TAY wee-bing, If you want to be a programmer that writes interesting and reliable code, you need to be willing to use the tools of the trade. I can't think of a bigger time-saver than Valgrind. I would suggest that you learn to use it and use it a lot. I bet it will lead you to the root of your problem pretty quickly.
John On Tue, May 8, 2012 at 2:17 PM, TAY wee-beng <zonexo at gmail.com> wrote: > Hi, > > I compiled and run my code under visual studio 2008 with intel fortran. > Everything works ok. > > However, when I tried to run the code in linux, I got the error as below. > The error happens when KSPSetUp(ksp,ierr) is called. > > However, I am not able to print VecView or MatView to view if there's any > errors. Is there any recommendation for debugging? I hope I do not need to > valgrind if possible. > > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > probably memory access out of range > [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger > [0]PETSC ERROR: or see > http://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind[0]PETSC > ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to find > memory corruption errors > [0]PETSC ERROR: likely location of problem given in stack below > [0]PETSC ERROR: --------------------- Stack Frames > ------------------------------------ > [0]PETSC ERROR: Note: The EXACT line numbers in the stack are not > available, > [0]PETSC ERROR: INSTEAD the line number of the start of the function > [0]PETSC ERROR: is given. > [0]PETSC ERROR: [0] DM user function line 0 unknownunknown > [0]PETSC ERROR: [0] DMComputeFunction line 2085 > /home/wtay/Codes/petsc-dev/src/dm/interface/dm.c > [0]PETSC ERROR: [0] KSPSetUp line 182 > /home/wtay/Codes/petsc-dev/src/ksp/ksp/interface/itfunc.c > [0]PETSC ERROR: --------------------- Error Message > ------------------------------------ > [0]PETSC ERROR: Signal received! > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: Petsc Development HG revision: > 7ecdd63ec420b1659b960e65d96e822c5ac1a968 HG Date: Mon May 07 21:42:26 2012 > -0500 > [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: ./ex29f on a petsc-3.2 named hpc12 by wtay Tue May 8 > 20:45:42 2012 > [0]PETSC ERROR: Libraries linked from > /home/wtay/Lib/petsc-3.2-dev_shared_debug/lib > [0]PETSC ERROR: Configure run at Tue May 8 10:47:59 2012 > [0]PETSC ERROR: Configure options --with-mpi-dir=/opt/openmpi-1.5.3/ > --with-blas-lapack-dir=/opt/intelcpro-11.1.059/mkl/lib/em64t/ > --with-debugging=1 --download-hypre=1 > --prefix=/home/wtay/Lib/petsc-3.2-dev_shared_debug --known-mpi-shared=1 > --with-shared-libraries > [0]PETSC ERROR: > ------------------------------------------------------------------------ > [0]PETSC ERROR: User provided function() line 0 in unknown directory > unknown file > -------------------------------------------------------------------------- > MPI_ABORT was invoked on rank 0 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. > > Yours sincerely, > > TAY wee-beng > > > On 5/5/2012 1:43 AM, Matthew Knepley wrote: > > On Fri, May 4, 2012 at 5:42 PM, TAY wee-beng <zonexo at gmail.com> wrote: > >> Hi, >> >> I wonder if you people are interested to include