] KSPSolve line 331 src/ksp/ksp/interface/itfunc.c [313]PETSC ERROR: [313] SNES_KSPSolve line 3394 src/snes/interface/snes.c [313]PETSC ERROR: [313] SNESSolve_LS line 142 src/snes/impls/ls/ls.c [401]PETSC ERROR: ------------------------------------------------------------------------ [401]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [401]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [401]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[401]P…: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [401]PETSC ERROR: likely location of problem given in stack below [401]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [313]PETSC ERROR: [313] SNESSolve line 2647 src/snes/interface/snes.c [313]PETSC ERROR: [313] TimeStep line 1554 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [313]PETSC ERROR: [313] SolveSteadyState line 1429 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [313]PETSC ERROR: [313] ComputefixedBoundary line 588 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 313 in communicator MPI_COMM_WORLD with errorcode 59. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: [313] SetReferenceElement line 424 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [313]PETSC ERROR: --------------------- Error Message ------------------------------------ [313]PETSC ERROR: Signal received! [313]PETSC ERROR: ------------------------------------------------------------------------ [313]PETSC ERROR: Petsc Release Version 3.2.0, Patch 1, Mon Sep 12 16:01:51 CDT 2011 [313]PETSC ERROR: See docs/changes/index.html for recent updates. [313]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [313]PETSC ERROR: See docs/index.html for manual pages. [313]PETSC ERROR: ------------------------------------------------------------------------ [313]PETSC ERROR: ./joab on a Janus-deb named node1739 by ronglian Sun Nov 27 12:50:41 2011 [313]PETSC ERROR: Libraries linked from /home/ronglian/soft/petsc-3.2-p1/Janus-debug/lib [313]PETSC ERROR: Configure run at Tue Sep 13 18:32:21 2011 [313]PETSC ERROR: Configure options --known-level1-dcache-size=32768 --known-level1-dcache-linesize=32 --known-level1-dcache-assoc=0 --known-memcmp-ok=1 --known-sizeof-char=1 --known-sizeof-void-p=8 --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8 --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8 --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-sizeof-MPI_Comm=8 --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --with-batch=1 --with-mpi-shared-libraries=1 --known-mpi-shared-libraries=0 --download-f-blas-lapack=1 --download-hypre=1 --download-superlu=1 --download-parmetis=1 --download-superlu_dist=1 --download-blacs=1 --download-scalapack=1 --with-debugging=1 [313]PETSC ERROR: ------------------------------------------------------------------------ [313]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [401]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, [401]PETSC ERROR: INSTEAD the line number of the start of the function [401]PETSC ERROR: is given. [401]PETSC ERROR: [401] MatLUFactorNumeric_SuperLU_DIST line 280 src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c [401]PETSC ERROR: [401] MatLUFactorNumeric line 2864 src/mat/interface/matrix.c [401]PETSC ERROR: [401] PCApply line 373 src/ksp/pc/interface/precon.c [401]PETSC ERROR: [401] FGMREScycle line 119 src/ksp/ksp/impls/gmres/fgmres/fgmres.c [401]PETSC ERROR: [401] KSPSolve_FGMRES line 282 src/ksp/ksp/impls/gmres/fgmres/fgmres.c [401]PETSC ERROR: [401] KSPSolve line 331 src/ksp/ksp/interface/itfunc.c [401]PETSC ERROR: [401] SNES_KSPSolve line 3394 src/snes/interface/snes.c [401]PETSC ERROR: [401] SNESSolve_LS line 142 src/snes/impls/ls/ls.c [401]PETSC ERROR: [401] SNESSolve line 2647 src/snes/interface/snes.c [401]PETSC ERROR: [401] TimeStep line 1554 