When running with just one mpi process it is often possible (on non-batch systems where one does not need to use mpiexec to start up a single rank run) to continue to just use
> gdb <the name of my exe.file> when running with more than 1 MPI process (or if the execuable requires mpiexec to start) you can use mpiexec -n 2 ./executable options -start_in_debugger and it will open two terminals with the debugger for each rank. See https://petsc.org/release/manual/other/#sec-debugging for more details. > On Jan 10, 2024, at 3:38 PM, Shatanawi, Sawsan Muhammad via petsc-users > <[email protected]> wrote: > > Hello all, > > I hope you are doing well. > > Generally, I use gdb <the name of my exe.file> to debug the code. > I got the attached error message. > > I have tried to add the flag -start_in_debugger in the make file, but it > didn't work, so it seems I was doing it in the wrong way > > This is the link for the whole code: sshatanawi/SS_GWM (github.com) > <https://github.com/sshatanawi/SS_GWM> > <https://github.com/sshatanawi/SS_GWM> > GitHub - sshatanawi/SS_GWM <https://github.com/sshatanawi/SS_GWM> > Contribute to sshatanawi/SS_GWM development by creating an account on GitHub. > github.com <http://github.com/> > > > You can read the description of the code in " Model Desprciption.pdf" > the compiling file is makefile_f90 where you can find the linked code files > > I really appreciate your help > > Bests, > Sawsan > From: Mark Adams <[email protected] <mailto:[email protected]>> > Sent: Friday, January 5, 2024 4:53 AM > To: Shatanawi, Sawsan Muhammad <[email protected] > <mailto:[email protected]>> > Cc: Matthew Knepley <[email protected] <mailto:[email protected]>>; > [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>> > Subject: Re: [petsc-users] Help with Integrating PETSc into Fortran > Groundwater Flow Simulation Code > > [EXTERNAL EMAIL] > This is a segv. As Matt said, you need to use a debugger for this or add > print statements to narrow down the place where this happens. > > You will need to learn how to use debuggers to do your project so you might > as well start now. > > If you have a machine with a GUI debugger that is easier but command line > debuggers are good to learn anyway. > > I tend to run debuggers directly (eg, lldb ./a.out -- program-args ...) and > use a GUI debugger (eg, Totalview or DDT) if available. > > Mark > > > On Wed, Dec 20, 2023 at 10:02 PM Shatanawi, Sawsan Muhammad via petsc-users > <[email protected] <mailto:[email protected]>> wrote: > Hello Matthew, > > Thank you for your help. I am sorry that I keep coming back with my error > messages, but I reached a point that I don't know how to fix them, and I > don't understand them easily. > The list of errors is getting shorter, now I am getting the attached error > messages > > Thank you again, > > Sawsan > From: Matthew Knepley <[email protected] <mailto:[email protected]>> > Sent: Wednesday, December 20, 2023 6:54 PM > To: Shatanawi, Sawsan Muhammad <[email protected] > <mailto:[email protected]>> > Cc: Barry Smith <[email protected] <mailto:[email protected]>>; > [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>> > Subject: Re: [petsc-users] Help with Integrating PETSc into Fortran > Groundwater Flow Simulation Code > > [EXTERNAL EMAIL] > On Wed, Dec 20, 2023 at 9:49 PM Shatanawi, Sawsan Muhammad via petsc-users > <[email protected] <mailto:[email protected]>> wrote: > Hello Barry, > > Thank you a lot for your help, Now I am getting the attached error message. > > Do not destroy the PC from KSPGetPC() > > THanks, > > Matt > > Bests, > Sawsan > From: Barry Smith <[email protected] <mailto:[email protected]>> > Sent: Wednesday, December 20, 2023 6:32 PM > To: Shatanawi, Sawsan Muhammad <[email protected] > <mailto:[email protected]>> > Cc: Mark Adams <[email protected] <mailto:[email protected]>>; > [email protected] <mailto:[email protected]> > <[email protected] <mailto:[email