my ex29 fortran version >> in the petsc examples, which can help people who are using fortran. >> > > Yes, we will definitely include it. Please send the source, and a > representative output with run options. > > Thanks, > > Matt > > >> Thanks. >> >> Yours sincerely, >> >> TAY wee-beng >> >> >> On 4/5/2012 9:28 PM, Matthew Knepley wrote: >> >> On Fri, May 4, 2012 at 3:24 PM, TAY wee-beng <zonexo at gmail.com> wrote: >> >>> >>> On 4/5/2012 9:16 PM, Barry Smith wrote: >>> >>>> Do an hg pull and then run make in src/mat/interface/ftn-custom/ >>>> >>>> Then it should link. >>>> >>>> Barry >>>> >>>> There was a E missing from the all caps name of the function. >>>> >>> After hg pull, I did: >>> >>> cd src//mat/interface/ftn-custom/ >>> >>> User at User-PC /cygdrive/c/temp/petsc-dev/src/mat/interface/ftn-custom >>> $ make >>> make[1]: Warning: File >>> `/cygdrive/c/temp/petsc-dev/petsc-3.2-dev_win32_vs2008/lib/libpetsc.lib(zmatregf.o)' >>> has modification time 787 s in the future >>> make[1]: Nothing to be done for `libc'. >>> make[1]: warning: Clock skew detected. Your build may be incomplete. >>> >>> But it still can't work. >>> >> >> Something is messed up with the clock on this machine. >> >> HOWEVER, development requires certain basic skills in order to debug >> your work. We >> cannot be the ones debugging your code. Now >> >> nm $PETSC_ARCH/lib/libpetsc.a | grep -i MatNullSpaceRemove >> >> will look for the symbol. >> >> Matt >> >> >>> >>>> >>>> On May 4, 2012, at 2:11 PM, Matthew Knepley wrote: >>>> >>>> On Fri, May 4, 2012 at 3:01 PM, TAY wee-beng<zonexo at gmail.com> wrote: >>>>> >>>>> On 4/5/2012 5:17 PM, Matthew Knepley wrote: >>>>> >>>>>> On Fri, May 4, 2012 at 11:05 AM, TAY wee-beng<zonexo at gmail.com> >>>>>> wrote: >>>>>> >>>>>> On 4/5/2012 3:05 PM, Matthew Knepley wrote: >>>>>> >>>>>>> On Fri, May 4, 2012 at 8:59 AM, TAY wee-beng<zonexo at gmail.com> >>>>>>> wrote: >>>>>>> >>>>>>> Hi, >>>>>>> >>>>>>> Is there anything else I can try to get it working right? >>>>>>> >>>>>>> The MatGetNullSpaceRemove() is missing. >>>>>>> >>>>>> Where should I add MatGetNullSpaceRemove and what are its syntax? I >>>>>> googled but there's no results. >>>>>> >>>>>> Fixed in p;etsc-dev: >>>>>> >>>>>> >>>>>> http://www.mcs.anl.gov/petsc/petsc-dev/docs/manualpages/Mat/MatNullSpaceRemove.html >>>>>> >>>>> I just compiled the updated petsc-dev but I got the same error msg >>>>> when I use: >>>>> >>>>> call MatNullSpaceRemove(nullspace,b,PETSC_NULL,ierr) >>>>> >>>>> error LNK2019: unresolved external symbol MATNULLSPACEREMOVE >>>>> referenced in function COMPUTERHS >>>>> 1>c:\obj_tmp\ex29f\Debug\ex29f.exe : fatal error LNK1120: 1 unresolved >>>>> externals >>>>> >>>>> That function is in: >>>>> >>>>> src/mat/interface/ftn-custom/zmatrixf.c >>>>> >>>>> Did that compile? Can you see the symbol in libpetsc.a? >>>>> >>>>> Matt >>>>> >>>>> Matt >>>>>> >>>>>> Thanks. >>>>>> >>>>>>> Matt >>>>>>> >>>>>>> Thanks? >>>>>>> >>>>>>> >>>>>>> On 2/5/2012 10:11 PM, Matthew Knepley wrote: >>>>>>> >>>>>>>> On Wed, May 2, 2012 at 1:55 PM, TAY wee-beng<zonexo at gmail.com> >>>>>>>> wrote: >>>>>>>> Hi, >>>>>>>> >>>>>>>> I did a MatView and VecView on both C