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [401]PETSC ERROR: [401] SolveSteadyState line 1429 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [401]PETSC ERROR: [401] ComputefixedBoundary line 588 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: [401] SetReferenceElement line 424 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [401]PETSC ERROR: --------------------- Error Message ------------------------------------ [401]PETSC ERROR: Signal received! [401]PETSC ERROR: ------------------------------------------------------------------------ [401]PETSC ERROR: Petsc Release Version 3.2.0, Patch 1, Mon Sep 12 16:01:51 CDT 2011 [401]PETSC ERROR: See docs/changes/index.html for recent updates. [401]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [401]PETSC ERROR: See docs/index.html for manual pages. [401]PETSC ERROR: ------------------------------------------------------------------------ [401]PETSC ERROR: ./joab on a Janus-deb named node1708 by ronglian Sun Nov 27 12:50:41 2011 [401]PETSC ERROR: Libraries linked from /home/ronglian/soft/petsc-3.2-p1/Janus-debug/lib [401]PETSC ERROR: Configure run at Tue Sep 13 18:32:21 2011 [401]PETSC ERROR: Configure options --known-level1-dcache-size=32768 --known-level1-dcache-linesize=32 --known-level1-dcache-assoc=0 --known-memcmp-ok=1 --known-sizeof-char=1 --known-sizeof-void-p=8 --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8 --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8 --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-sizeof-MPI_Comm=8 --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --with-batch=1 --with-mpi-shared-libraries=1 --known-mpi-shared-libraries=0 --download-f-blas-lapack=1 --download-hypre=1 --download-superlu=1 --download-parmetis=1 --download-superlu_dist=1 --download-blacs=1 --download-scalapack=1 --with-debugging=1 [401]PETSC ERROR: ------------------------------------------------------------------------ [401]PETSC ERROR: User provided function() line 0 in unknown directory unknown file ***ASSERTION failed on line 169 of file ccgraph.c: cadjwgtsum[cnvtxs] == idxsum(nedges, cadjwgt) 0 107 106 107 0 [511]PETSC ERROR: ------------------------------------------------------------------------ [511]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [511]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [511]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[511]P…: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [511]PETSC ERROR: likely location of problem given in stack below [511]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [511]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, [511]PETSC ERROR: INSTEAD the line number of the start of the function [511]PETSC ERROR: is given. [511]PETSC ERROR: [511] MatLUFactorNumeric_SuperLU_DIST line 280 src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c [511]PETSC ERROR: [511] MatLUFactorNumeric line 2864 src/mat/interface/matrix.c [511]PETSC ERROR: [511] PCApply line 373 src/ksp/pc/interface/precon.c [511]PETSC ERROR: [511] FGMREScycle line 119 src/ksp/ksp/impls/gmres/fgmres/fgmres.c [511]PETSC ERROR: [511] KSPSolve_FGMRES line 282 src/ksp/ksp/impls/gmres/fgmres/fgmres.c [511]PETSC ERROR: [511] KSPSolve line 331 src/ksp/ksp/interface/itfunc.c [511]PETSC ERROR: [511] SNES_KSPSolve line 3394 src/snes/interface/snes.c [511]PETSC ERROR: [511] SNESSolve_LS line 142 src/snes/impls/ls/ls.c [511]PETSC ERROR: [511] SNESSolve line 2647 src/snes/interface/snes.c [511]PETSC ERROR: [511] TimeStep line 1554 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [511]PETSC ERROR: [511] SolveSteadyState line 1429 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [511]PETSC ERROR: [511] ComputefixedBoundary line 588 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: [511] SetReferenceElement line 424 