protected]>> > Subject: Re: [petsc-users] Help with Integrating PETSc into Fortran > Groundwater Flow Simulation Code > > [EXTERNAL EMAIL] > > Instead of > > call PCCreate(PETSC_COMM_WORLD, pc, ierr) > call PCSetType(pc, PCILU,ierr) ! Choose a preconditioner type (ILU) > call KSPSetPC(ksp, pc,ierr) ! Associate the preconditioner with the KSP > solver > > do > > call KSPGetPC(ksp,pc,ierr) > call PCSetType(pc, PCILU,ierr) > > Do not call KSPSetUp(). It will be taken care of automatically during the > solve > > > >> On Dec 20, 2023, at 8:52 PM, Shatanawi, Sawsan Muhammad via petsc-users >> <[email protected] <mailto:[email protected]>> wrote: >> >> Hello, >> I don't think that I set preallocation values when I created the matrix, >> would you please have look at my code. It is just the petsc related part >> from my code. >> I was able to fix some of the error messages. Now I have a new set of error >> messages related to the KSP solver (attached) >> >> I appreciate your help >> >> Sawsan >> From: Mark Adams <[email protected] <mailto:[email protected]>> >> Sent: Wednesday, December 20, 2023 6:44 AM >> To: Shatanawi, Sawsan Muhammad <[email protected] >> <mailto:[email protected]>> >> Cc: [email protected] <mailto:[email protected]> >> <[email protected] <mailto:[email protected]>> >> Subject: Re: [petsc-users] Help with Integrating PETSc into Fortran >> Groundwater Flow Simulation Code >> >> [EXTERNAL EMAIL] >> Did you set preallocation values when you created the matrix? >> Don't do that. >> >> On Wed, Dec 20, 2023 at 9:36 AM Shatanawi, Sawsan Muhammad >> <[email protected] <mailto:[email protected]>> wrote: >> Hello, >> >> I am trying to create a sparse matrix( which is as I believe a zero matrix) >> then adding some nonzero elements to it over a loop, then assembling it >> >> Get Outlook for iOS >> <https://urldefense.com/v3/__https://aka.ms/o0ukef__;!!JmPEgBY0HMszNaDT!uUJ_jeYf45gcXDGR_PeMjhU7hbd_fKcXJPn0pM9eb-YQihKNYuXMYM9x-hglsbXsCFIwNBWgHXdetHODupsOloE$> >> From: Mark Adams <[email protected] <mailto:[email protected]>> >> Sent: Wednesday, December 20, 2023 2:48 AM >> To: Shatanawi, Sawsan Muhammad <[email protected] >> <mailto:[email protected]>> >> Cc: [email protected] <mailto:[email protected]> >> <[email protected] <mailto:[email protected]>> >> Subject: Re: [petsc-users] Help with Integrating PETSc into Fortran >> Groundwater Flow Simulation Code >> >> [EXTERNAL EMAIL] >> I am guessing that you are creating a matrix, adding to it, finalizing it >> ("assembly"), and then adding to it again, which is fine, but you are adding >> new non-zeros to the sparsity pattern. >> If this is what you want then you can tell the matrix to let you do that. >> Otherwise you have a bug. >> >> Mark >> >> On Tue, Dec 19, 2023 at 9:50 PM Shatanawi, Sawsan Muhammad via petsc-users >> <[email protected] <mailto:[email protected]>> wrote: >> Hello everyone, >> >> I hope this email finds you well. >> >> My Name is Sawsan Shatanawi, and I am currently working on developing a >> Fortran code for simulating groundwater flow in a 3D system. The code >> involves solving a nonlinear system, and I have created the matrix to be >> solved using the PCG solver and Picard iteration. However, when I tried to >> assign it as a PETSc matrix I started getting a lot of error messages. >> >> I am kindly asking if someone can help me, I would be happy to share my code >> with him/her. >> >> Please find the attached file contains a list of errors I have gotten >> >> Thank you in advance for your time and assistance. >> Best regards, >> >> Sawsan >> >> >> <Matrix_RHS.F90><out.txt><solver.F90> > > > > -- > 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 > > https://www.cse.buffalo.edu/~knepley/ > <https://urldefense.com/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!JmPEgBY0HMszNaDT!uskvAyF0pMMWDbMIexr9g4qN46V7Rea17GQdNIVG2vH_HMaX7mXgie4ZYgusmPpss_DS7H1_8vn8arGQNSkC$> > <out4.txt>
