February 2012 - 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

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PCGASMSetLocalSubdomains
by Hui Zhang 22 May '12

22 May '12

About PCGASMSetLocalSubdomains(), in the case of one subdomain supported by multiple processors, shall I always create the arguments 'is[s]' and 'is_local[s]' in a subcommunicator consisting of processors supporting the subdomain 's'? The source code of PCGASMCreateSubdomains2D() seemingly does so. Thanks, Hui

4 32

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

MKL BLAS interface inconsistency
by Alexander Grayver 05 Apr '12

05 Apr '12

Dear petsc team, I've been struggling with this problem for a long time and seeking for your advice now. Let's take simple petsc program: #include <petscksp.h> int main(int argc,char **args) { Vec b; PetscReal norm; PetscInitialize(&argc,&args,(char *)0,NULL); VecCreateSeq(PETSC_COMM_SELF,100,&b); VecSet(b,2.0); VecNorm(b,NORM_1_AND_2,&norm); return 0; } This program works well if I compile petsc with non-mkl blas/lapack. However, if I compile petsc with mkl blas/lapack this program crashes: zdotc, FP=7fff8f121e30 VecNorm_Seq, FP=7fff8f121f90 VecNorm_Seq, FP=7fff8f1220f0 VecNorm, FP=7fff8f122230 main, FP=7fff8f122290 It crashes in zdotc. You call this routine as following: *z = BLASdot_(&bn,xx,&one,xx,&one); When I look at the zdotc interface in mkl.h I see: void ZDOTC(MKL_Complex16 *pres, const MKL_INT *n, const MKL_Complex16 *x, const MKL_INT *incx, const MKL_Complex16 *y, const MKL_INT *incy); I also found example here: http://software.intel.com/en-us/articles/intel-math-kernel-library-intel-mk… There are 6 input parameters. But in "classical" BLAS implementation 5 input and 1 output. For example, NORM_1 works well since interface to dzasum is the same. Any ideas? -- Regards, Alexander

4 9

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)

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Re: [petsc-users] Matrix format mpiaij does not have a built-in PETSc XXX!
by Aron Roland 06 Mar '12

06 Mar '12

Dear All, I hope somebody can help us on this or give at least some clearance. We have just included PETSc as an solver for our sparse matrix evolving from an unstructured mesh advection scheme. The problem is that we are using the mpiaij matrix type, since our matrix is naturally sparse. However it seems that PETSc has no PC for this, except the PCSOR, which showed to be not very effective for our problem. All others give the error msg. of the mail subject, where XXX are the different PC tried. The manual is a bit diffuse on this e.g. http://www.mcs.anl.gov/petsc/documentation/linearsolvertable.html it is claimed that certain PC's are running on aij matrices ... but these are to be defined either as seq. or parallel (mpiaij) matrices. Moreover in the above mentioned list are two columns parallel/seriel, what is the intention of parallel capability when not applicable to matrices stored within the parallel mpiaij framework. I guess we just not understanding the concept or have some other difficulties of understanding of all this. Any comments help is welcome Aron

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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

Configuring without debug
by Bojan Niceno 28 Feb '12

28 Feb '12

Dear all, I am trying to configure PETSc with*out* debugging. I am issuing the following command: ./configure --with-mpi-dir=/opt/mpi/openmpi-1.2.6-gcc-4.1 --with-debugging=0 COPTFLAGS='-O3 -march=p4 -mtune=p4' FOPTFLAGS='-O3 -qarch=p4 -qtune=p4'. The configuration procedure starts well, saying: =============================================================================== WARNING! Compiling PETSc with no debugging, this should only be done for timing and production runs. All development should be done when configured using --with-debugging=1 =============================================================================== which is is fine, which is what I wanted, but it ends with the message: xxx=========================================================================xxx Configure stage complete. Now build PETSc libraries with (legacy build): make PETSC_DIR=/homecfd/niceno/PETSc-3.2-p6-O PETSC_ARCH=arch-linux2-c-debug all Judging from the proposed PETSC_ARCH, it seems that debugging got switched back on :-( Then I type make, and, after a while, get the message: Completed building libraries ========================================= Now to check if the libraries are working do: make PETSC_DIR=/homecfd/niceno/PETSc-3.2-p6-O PETSC_ARCH=arch-linux2-c-debug test ========================================= Is there a way to build PETSc with*out* debugging option? Kind regards, Bojan --

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