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [511]PETSC ERROR: --------------------- Error Message ------------------------------------ [511]PETSC ERROR: Signal received! [511]PETSC ERROR: ------------------------------------------------------------------------ [511]PETSC ERROR: Petsc Release Version 3.2.0, Patch 1, Mon Sep 12 16:01:51 CDT 2011 [511]PETSC ERROR: See docs/changes/index.html for recent updates. [511]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [511]PETSC ERROR: See docs/index.html for manual pages. [511]PETSC ERROR: ------------------------------------------------------------------------ [511]PETSC ERROR: ./joab on a Janus-deb named node1376 by ronglian Sun Nov 27 12:50:41 2011 [511]PETSC ERROR: Libraries linked from /home/ronglian/soft/petsc-3.2-p1/Janus-debug/lib [511]PETSC ERROR: Configure run at Tue Sep 13 18:32:21 2011 [511]PETSC ERROR: Configure options --known-level1-dcache-size=32768 --known-level1-dcache-linesize=32 --known-level1-dcache-assoc=0 --known-memcmp-ok=1 --known-sizeof-char=1 --known-sizeof-void-p=8 --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8 --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8 --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-sizeof-MPI_Comm=8 --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --with-batch=1 --with-mpi-shared-libraries=1 --known-mpi-shared-libraries=0 --download-f-blas-lapack=1 --download-hypre=1 --download-superlu=1 --download-parmetis=1 --download-superlu_dist=1 --download-blacs=1 --download-scalapack=1 --with-debugging=1 [511]PETSC ERROR: ------------------------------------------------------------------------ [511]PETSC ERROR: User provided function() line 0 in unknown directory unknown file ***ASSERTION failed on line 169 of file ccgraph.c: cadjwgtsum[cnvtxs] == idxsum(nedges, cadjwgt) 0 107 106 107 0 [404]PETSC ERROR: ------------------------------------------------------------------------ [404]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [404]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [404]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[404]P…: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [404]PETSC ERROR: likely location of problem given in stack below [404]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [404]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, [404]PETSC ERROR: INSTEAD the line number of the start of the function [404]PETSC ERROR: is given. [404]PETSC ERROR: [404] MatLUFactorNumeric_SuperLU_DIST line 280 src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c [404]PETSC ERROR: [404] MatLUFactorNumeric line 2864 src/mat/interface/matrix.c [404]PETSC ERROR: [404] PCApply line 373 src/ksp/pc/interface/precon.c [404]PETSC ERROR: [404] FGMREScycle line 119 src/ksp/ksp/impls/gmres/fgmres/fgmres.c [404]PETSC ERROR: [404] KSPSolve_FGMRES line 282 src/ksp/ksp/impls/gmres/fgmres/fgmres.c [404]PETSC ERROR: [404] KSPSolve line 331 src/ksp/ksp/interface/itfunc.c [404]PETSC ERROR: [404] SNES_KSPSolve line 3394 src/snes/interface/snes.c [404]PETSC ERROR: [404] SNESSolve_LS line 142 src/snes/impls/ls/ls.c [404]PETSC ERROR: [404] SNESSolve line 2647 src/snes/interface/snes.c [404]PETSC ERROR: [404] TimeStep line 1554 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [404]PETSC ERROR: [404] SolveSteadyState line 1429 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [404]PETSC ERROR: [404] ComputefixedBoundary line 588 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: [404] SetReferenceElement line 424 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [404]PETSC ERROR: --------------------- Error Message ------------------------------------ [404]PETSC ERROR: Signal received! [404]PETSC ERROR: ------------------------------------------------------------------------ [404]PETSC ERROR: Petsc Release Version 