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> On May 7, 2024, at 2:22 PM, Shatanawi, Sawsan Muhammad via petsc-users > <[email protected]> wrote: > > This Message Is From an External Sender > This message came from outside your organization. > Hello everyone, > > I hope this email finds you well. > > > My Name is Sawsan Shatanawi, and I was developing a Fortran code for > simulating groundwater flow in a 3D system with nonlinear behavior. I solved > the nonlinear system using the PCG solver and Picard iteration, but I did not > get good results although I checked my matrix and RHS and everything, I > decided to change my solver to Newton Rapson method. > I checked PETSc documents but I have a few questions: > 1) My groundwater system is time-dependent, so should I use TS only instead > of SNES? > 2) My system has its deltaT, would using deltaT as dt affect my solver, or is > it better to use TS-PETSc dt? Also, would using PETSc dt affect the > simulation of the groundwater system > 3) I want my Jacobian matrix to be calculated by PETSc automatically > 4) Do I need to define and calculate the residual vector? > > My A-Matrix contains coefficients and external sources and my RHS vector > includes the boundary conditions > > > Please find the attached file contains a draft of my code > > Thank you in advance for your time and help. > > Best regards, > > Sawsan > > > From: Shatanawi, Sawsan Muhammad <[email protected] > <mailto:[email protected]>> > Sent: Tuesday, January 16, 2024 10:43 AM > To: Junchao Zhang <[email protected] <mailto:[email protected]>> > Cc: Barry Smith <[email protected] <mailto:[email protected]>>; Matthew Knepley > <[email protected] <mailto:[email protected]>>; Mark Adams <[email protected] > <mailto:[email protected]>>; [email protected] > <mailto:[email protected]> <[email protected] > <mailto:[email protected]>> > Subject: Re: [petsc-users] Help with Integrating PETSc into Fortran > Groundwater Flow Simulation Code > > Hello all, > > Thank you for your valuable help. I will do your recommendations and hope it > will run without any issues. > > Bests, > Sawsan > > From: Junchao Zhang <[email protected] <mailto:[email protected]>> > Sent: Friday, January 12, 2024 8:46 AM > To: Shatanawi, Sawsan Muhammad <[email protected] > <mailto:[email protected]>> > Cc: Barry Smith <[email protected] <mailto:[email protected]>>; Matthew Knepley > <[email protected] <mailto:[email protected]>>; Mark Adams <[email protected] > <mailto:[email protected]>>; [email protected] > <mailto:[email protected]> <[email protected] > <mailto:[email protected]>> > Subject: Re: [petsc-users] Help with Integrating PETSc into Fortran > Groundwater Flow Simulation Code > > [EXTERNAL EMAIL] > 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 > <[email protected] <mailto:[email protected]>> 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@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 > <https://urldefense.us/v3/__http://gnu.org/licenses/gpl.html__;!!G_uCfscf7eWS!eZkBlApyezAyEBaDxGemEyUmTe87omvkv59rrf0Mq8L4bOTqEL9wynuMJ1ci9kRDOqucZBiYdGT2tRTVguZ5eGs$ > > <https://urldefense.com/v3/__http://gnu.org/licenses/gpl.html__;!!JmPEgBY0HMszNaDT!o4qS1zaFLg2L8PlawWJVyYsJpnwYHuL6SIIZsmzTO98RCzbP26HwTi_0-ipCS_D2SBG0X4gtEnM13-nbzFEFKvtraKaM$>> > This is free software: you are free to change and redistribute it. > There is NO WARRANTY, to the extent permitted by law. Type "show copying" > and "show warranty" for details. > This GDB was configured as "x86_64-redhat-linux-gnu". > For bug reporting instructions, please see: > <https://urldefense.us/v3/__http://www.gnu.org/software/gdb/bugs/__;!!G_uCfscf7eWS!eZkBlApyezAyEBaDxGemEyUmTe87omvkv59rrf0Mq8L4bOTqEL9wynuMJ1ci9kRDOqucZBiYdGT2tRTVn6ndgxI$ > > <https://urldefense.com/v3/__http://www.gnu.org/software/gdb/bugs/__;!!JmPEgBY0HMszNaDT!o4qS1zaFLg2L8PlawWJVyYsJpnwYHuL6SIIZsmzTO98RCzbP26HwTi_0-ipCS_D2SBG0X4gtEnM13-nbzFEFKjO8jNfs$>>... > ./GW/exe: No such file or directory. > (gdb) run > Starting program: > No executable file specified. > Use the "file" or "exec-file" command. > (gdb) bt > No stack. > (gdb) > > If the highlighted line is the error, I don't know why when I write gdb , it > does not show me the location of error > The code : sshatanawi/SS_GWM (github.com) > <https://urldefense.com/v3/__https://github.com/sshatanawi/SS_GWM__;!!JmPEgBY0HMszNaDT!o4qS1zaFLg2L8PlawWJVyYsJpnwYHuL6SIIZsmzTO98RCzbP26HwTi_0-ipCS_D2SBG0X4gtEnM13-nbzFEFKp8i33ur$> > > > I really appreciate your helps > > Sawsan > From: Barry Smith <[email protected] <mailto:[email protected]>> > Sent: Wednesday, January 10, 2024 5:35 PM > To: Junchao Zhang <[email protected] <mailto:[email protected]>> > Cc: Shatanawi, Sawsan Muhammad <[email protected] > <mailto:[email protected]>>; Mark Adams <[email protected] > <mailto:[email protected]>>; [email protected] > <mailto:[email protected]> <[email protected] > <mailto:[email protected]>> > 