[petsc-users] Help with Integrating PETSc into Fortran Groundwater Flow Simulation Code

[Junchao Zhang]

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 at 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 <mfadams at lbl.gov>
> *Sent:* Friday, January 5, 2024 4:53 AM
> *To:* Shatanawi, Sawsan Muhammad <sawsan.shatanawi at wsu.edu>
> *Cc:* Matthew Knepley <knepley at gmail.com>; petsc-users at mcs.anl.gov <
> petsc-users at 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 at 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 <knepley at gmail.com>
> *Sent:* Wednesday, December 20, 2023 6:54 PM
> *To:* Shatanawi, Sawsan Muhammad <sawsan.shatanawi at wsu.edu>
> *Cc:* Barry Smith <bsmith at petsc.dev>; petsc-users at mcs.anl.gov <
> petsc-users at 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 at 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 <bsmith at petsc.dev>
> *Sent:* Wednesday, December 20, 2023 6:32 PM
> *To:* Shatanawi, Sawsan Muhammad <sawsan.shatanawi at wsu.edu>
> *Cc:* Mark Adams <mfadams at lbl.gov>; petsc-users at mcs.anl.gov <
> petsc-users at 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 at 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 <mfadams at lbl.gov>
> *Sent:* Wednesday, December 20, 2023 6:44 AM
> *To:* Shatanawi, Sawsan Muhammad <sawsan.shatanawi at wsu.edu>
> *Cc:* petsc-users at mcs.anl.gov <petsc-users at 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.shatanawi at 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$>
> ------------------------------
> *From:* Mark Adams <mfadams at lbl.gov>
> *Sent:* Wednesday, December 20, 2023 2:48 AM
> *To:* Shatanawi, Sawsan Muhammad <sawsan.shatanawi at wsu.edu>
> *Cc:* petsc-users at mcs.anl.gov <petsc-users at mcs.anl.gov>
> *Subject:* Re: [petsc-users] Help with Integrating PETSc into Fortran
> Groundwater Flow Simulation Code
>
> *[EXTERNAL EMAIL]*
> I am guessing that you are creating a matrix, adding to it, finalizing it
> ("assembly"), and then adding to it again, which is fine, but you are
> adding new non-zeros to the sparsity pattern.
> If this is what you want then you can tell the matrix to let you do that.
> Otherwise you have a bug.
>
> Mark
>
> On Tue, Dec 19, 2023 at 9:50 PM Shatanawi, Sawsan Muhammad via petsc-users
> <petsc-users at mcs.anl.gov> wrote:
>
> Hello everyone,
>
> I hope this email finds you well.
>
>  My Name is Sawsan Shatanawi, and I am currently working on developing a
> Fortran code for simulating groundwater flow in a 3D system. The code
> involves solving a nonlinear system, and I have created the matrix to be
> solved using the PCG solver and Picard iteration. However, when I tried
> to assign it as a PETSc matrix I started getting a lot of error messages.
>
> I am kindly asking if someone can help me, I would be happy to share my
> code with him/her.
>
> Please find the attached file contains a list of errors I have gotten
>
> Thank you in advance for your time and assistance.
>
> Best regards,
>
>  Sawsan
>
> <Matrix_RHS.F90><out.txt><solver.F90>
>
>
>
>
> --
> What most experimenters take for granted before they begin their
> experiments is infinitely more interesting than any results to which their
> experiments lead.
> -- Norbert Wiener
>
> https://www.cse.buffalo.edu/~knepley/
> <https://urldefense.com/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!JmPEgBY0HMszNaDT!uskvAyF0pMMWDbMIexr9g4qN46V7Rea17GQdNIVG2vH_HMaX7mXgie4ZYgusmPpss_DS7H1_8vn8arGQNSkC$>
>
>
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