Sawsan, Also, another error at https://github.com/sshatanawi/SS_GWM/blob/main/GW_solver_try.F90#L170. You can not destroy the vector BEFORE calling VecRestoreArray(),
--Junchao Zhang On Wed, Jan 10, 2024 at 5:49 PM Junchao Zhang <junchao.zh...@gmail.com> wrote: > Hi, Sawsan, > I could build your code and I also could gdb it. > > $ gdb ./GW.exe > ... > $ Thread 1 "GW.exe" received signal SIGSEGV, Segmentation fault. > 0x00007ffff1e6d44f in vecgetarray_ (x=0x7fffffffa718, fa=0x0, > ia=0x7fffffffa75c, ierr=0x0) at > /scratch/jczhang/petsc/src/vec/vec/interface/ftn-custom/zvectorf.c:257 > 257 *ierr = VecGetArray(*x, &lx); > (gdb) bt > #0 0x00007ffff1e6d44f in vecgetarray_ (x=0x7fffffffa718, fa=0x0, > ia=0x7fffffffa75c, ierr=0x0) at > /scratch/jczhang/petsc/src/vec/vec/interface/ftn-custom/zvectorf.c:257 > #1 0x000000000040b6e3 in gw_solver (t_s=1.40129846e-45, n=300) at > GW_solver_try.F90:169 > #2 0x000000000040c6a8 in test_gw () at test_main.F90:35 > > ierr=0x0 caused the segfault. See > https://petsc.org/release/manualpages/Vec/VecGetArray/#vecgetarray, you > should use VecGetArrayF90 instead. > > BTW, Barry, the code > https://github.com/sshatanawi/SS_GWM/blob/main/GW_solver_try.F90#L169 has > "call VecGetArray(temp_solution, H_vector, ierr)". I don't find petsc > Fortran examples doing VecGetArray. Do we still support it? > > --Junchao Zhang > > > On Wed, Jan 10, 2024 at 2:38 PM Shatanawi, Sawsan Muhammad via petsc-users > <petsc-users@mcs.anl.gov> 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 >> ** >> >> 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 <mfad...@lbl.gov> >> *Sent:* Friday, January 5, 2024 4:53 AM >> *To:* Shatanawi, Sawsan Muhammad <sawsan.shatan...@wsu.edu> >> *Cc:* Matthew Knepley <knep...@gmail.com>; petsc-users@mcs.anl.gov < >> petsc-users@mcs.anl.gov> >> *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 <petsc-users@mcs.anl.gov> 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 <knep...@gmail.com> >> *Sent:* Wednesday, December 20, 2023 6:54 PM >> *To:* Shatanawi, Sawsan Muhammad <sawsan.shatan...@wsu.edu> >> *Cc:* Barry Smith <bsm...@petsc.dev>; petsc-users@mcs.anl.gov < >> petsc-users@mcs.anl.gov> >> *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 <petsc-users@mcs.anl.gov> 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 <bsm...@petsc.dev> >> *Sent:* Wednesday, December 20, 2023 6:32 PM >> *To:* Shatanawi, Sawsan Muhammad <sawsan.shatan...@wsu.edu> >> *Cc:* Mark Adams <mfad...@lbl.gov>; petsc-users@mcs.anl.gov < >> petsc-users@mcs.anl.gov> >> *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 < >> petsc-users@mcs.anl.gov> 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 <mfad...@lbl.gov> >> *Sent:* Wednesday, December 20, 2023 6:44 AM >> *To:* Shatanawi, Sawsan Muhammad <sawsan.shatan...@wsu.edu> >> *Cc:* petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> >> *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 < >> sawsan.shatan...@wsu.edu> 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$> >> ------------------------------ >> *From:* Mark Adams <mfad...@lbl.gov> >> *Sent:* Wednesday, December 20, 2023 2:48 AM >> *To:* Shatanawi, Sawsan Muhammad <sawsan.shatan...@wsu.edu> >> *Cc:* petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> >> *Subject:* Re: [petsc-users] Help with Integrating PETSc into Fortran >> Groundwater Flow Simulation Code >> >> *[EXTERNAL EMAIL]* >> I am guessing that you are creating a matrix, adding to it, finalizing it >> ("assembly"), and then adding to it again, which is fine, but you are >> adding new non-zeros to the sparsity pattern. >> If this is what you want then you can tell the matrix to let you do that. >> Otherwise you have a bug. >> >> Mark >> >> On Tue, Dec 19, 2023 at 9:50 PM Shatanawi, Sawsan Muhammad via >> petsc-users <petsc-users@mcs.anl.gov> wrote: >> >> Hello everyone, >> >> I hope this email finds you well. >> >> My Name is Sawsan Shatanawi, and I am currently working on developing a >> Fortran code for simulating groundwater flow in a 3D system. The code >> involves solving a nonlinear system, and I have created the matrix to be >> solved using the PCG solver and Picard iteration. However, when I tried >> to assign it as a PETSc matrix I started getting a lot of error messages. >> >> I am kindly asking if someone can help me, I would be happy to share my >> code with him/her. >> >> Please find the attached file contains a list of errors I have gotten >> >> Thank you in advance for your time and assistance. >> >> Best regards, >> >> Sawsan >> >> <Matrix_RHS.F90><out.txt><solver.F90> >> >> >> >> >> -- >> What most experimenters take for granted before they begin their >> experiments is infinitely more interesting than any results to which their >> experiments lead. >> -- Norbert Wiener >> >> https://www.cse.buffalo.edu/~knepley/ >> <https://urldefense.com/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!JmPEgBY0HMszNaDT!uskvAyF0pMMWDbMIexr9g4qN46V7Rea17GQdNIVG2vH_HMaX7mXgie4ZYgusmPpss_DS7H1_8vn8arGQNSkC$> >> >>