3.2.0, Patch 1, Mon Sep 12 16:01:51 CDT 2011 [404]PETSC ERROR: See docs/changes/index.html for recent updates. [404]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [404]PETSC ERROR: See docs/index.html for manual pages. [404]PETSC ERROR: ------------------------------------------------------------------------ [404]PETSC ERROR: ./joab on a Janus-deb named node1708 by ronglian Sun Nov 27 12:50:41 2011 [404]PETSC ERROR: Libraries linked from /home/ronglian/soft/petsc-3.2-p1/Janus-debug/lib [404]PETSC ERROR: Configure run at Tue Sep 13 18:32:21 2011 [404]PETSC ERROR: Configure options --known-level1-dcache-size=32768 --known-level1-dcache-linesize=32 --known-level1-dcache-assoc=0 --known-memcmp-ok=1 --known-sizeof-char=1 --known-sizeof-void-p=8 --known-sizeof-short=2 --known-sizeof-int=4 --known-sizeof-long=8 --known-sizeof-long-long=8 --known-sizeof-float=4 --known-sizeof-double=8 --known-sizeof-size_t=8 --known-bits-per-byte=8 --known-sizeof-MPI_Comm=8 --known-sizeof-MPI_Fint=4 --known-mpi-long-double=1 --with-batch=1 --with-mpi-shared-libraries=1 --known-mpi-shared-libraries=0 --download-f-blas-lapack=1 --download-hypre=1 --download-superlu=1 --download-parmetis=1 --download-superlu_dist=1 --download-blacs=1 --download-scalapack=1 --with-debugging=1 [404]PETSC ERROR: ------------------------------------------------------------------------ [404]PETSC ERROR: User provided function() line 0 in unknown directory unknown file ***ASSERTION failed on line 169 of file ccgraph.c: cadjwgtsum[cnvtxs] == idxsum(nedges, cadjwgt) 0 107 106 107 0 [371]PETSC ERROR: ------------------------------------------------------------------------ [371]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [371]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [371]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/faq.html#valgrind[371]P…: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find memory corruption errors [371]PETSC ERROR: likely location of problem given in stack below [371]PETSC ERROR: --------------------- Stack Frames ------------------------------------ [371]PETSC ERROR: Note: The EXACT line numbers in the stack are not available, [371]PETSC ERROR: INSTEAD the line number of the start of the function [371]PETSC ERROR: is given. [371]PETSC ERROR: [371] MatLUFactorNumeric_SuperLU_DIST line 280 src/mat/impls/aij/mpi/superlu_dist/superlu_dist.c [371]PETSC ERROR: [371] MatLUFactorNumeric line 2864 src/mat/interface/matrix.c [371]PETSC ERROR: [371] PCApply line 373 src/ksp/pc/interface/precon.c [371]PETSC ERROR: [371] FGMREScycle line 119 src/ksp/ksp/impls/gmres/fgmres/fgmres.c [371]PETSC ERROR: [371] KSPSolve_FGMRES line 282 src/ksp/ksp/impls/gmres/fgmres/fgmres.c [371]PETSC ERROR: [371] KSPSolve line 331 src/ksp/ksp/interface/itfunc.c [371]PETSC ERROR: [371] SNES_KSPSolve line 3394 src/snes/interface/snes.c [371]PETSC ERROR: [371] SNESSolve_LS line 142 src/snes/impls/ls/ls.c [371]PETSC ERROR: [371] SNESSolve line 2647 src/snes/interface/snes.c [371]PETSC ERROR: [371] TimeStep line 1554 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [371]PETSC ERROR: [371] SolveSteadyState line 1429 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [371]PETSC ERROR: [371] ComputefixedBoundary line 588 /home/rlchen/rlchen/soft/fixedmesh/code_changed/joab.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] Elements line 290 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c [371]PETSC ERROR: [371] SetReferenceElement line 424 /home/rlchen/rlchen/soft/fixedmesh/code_changed/setelement.c > This is part of the graph library Metis. Perhaps an invalid graph was > passed to Metis? Without a stack trace (you can configure > -with-debugging=1, the default), we don't even know whether this error was > reached through PETSc, through your code, or through another library. >