and Fortran, right after Mat >>>>>>>> and Vec assembly. I have attached the printout below. They are exactly >>>>>>>> the >>>>>>>> same, but yet the result is different in Neumann condition. However, >>>>>>>> the >>>>>>>> dirichlet condition gives the correct ans. Is there anything else that >>>>>>>> could be wrong even if the Mat and Vec are the same? >>>>>>>> >>>>>>>> Did you set the null space for the matrix when you have Neumann >>>>>>>> conditions? >>>>>>>> >>>>>>> Yes, for the matrix, I set as: >>>>>>> >>>>>>> call >>>>>>> MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,PETSC_NULL_OBJECT,nullspace,ierr) >>>>>>> >>>>>>> call MatSetNullSpace(jac,nullspace,ierr) >>>>>>> >>>>>>> call MatNullSpaceDestroy(nullspace,ierr) >>>>>>> >>>>>>> for the Vec, >>>>>>> >>>>>>> call >>>>>>> MatNullSpaceCreate(PETSC_COMM_WORLD,PETSC_TRUE,0,PETSC_NULL_OBJECT,nullspace,ierr) >>>>>>> >>>>>>> !call MatNullSpaceRemove(nullspace,b,PETSC_NULL,ierr) >>>>>>> >>>>>>> call MatNullSpaceDestroy(nullspace,ierr) >>>>>>> >>>>>>> MatNullSpaceRemove was comment out because there's error during >>>>>>> linking >>>>>>> >>>>>>> >>>>>>> Matt >>>>>>>> >>>>>>>> Thanks! >>>>>>>> >>>>>>>> Fortran: >>>>>>>> >>>>>>>> Matrix Object: 1 MPI processes >>>>>>>> type: seqaij >>>>>>>> row 0: (0, 2) (1, -1) (3, -1) >>>>>>>> row 1: (0, -1) (1, 3) (2, -1) (4, -1) >>>>>>>> row 2: (1, -1) (2, 2) (5, -1) >>>>>>>> row 3: (0, -1) (3, 3) (4, -1) (6, -1) >>>>>>>> row 4: (1, -1) (3, -1) (4, 4) (5, -1) (7, -1) >>>>>>>> row 5: (2, -1) (4, -1) (5, 3) (8, -1) >>>>>>>> row 6: (3, -1) (6, 2) (7, -1) >>>>>>>> row 7: (4, -1) (6, -1) (7, 3) (8, -1) >>>>>>>> row 8: (5, -1) (7, -1) (8, 2) >>>>>>>> Vector Object:Vec_0000000084000000_0 1 MPI processes >>>>>>>> type: mpi >>>>>>>> Process [0] >>>>>>>> 0.25 >>>>>>>> 0.0205213 >>>>>>>> 1.135e-005 >>>>>>>> 0.0205213 >>>>>>>> 0.00168449 >>>>>>>> 9.31663e-007 >>>>>>>> 1.135e-005 >>>>>>>> 9.31663e-007 >>>>>>>> 5.15289e-010 >>>>>>>> Vector Object:Vec_0000000084000000_1 1 MPI processes >>>>>>>> type: mpi >>>>>>>> Process [0] >>>>>>>> 0.14924 >>>>>>>> 0.0242397 >>>>>>>> -0.0260347 >>>>>>>> 0.0242397 >>>>>>>> -0.0256192 >>>>>>>> -0.0400102 >>>>>>>> -0.0260347 >>>>>>>> -0.0400102 >>>>>>>> -0.0400102 >>>>>>>> Press any key to continue . . . >>>>>>>> >>>>>>>> C: >>>>>>>> >>>>>>>> Matrix Object: 1 MPI processes >>>>>>>> type: seqaij >>>>>>>> row 0: (0, 2) (1, -1) (3, -1) >>>>>>>> row 1: (0, -1) (1, 3) (2, -1) (4, -1) >>>>>>>> row 2: (1, -1) (2, 2) (5, -1) >>>>>>>> row 3: (0, -1) (3, 3) (4, -1) (6, -1) >>>>>>>> row 4: (1, -1) (3, -1) (4, 4) (5, -1) (7, -1) >>>>>>>> row 5: (2, -1) (4, -1) (5, 3) (8, -1) >>>>>>>> row 6: (3, -1) (6, 2) (7, -1) >>>>>>>> row 7: (4, -1) (6, -1) (7, 3) (8, -1) >>>>>>>> row 8: (5, -1) (7, -1) (8, 2) >>>>>>>> Vector Object:Vec_0x1d3b000_0 1 MPI processes >>>>>>>> type: mpi >>>>>>>> Process [0] >>>>>>>> 0.25 >>>>>>>> 0.0205212 >>>>>>>> 1.135e-05 >>>>>>>> 0.0205212 >>>>>>>> 0.00168449 >>>>>>>> 9.31663e-07 >>>>>>>> 1.135e-05 >>>>>>>> 9.31663e-07 >>>>>>>> 5.15288e-10 >>>>>>>> Vector Object:Vec_0x1d3b000_1 1 MPI processes >>>>>>>> type: mpi >>>>>>>> Process [0] >>>>>>>> 0.139311 >>>>>>>> 0.0305751 >>>>>>>> -0.0220633 >>>>>>>> 0.0305751 >>>>>>>> -0.0135158 >>>>>>>> -0.042185 >>>>>>>> -0.0220633 >>>>>>>> -0.042185 >>>>>>>> -0.058449 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> Yours sincerely, >>>>>>>> >>>>>>>> TAY wee-beng >>>>>>>> >>>>>>>> >>>>>>>> On 1/5/2012 11:54 PM, Matthew Knepley wrote: >>>>>>>> >>>>>>>>> On Tue, May 1, 2012 at 5:48 PM, TAY wee-beng<zonexo at gmail.com> >>>>>>>>> wrote: >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> Do you mean my method is wrong? >>>>>>>>> >>>>>>>>> I am following the template of ex22f, >>>>>>>>> >>>>>>>>> where the variables are declared as : >>>>>>>>> >>>>>>>>> PetscScalar v(5) >>>>>>>>> >>>>>>>>> MatStencil row(4),col(4,5) >>>>>>>>> >>>>>>>>> Hence, >>>>>>>>> >>>>>>>>> for the neumann BC >>>>>>>>> >>>>>>>>> num = 1 >>>>>>>>> >>>>>>>>> if (j/=0) then >>>>>>>>> >>>>>>>>> v(num) = -rho*HxdHy >>>>>>>>> >>>>>>>>> col(MatStencil_i,num) = i >>>>>>>>> >>>>>>>>> col(MatStencil_j,num) = j-1 >>>>>>>>> >>>>>>>>> num = num + 1 >>>>>>>>> >>>>>>>>> end if >>>>>>>>> >>>>>>>>> if (i/=0) then >>>>>>>>> >>>>>>>>> v(num) = -rho*HydHx >>>>>>>>> >>>>>>>>> col(MatStencil_i,num) = i-1 >>>>>>>>> >>>>>>>>> col(MatStencil_j,num) = j >>>>>>>>> >>>>>>>>> num = num + 1 >>>>>>>>> >>>>>>>>> end if >>>>>>>>> >>>>>>>>> if (i/=mx-1) then >>>>>>>>> >>>>>>>>> v(num) = -rho*HydHx >>>>>>>>> >>>>>>>>> col(MatStencil_i,num) = i+1 >>>>>>>>> >>>>>>>>> col(MatStencil_j,num) = j >>>>>>>>> >>>>>>>>> num = num + 1 >>>>>>>>> >>>>>>>>> end if >>>>>>>>> >>>>>>>>> if (j/=my-1) then >>>>>>>>> >>>>>>>>> v(num) = -rho*HxdHy >>>>>>>>> >>>>>>>>> col(MatStencil_i,num) = i >>>>>>>>> >>>>>>>>> col(MatStencil_j,num) = j+1 >>>>>>>>> >>>>>>>>> num = num + 1 >>>>>>>>> >>>>>>>>> end if >>>>>>>>> >>>>>>>>> v(num) = ((num-1)/2.0)*rho*(HxdHy + HydHx) >>>>>>>>> >>>>>>>>> print *, v >>>>>>>>> >>>>>>>>> col(MatStencil_i,num) = i >>>>>>>>> >>>>>>>>> col(MatStencil_j,num) = j >>>>>>>>> >>>>>>>>> !num = num + 1 >>>>>>>>> >>>>>>>>> call >>>>>>>>> MatSetValuesStencil(jac,i1,row,num,col,v,INSERT_VALUES,ierr) >>>>>>>>> >>>>>>>>> I do not get any more out of range error. However,my ans is still >>>>>>>>> different from that of ex29 in C. >>>>>>>>> >>>>>>>>> This is very simple. You have an error in your code. Checking it >>>>>>>>> is very simple: run the code and >>>>>>>>> break in MatSetValues(). Make sure ex29 makes calls with exactly >>>>>>>>> the same indices as your ex29f. >>>>>>>>> >>>>>>>>> Matt >>>>>>>>> >>>>>>>>> Yours sincerely, >>>>>>>>> >>>>>>>>> TAY wee-beng >>>>>>>>> >>>>>>>>> -- >>>>>>>>> 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 >>>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> 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 >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> 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 >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> 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 >>>>>> >>>>> >>>>> >>>>> -- >>>>> 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 >>>>> >>>> >> >> >> -- >> 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 >> >> > > > -- > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... 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