[petsc-users] Help with Integrating PETSc into Fortran Groundwater Flow Simulation Code
Junchao Zhang
junchao.zhang at gmail.com
Fri Jan 12 10:46:41 CST 2024
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.shatanawi at 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 at 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 <bsmith at petsc.dev>
> *Sent:* Wednesday, January 10, 2024 5:35 PM
> *To:* Junchao Zhang <junchao.zhang at gmail.com>
> *Cc:* Shatanawi, Sawsan Muhammad <sawsan.shatanawi at wsu.edu>; 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]*
>
>
> 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
> <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 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://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 <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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