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

Wed Jan 10 17:52:05 CST 2024

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.zhang at 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 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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