7 15

Infinite or not-a-number generated in norm!
by Dominik Szczerba 30 Dec '11

30 Dec '11

Hi, I am getting the below error with fgmres. I was wondering how to start debugging the problem. All the values in the matrix and rhs seem fine. Any suggestions are very welcome. Best regards, Dominik ||b|| = 3.102831e-05 Starting KSPSolve... 0 KSP Residual norm 2.071556923444e-05 [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Floating point exception! [0]PETSC ERROR: Infinite or not-a-number generated in norm! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 3.2.0, Patch 5, Sat Oct 29 13:45:54 CDT 2011 [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: /home/dsz/build/framework-debug/sandbox/cscs/bin/FluidSolver on a linux-gnu named tharsis by dsz Fri Dec 30 15:31:20 2011 [0]PETSC ERROR: Libraries linked from /home/dsz/pack/petsc-3.2-p5/linux-gnu-c-debug/lib [0]PETSC ERROR: Configure run at Wed Nov 23 13:57:33 2011 [0]PETSC ERROR: Configure options PETSC_DIR=/home/dsz/pack/petsc-3.2-p5 PETSC_ARCH=linux-gnu-c-debug --with-debugging=1 --with-x=0 --download-f-blas-lapack=1 --download-mpich=1 --download-hypre=1 --download-parmetis=1 --download-scalapack --download-blacs --download-mumps --with-hdf5 --with-hdf5-dir=/usr [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: VecNorm() line 167 in /home/dsz/pack/petsc-3.2-p5/src/vec/vec/interface/rvector.c [0]PETSC ERROR: FGMREScycle() line 132 in /home/dsz/pack/petsc-3.2-p5/src/ksp/ksp/impls/gmres/fgmres/fgmres.c [0]PETSC ERROR: KSPSolve_FGMRES() line 299 in /home/dsz/pack/petsc-3.2-p5/src/ksp/ksp/impls/gmres/fgmres/fgmres.c [0]PETSC ERROR: KSPSolve() line 423 in /home/dsz/pack/petsc-3.2-p5/src/ksp/ksp/interface/itfunc.c [0]PETSC ERROR: ApplyPreconditioner() line 3721 in "unknowndirectory/"/home/dsz/src/framework/sandbox/dsz/cscs/solve/FluidSolver.cxx [0]PETSC ERROR: PCApply_Shell() line 121 in /home/dsz/pack/petsc-3.2-p5/src/ksp/pc/impls/shell/shellpc.c [0]PETSC ERROR: PCApply() line 383 in /home/dsz/pack/petsc-3.2-p5/src/ksp/pc/interface/precon.c [0]PETSC ERROR: FGMREScycle() line 174 in /home/dsz/pack/petsc-3.2-p5/src/ksp/ksp/impls/gmres/fgmres/fgmres.c [0]PETSC ERROR: KSPSolve_FGMRES() line 299 in /home/dsz/pack/petsc-3.2-p5/src/ksp/ksp/impls/gmres/fgmres/fgmres.c [0]PETSC ERROR: KSPSolve() line 423 in /home/dsz/pack/petsc-3.2-p5/src/ksp/ksp/interface/itfunc.c

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Flops pf MatMult is less than expected
by Junchao Zhang 30 Dec '11

30 Dec '11

Hello, I have a sparse matrix A. Its size is 494 x 494. It has 1666 nonzeros. I call MatMult(A, x, y). From the profiling result (got by -log_summary), I find MatMult's flops is 2838. I think the flops should be nnz x 2 = 1666 x 2 = 3332. I don't know how PETSc got this number (2838). I also observed the phenomena with other matrices. It seems PETSc always give smaller flops. Why? Thank you! -- Junchao Zhang

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How to get number of local nonzeros of a matrix?
by Junchao Zhang 29 Dec '11

29 Dec '11

Hello, I create a MPIAIJ matrix. How can I know the # of nonzeros stored locally? Furthermore, in case it is needed, how can I get access to the Compress Sparse Row(CSR) data structure of the local matrix, i.e., the row pointer array, column index array, value array? Thank you! -- Junchao Zhang

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Re: [petsc-users] Strongly nonlinear equation solved within the framework of PETSc
by Fatcharm 29 Dec '11

