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

Barry Smith bsmith at petsc.dev
Wed Jan 10 16:50:12 CST 2024 

   When running with just one mpi process it is often possible (on non-batch systems where one does not need to use mpiexec to start up a single rank run) to continue to just use

> gdb <the name of my exe.file> 

when running with more than 1 MPI process (or if the execuable requires mpiexec to start) you can use

mpiexec -n 2 ./executable options -start_in_debugger 

and it will open two terminals with the debugger for each rank. See https://petsc.org/release/manual/other/#sec-debugging for more details.



> On Jan 10, 2024, at 3:38 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 <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$>
> <out4.txt>

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