[petsc-users] Help with Integrating PETSc into Fortran Groundwater Flow Simulation Code
Barry Smith
bsmith at petsc.dev
Wed Jan 10 19:35:37 CST 2024
> On Jan 10, 2024, at 6:49 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?
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 at mcs.anl.gov <mailto: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 <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 <mfadams at lbl.gov <mailto:mfadams at lbl.gov>>
>> Sent: Friday, January 5, 2024 4:53 AM
>> To: Shatanawi, Sawsan Muhammad <sawsan.shatanawi at wsu.edu <mailto:sawsan.shatanawi at wsu.edu>>
>> Cc: Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>>; petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto: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 <mailto: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 <mailto:knepley at gmail.com>>
>> Sent: Wednesday, December 20, 2023 6:54 PM
>> To: Shatanawi, Sawsan Muhammad <sawsan.shatanawi at wsu.edu <mailto:sawsan.shatanawi at wsu.edu>>
>> Cc: Barry Smith <bsmith at petsc.dev <mailto:bsmith at petsc.dev>>; petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto: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 <mailto: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 <mailto:bsmith at petsc.dev>>
>> Sent: Wednesday, December 20, 2023 6:32 PM
>> To: Shatanawi, Sawsan Muhammad <sawsan.shatanawi at wsu.edu <mailto:sawsan.shatanawi at wsu.edu>>
>> Cc: Mark Adams <mfadams at lbl.gov <mailto:mfadams at lbl.gov>>; petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto: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 <mailto: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 <mailto:mfadams at lbl.gov>>
>>> Sent: Wednesday, December 20, 2023 6:44 AM
>>> To: Shatanawi, Sawsan Muhammad <sawsan.shatanawi at wsu.edu <mailto:sawsan.shatanawi at wsu.edu>>
>>> Cc: petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto: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 <mailto: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 <mailto:mfadams at lbl.gov>>
>>> Sent: Wednesday, December 20, 2023 2:48 AM
>>> To: Shatanawi, Sawsan Muhammad <sawsan.shatanawi at wsu.edu <mailto:sawsan.shatanawi at wsu.edu>>
>>> Cc: petsc-users at mcs.anl.gov <mailto:petsc-users at mcs.anl.gov> <petsc-users at mcs.anl.gov <mailto: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 <mailto: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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