29 Dec '11

2011/12/28, petsc-users-request(a)mcs.anl.gov <petsc-users-request(a)mcs.anl.gov>: > Send petsc-users mailing list submissions to > petsc-users(a)mcs.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.mcs.anl.gov/mailman/listinfo/petsc-users > or, via email, send a message with subject or body 'help' to > petsc-users-request(a)mcs.anl.gov > > You can reach the person managing the list at > petsc-users-owner(a)mcs.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of petsc-users digest..." > > > Today's Topics: > > 1. Re: Strongly nonlinear equation solved within the framework > of PETSc (Jed Brown) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 27 Dec 2011 22:01:15 -0600 > From: Jed Brown <jedbrown(a)mcs.anl.gov> > Subject: Re: [petsc-users] Strongly nonlinear equation solved within > the framework of PETSc > To: PETSc users list <petsc-users(a)mcs.anl.gov> > Message-ID: > <CAM9tzSnvqS5zci5AHmZHzidnLt0LAeXKFsQgZ9O+uLMX7mtr=g(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > On Tue, Dec 27, 2011 at 19:58, Feng-Chao Wang <wolfshow(a)gmail.com> wrote: > >> ** >> Dear all, >> >> I want to numerically solve a strongly nonlinear fourth-order equation >> (2-D), which is used to describe the dynamics of a liquid film. >> please find the form of the equation below or in the attachment, The >> thickness of the film, H(X,Y,T) is the function to be solved, C, G, A0 >> are >> constant parameters. >> >> >> I wrote a PETSc programs for this problem, using CN method in time. >> However, it does not work well. In some cases, there are some >> negativevalues in the solution (Obviously, the thickness of the liquid >> film >> could not be negative.) While in some other cases, the solution remains as >> the initial condition, looking like the governing equation doesn't work at >> all. >> > > 1. Make sure that the equations are actually being solved, for instance > with -snes_monitor -snes_converged_reason -ksp_converged_reason. > Dear Jed, Follow your suggestions, I examined my problem. For the cases that the equations are not being solved, I got these message: timestep 0: time 0, solution norm 10.201, max 0.00195106, min 4.89435e-05 0 SNES Function norm 2.772465906990e+07 Linear solve did not converge due to DIVERGED_DTOL iterations 3270 Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE timestep 1: time 0.0001, solution norm 10.201, max 0.00195106, min 4.89435e-05 0 SNES Function norm 2.772465906990e+07 Linear solve did not converge due to DIVERGED_DTOL iterations 3270 Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE timestep 2: time 0.0002, solution norm 10.201, max 0.00195106, min 4.89435e-05 0 SNES Function norm 2.772465906990e+07 Linear solve did not converge due to DIVERGED_DTOL iterations 3270 Nonlinear solve did not converge due to DIVERGED_LINEAR_SOLVE We can see that the SNES Function norm is extremely large. I think it is because that the initial value for the unknown function H(X,T) is quite small and there is some terms like (1/H)(dH/dX) or (1/H^2)(dH/dX) in my equations. For "Linear solve did not converge due to DIVERGED_DTOL iterations 3270", does this mean I should change the ksp_type? Thank you very much! Feng-Chao > 2. Start with a time integration method that has a discrete maximum > principle. Implicit Euler has this property for many classes of systems, > but CN does not. > > 3. Consider writing the system as a variational inequality if positivity is > still a problem with the time steps you want to take. Then use SNESVIRS (or > SNESVIRSAUG or SNESVISS). > > >> >> I think it is because that the solution of this equation may form infinite >> fradient when the equation is developed. >> >> Some literatures reported that the similar problem was solved successfully >> using the ADI (Alternating Direction Implicit) method. Unfortunately, I >> found that the current PETSc doesn't support ADI. >> >> I also read a paper in which the similar equation was solved by using the >> CN scheme in time. Besides, the author employed the modified second-order >> upwind difference method to handle the nonlinear terms due to the >> inability >> of the centered differences in space. >> >> I prefer to use PETSc because this powerful toolkit enables easy parallel >> computation of PDE since I am not familar with MPI. Could anyone please >> give me some suggestions on how I can solve the above equation within the >> framework of PETSc? >> >> Thanks very much in advance! >> >> Feng-Chao Wang >> >> 2011-12-28 >> ------------------------------ >> >> >

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