Hi, Sawsan, First in test_main.F90, you need to call VecGetArrayF90(temp_solution, H_vector, ierr) and VecRestoreArrayF90 (temp_solution, H_vector, ierr) as Barry mentioned. Secondly, in the loop of test_main.F90, it calls GW_solver(). Within it, it calls PetscInitialize()/PetscFinalize(). But without MPI being initialized, PetscInitialize()/PetscFinalize()* can only be called once. * do timestep =2 , NTSP call GW_boundary_conditions(timestep-1) !print *,HNEW(1,1,1) call GW_elevation() ! print *, GWTOP(2,2,2) call GW_conductance() ! print *, CC(2,2,2) call GW_recharge() ! print *, B_Rech(5,4) call GW_pumping(timestep-1) ! print *, B_pump(2,2,2) call GW_SW(timestep-1) print *,B_RIVER (2,2,2) call GW_solver(timestep-1,N) call GW_deallocate_loop() end do
A solution is to delete PetscInitialize()/PetscFinalize() in GW_solver_try.F90 and move it to test_main.F90, outside the do loop. diff --git a/test_main.F90 b/test_main.F90 index b5997c55..107bd3ee 100644 --- a/test_main.F90 +++ b/test_main.F90 @@ -1,5 +1,6 @@ program test_GW +#include <petsc/finclude/petsc.h> use petsc use GW_constants use GW_param_by_user @@ -8,6 +9,9 @@ program test_GW implicit none integer :: N integer :: timestep + PetscErrorCode ierr + + call PetscInitialize(ierr) call GW_domain(N) !print *, "N=",N !print *, DELTAT @@ -37,4 +41,5 @@ program test_GW end do print *, HNEW(NCOL,3,2) call GW_deallocate () + call PetscFinalize(ierr) end program test_GW With that, the MPI error will be fixed. The code could run to gw_deallocate () before abort. There are other memory errors. You can install/use valgrind to fix them. Run it with valgrind ./GW.exe and look through the output Thanks. --Junchao Zhang On Thu, Jan 11, 2024 at 10:49 PM Shatanawi, Sawsan Muhammad < sawsan.shatan...@wsu.edu> wrote: > Hello, > > Thank you all for your help. > > I have changed VecGetArray to VecGetArrayF90, and the location of destory > call. but I want to make sure that VecGet ArrayF90 is to make a new array( > vector) that I can use in the rest of my Fortran code? > > when I run it and debugged it, I got > > 5.2000000E-03 > 50.00000 > 10.00000 > 0.0000000E+00 > PETSC: Attaching gdb to > /weka/data/lab/richey/sawsan/GW_CODE/code2024/SS_GWM/./GW.exe of pid 33065 > on display :0.0 on machine sn16 > Unable to start debugger in xterm: No such file or directory > 0.0000000E+00 > Attempting to use an MPI routine after finalizing MPICH > srun: error: sn16: task 0: Exited with exit code 1 > [sawsan.shatanawi@login-p2n02 SS_GWM]$ gdb ./GW/exe > GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-100.el7 > Copyright (C) 2013 Free Software Foundation, Inc. > License GPLv3+: GNU GPL version 3 or later < > http://gnu.org/licenses/gpl.html> > This is free software: you are free to change and redistribute it. > There is NO WARRANTY, to the extent permitted by law. Type "show copying" > and "show warranty" for details. > This GDB was configured as "x86_64-redhat-linux-gnu". > For bug reporting instructions, please see: > <http://www.gnu.org/software/gdb/bugs/>... > ./GW/exe: No such file or directory. > (gdb) run > Starting program: > No executable file specified. > Use the "file" or "exec-file" command. > (gdb) bt > No stack. > (gdb) > > If the highlighted line is the error, I don't know why when I write gdb , > it does not show me the location of error > The code : sshatanawi/SS_GWM (github.com) > <https://github.com/sshatanawi/SS_GWM> > > I really appreciate your helps > > Sawsan > ------------------------------ > *From:* Barry Smith <bsm...@petsc.dev> > *Sent:* Wednesday, January 10, 2024 5:35 PM > *To:* Junchao Zhang <junchao.zh...@gmail.com> > *Cc:* Shatanawi, Sawsan Muhammad <sawsan.shatan...