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 <[email protected] >> <mailto:[email protected]>> 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://urldefense.us/v3/__https://petsc.org/release/manualpages/Vec/VecGetArray/*vecgetarray__;Iw!!G_uCfscf7eWS!eZkBlApyezAyEBaDxGemEyUmTe87omvkv59rrf0Mq8L4bOTqEL9wynuMJ1ci9kRDOqucZBiYdGT2tRTV25yWFSQ$ >> >> <https://urldefense.com/v3/__https://petsc.org/release/manualpages/Vec/VecGetArray/*vecgetarray__;Iw!!JmPEgBY0HMszNaDT!tqBApprMfYxwNz4Zvnk8coNE5AeWjA9wSdAM7QJcIIVP1z0VDsVIalo4Sew2b0fW3bZtTAbPh-h0MUsZ9Km12jA$>, >> you should use VecGetArrayF90 instead. >> >> BTW, Barry, the code >> https://urldefense.us/v3/__https://github.com/sshatanawi/SS_GWM/blob/main/GW_solver_try.F90*L169__;Iw!!G_uCfscf7eWS!eZkBlApyezAyEBaDxGemEyUmTe87omvkv59rrf0Mq8L4bOTqEL9wynuMJ1ci9kRDOqucZBiYdGT2tRTVocqNAbg$ >> >> <https://urldefense.com/v3/__https://github.com/sshatanawi/SS_GWM/blob/main/GW_solver_try.F90*L169__;Iw!!JmPEgBY0HMszNaDT!tqBApprMfYxwNz4Zvnk8coNE5AeWjA9wSdAM7QJcIIVP1z0VDsVIalo4Sew2b0fW3bZtTAbPh-h0MUsZh2eAi4o$> >> has "call VecGetArray(temp_solution, H_vector, ierr)". I don't find >> petsc Fortran examples doing VecGetArray. Do we still support it? > > This is not the correct calling sequence for VecGetArray() from Fortran. > > Regardless, definitely should not be writing any new code that uses > VecGetArray() from Fortran. Should use VecGetArrayF90(). > >> >> --Junchao Zhang >> >> >> On Wed, Jan 10, 2024 at 2:38 PM Shatanawi, Sawsan Muhammad via petsc-users >> <[email protected] <mailto:[email protected]>> wrote: >> Hello all, >> >> I hope you are doing well. >> >> Generally, I use gdb <the name of my exe.file> to debug the code. >> I got the attached error message. >> >> I have tried to add the flag -start_in_debugger in the make file, but it >> didn't work, so it seems I was doing it in the wrong way >> >> This is the link for the whole code: sshatanawi/SS_GWM (github.com) >> <https://urldefense.com/v3/__https://github.com/sshatanawi/SS_GWM__;!!JmPEgBY0HMszNaDT!tqBApprMfYxwNz4Zvnk8coNE5AeWjA9wSdAM7QJcIIVP1z0VDsVIalo4Sew2b0fW3bZtTAbPh-h0MUsZ1Veab3M$> >> >> <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 <[email protected] <mailto:[email protected]>> >> Sent: Friday, January 5, 2024 4:53 AM >> To: Shatanawi, Sawsan Muhammad <[email protected] >> <mailto:[email protected]>> >> Cc: Matthew Knepley <[email protected] <mailto:[email protected]>>; >> [email protected] <mailto:[email protected]> >> <[email protected] <mailto:[email protected]>> >> 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 >> <[email protected] <mailto:[email protected]>> 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 <[email protected] <mailto:[email protected]>> >> Sent: Wednesday, December 20, 2023 6:54 PM >> To: Shatanawi, Sawsan Muhammad <[email protected] >> <mailto:[email protected]>> >> Cc: Barry Smith <[email protected] <mailto:[email protected]>>; >> [email protected] <mailto:[email protected]> >> <[email protected] <mailto:[email protected]>> >> 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 >> <[email protected] <mailto:[email protected]>> 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 <[email protected] <mailto:[email protected]>> >> Sent: Wednesday, December 20, 2023 6:32 PM >> To: Shatanawi, Sawsan Muhammad <[email protected] >> <mailto:[email protected]>> >> Cc: Mark Adams <[email protected] <mailto:[email protected]>>; >> [email protected] <mailto:[email protected]> >> <[email protected] <mailto:[email protected]>> >> 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 >>> <[email protected] <mailto:[email protected]>> 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 <[email protected] <mailto:[email protected]>> >>> Sent: Wednesday, December 20, 2023 6:44 AM >>> To: Shatanawi, Sawsan Muhammad <[email protected] >>> <mailto:[email protected]>> >>> Cc: [email protected] <mailto:[email protected]> >>> <[email protected] <mailto:[email protected]>> >>> 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 >>> <[email protected] <mailto:[email protected]>> 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 <[email protected] <mailto:[email protected]>> >>> Sent: Wednesday, December 20, 2023 2:48 AM >>> To: Shatanawi, Sawsan Muhammad <[email protected] >>> <mailto:[email protected]>> >>> Cc: [email protected] <mailto:[email protected]> >>> <[email protected] <mailto:[email protected]>> >>> 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 >>> <[email protected] <mailto:[email protected]>> 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://urldefense.us/v3/__https://www.cse.buffalo.edu/*knepley/__;fg!!G_uCfscf7eWS!eZkBlApyezAyEBaDxGemEyUmTe87omvkv59rrf0Mq8L4bOTqEL9wynuMJ1ci9kRDOqucZBiYdGT2tRTVcuRVDQ4$ >> >> <https://urldefense.com/v3/__http://www.cse.buffalo.edu/*knepley/__;fg!!JmPEgBY0HMszNaDT!uskvAyF0pMMWDbMIexr9g4qN46V7Rea17GQdNIVG2vH_HMaX7mXgie4ZYgusmPpss_DS7H1_8vn8arGQNSkC$> > > <Newton_PETSc.txt>
