Updates to geoclaw bouss calling of PETSc to support shared memory

[BarrySmith]

Shared memory is used to transfer data from OpenMP code to MPI processes instead of nonscalable message passing

[BarrySmith]

Note this new code requires petsc 3.21 or later (3.21 was released in march).

We should talk about adding the version test to the geoclaw makefiles later.

[rjleveque]

Thanks @BarrySmith!

@mjberger tells me we still need to do some more timing comparisons between this and the original version, which I will try to work with her on in the near future.

[rjleveque]

I tried running this along with my new petscMPIoptions file from #631. It still runs fine with

    -mpi_linear_solver_server_use_shared_memory false

but with

   -mpi_linear_solver_server_use_shared_memory true

I get the following...

[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Error in external library
[0]PETSC ERROR: shmat() of shmid 65544 returned 0xffffffffffffffff Too many open files
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR:   Option left: name:-ksp_max_it value: 200 source: file
[0]PETSC ERROR:   Option left: name:-ksp_reuse_preconditioner (no value) source: file
[0]PETSC ERROR:   Option left: name:-ksp_rtol value: 1.e-9 source: file
[0]PETSC ERROR:   Option left: name:-ksp_type value: gmres source: file
[0]PETSC ERROR:   Option left: name:-mpi_linear_solver_server_minimum_count_per_rank value: 5000 source: file
[0]PETSC ERROR:   Option left: name:-mpi_linear_solver_server_view (no value) source: file
[0]PETSC ERROR:   Option left: name:-pc_type value: gamg source: file
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.22.1, unknown 

[0]PETSC ERROR: /Users/rjl/git/clawpack/geoclaw/examples/bouss/radial_flat/xgeoclaw with 6 MPI process(es) and PETSC_ARCH arch-darwin-c-opt on niwot by rjl Sat Nov  9 09:07:05 2024
[0]PETSC ERROR: Configure options: --with-debugging=0
[0]PETSC ERROR: #1 PetscShmgetAllocateArray() at /Users/rjl/git/Clones/petsc/src/sys/utils/server.c:279
[0]PETSC ERROR: #2 VecCreate_Seq() at /Users/rjl/git/Clones/petsc/src/vec/vec/impls/seq/bvec3.c:33
[0]PETSC ERROR: #3 VecSetType() at /Users/rjl/git/Clones/petsc/src/vec/vec/interface/vecreg.c:161
[0]PETSC ERROR: #4 VecCreateSeq() at /Users/rjl/git/Clones/petsc/src/vec/vec/impls/seq/vseqcr.c:34
[0]PETSC ERROR: #5 /Users/rjl/git/clawpack/geoclaw/src/2d/bouss/implicit_update_bouss_2Calls.f90:47
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_SELF
with errorcode 76.

[rjleveque]

I just tried this on a different problem, and again it runs ok with ..use_shared_memory false but when true I now get a different error, see below. This problem is set to use SWE for the first 60 seconds and then switch to the Boussinesq equations. So PETSc is not used at earlier times and it dies at t=60:

[...]
 AMRCLAW: level  1  CFL = .406E+00  dt = 0.1000E+02  final t = 0.600000E+02
Writing fgout grid #   1  frame   12 at time =    0.55000000E+02
Writing fgout grid #   2  frame   12 at time =    0.55000000E+02
Writing fgout grid #   1  frame   13 at time =    0.60000000E+02
Writing fgout grid #   2  frame   13 at time =    0.60000000E+02
 Using/Switching to Boussinesq equations
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Petsc has generated inconsistent data
[0]PETSC ERROR: Unable to locate PCMPI allocated shared address 0x141208000
[0]PETSC ERROR: WARNING! There are unused option(s) set! Could be the program crashed before usage or a spelling mistake, etc!
[0]PETSC ERROR:   Option left: name:-ksp_max_it value: 200 source: file
[0]PETSC ERROR:   Option left: name:-ksp_reuse_preconditioner (no value) source: file
[0]PETSC ERROR:   Option left: name:-ksp_rtol value: 1.e-9 source: file
[0]PETSC ERROR:   Option left: name:-ksp_type value: gmres source: file
[0]PETSC ERROR:   Option left: name:-mpi_linear_solver_server_view (no value) source: file
[0]PETSC ERROR:   Option left: name:-pc_type value: gamg source: file
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.22.1, unknown 
[0]PETSC ERROR: /Users/rjl/git/CopesHubTsunamis/geoclaw_runs/xgeoclaw_bouss_v511_sharedmem with 6 MPI process(es) and PETSC_ARCH arch-darwin-c-opt on niwot.local by rjl Sat Nov 16 06:31:46 2024
[0]PETSC ERROR: Configure options: --with-debugging=0
[0]PETSC ERROR: #1 PetscShmgetMapAddresses() at /Users/rjl/git/Clones/petsc/src/sys/utils/server.c:114
[0]PETSC ERROR: #2 PCMPISetMat() at /Users/rjl/git/Clones/petsc/src/ksp/pc/impls/mpi/pcmpi.c:269
[0]PETSC ERROR: #3 PCSetUp_MPI() at /Users/rjl/git/Clones/petsc/src/ksp/pc/impls/mpi/pcmpi.c:853
[0]PETSC ERROR: #4 PCSetUp() at /Users/rjl/git/Clones/petsc/src/ksp/pc/interface/precon.c:1071
[0]PETSC ERROR: #5 KSPSetUp() at /Users/rjl/git/Clones/petsc/src/ksp/ksp/interface/itfunc.c:415
[0]PETSC ERROR: #6 KSPSolve_Private() at /Users/rjl/git/Clones/petsc/src/ksp/ksp/interface/itfunc.c:826
[0]PETSC ERROR: #7 KSPSolve() at /Users/rjl/git/Clones/petsc/src/ksp/ksp/interface/itfunc.c:1075