@wsu.edu>; 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]* > > > On Jan 10, 2024, at 6:49 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 > <https://urldefense.com/v3/__https://petsc.org/release/manualpages/Vec/VecGetArray/*vecgetarray__;Iw!!JmPEgBY0HMszNaDT!tqBApprMfYxwNz4Zvnk8coNE5AeWjA9wSdAM7QJcIIVP1z0VDsVIalo4Sew2b0fW3bZtTAbPh-h0MUsZ9Km12jA$>, > you should use VecGetArrayF90 instead. > > BTW, Barry, the code > https://github.com/sshatanawi/SS_GWM/blob/main/GW_solver_try.F90#L169 > <https://urldefense.com/v3/__https://github.com/sshatanawi/SS_GWM/blob/main/GW_solver_try.F90*L169__;Iw!!JmPEgBY0HMszNaDT!tqBApprMfYxwNz4Zvnk8coNE5AeWjA9wSdAM7QJcIIVP1z0VDsVIalo4Sew2b0fW3bZtTAbPh-h0MUsZh2eAi4o$> > has "call VecGetArray(temp_solution, H_vector, ierr)". I don't find > petsc Fortran examples doing VecGetArray. Do we still support it? > > > This is not the correct calling sequence for VecGetArray() from > Fortran. > > Regardless, definitely should not be writing any new code that uses > VecGetArray() from Fortran. Should use VecGetArrayF90(). > > > --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://urldefense.com/v3/__https://github.com/sshatanawi/SS_GWM__;!!JmPEgBY0HMszNaDT!tqBApprMfYxwNz4Zvnk8coNE5AeWjA9wSdAM7QJcIIVP1z0VDsVIalo4Sew2b0fW3bZtTAbPh-h0MUsZ1Veab3M$> > > <https://urldefense.com/v3/__https://github.com/sshatanawi/SS_GWM__;!!JmPEgBY0HMszNaDT!tqBApprMfYxwNz4Zvnk8coNE5AeWjA9wSdAM7QJcIIVP1z0VDsVIalo4Sew2b0fW3bZtTAbPh-h0MUsZ1Veab3M$> > GitHub - sshatanawi/SS_GWM > <https://urldefense.com/v3/__https://github.com/sshatanawi/SS_GWM__;!!JmPEgBY0HMszNaDT!tqBApprMfYxwNz4Zvnk8coNE5AeWjA9wSdAM7QJcIIVP1z0VDsVIalo4Sew2b0fW3bZtTAbPh-h0MUsZ1Veab3M$> > Contribute to sshatanawi/SS_GWM development by creating an account on > GitHub. > github.com > <https://urldefense.com/v3/__http://github.com/__;!!JmPEgBY0HMszNaDT!tqBApprMfYxwNz4Zvnk8coNE5AeWjA9wSdAM7QJcIIVP1z0VDsVIalo4Sew2b0fW3bZtTAbPh-h0MUsZ8rcrPiA$> > ** > > 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$> > ------------------------------ > *From:* Mark Adams <mfad...@lbl.gov> > *Sent:* Wednesday, December 20, 2023 2:48 AM > *To:* Shatanawi, Sawsan Muhammad <sawsan.shatan...@wsu.edu> > *Cc:* petsc-users@mcs.anl.gov <petsc-users@mcs.anl.gov> > *Subject:* Re: [petsc-users] Help with Integrating PETSc into Fortran > Groundwater Flow Simulation Code > > *[EXTERNAL EMAIL]* > I am guessing that you are creating a matrix, adding to it, finalizing it > ("assembly"), and then adding to it again, which is fine, but you are > adding new non-zeros to the sparsity pattern. > If this is what you want then you can tell the matrix to let you do that. > Otherwise you have a bug. > > Mark > > On Tue, Dec 19, 2023 at 9:50 PM Shatanawi, Sawsan Muhammad via petsc-users > <petsc-users@mcs.anl.gov> wrote: > > Hello everyone, > > I hope this email finds you well. > > My Name is Sawsan Shatanawi, and I am currently working on developing a > Fortran code for simulating groundwater flow in a 3D system. The code > involves solving a nonlinear system, and I have created the matrix to be > solved using the PCG solver and Picard iteration. However, when I tried > to assign it as a PETSc matrix I started getting a lot of error messages. > > I am kindly asking if someone can help me, I would be happy to share my > code with him/her. > > Please find the attached file contains a list of errors I have gotten > > Thank you in advance for your time and assistance. > > Best regards, > > Sawsan > > <Matrix_RHS.F90><out.txt><solver.F90> > > > > > -- > What most experimenters take for granted before they begin their > experiments is infinitely more interesting than any results to which their > experiments lead. > -- Norbert Wiener > > https://www.cse.buffalo.edu/~knepley/ > <https://urldefense.com/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!JmPEgBY0HMszNaDT!uskvAyF0pMMWDbMIexr9g4qN46V7Rea17GQdNIVG2vH_HMaX7mXgie4ZYgusmPpss_DS7H1_8vn8arGQNSkC$> > > >