[petsc-users] MPI barrier issue using MatZeroRows
Amneet Bhalla
mail2amneet at gmail.com
Tue Nov 28 21:23:43 CST 2023
On Tue, Nov 28, 2023 at 6:42 PM Barry Smith <bsmith at petsc.dev> wrote:
>
> for (int comp = 0; comp < 2; ++comp)
> {
> .......
> for (Box<NDIM>::Iterator bc(bc_coef_box); bc; bc++)
> {
> ......
> if (IBTK::abs_equal_eps(b, 0.0))
> {
> const double diag_value = a;
> ierr = MatZeroRows(mat, 1, &u_dof_index,
> diag_value, NULL, NULL);
> IBTK_CHKERRQ(ierr);
> }
> }
> }
>
> In general, this code will not work because each process calls MatZeroRows
> a different number of times, so it cannot match up with all the processes.
>
> If u_dof_index is always local to the current process, you can call
> MatSetOption(mat, MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) above the for loop
> and
> the MatZeroRows will not synchronize across the MPI processes (since it
> does not need to and you told it that).
>
Yes, u_dof_index is going to be local and I put a check on it a few lines
before calling MatZeroRows.
Can MatSetOption() be called after the matrix has been assembled?
> If the u_dof_index will not always be local, then you need, on each
> process, to list all the u_dof_index for each process in an array and then
> call MatZeroRows()
> once after the loop so it can exchange the needed information with the
> other MPI processes to get the row indices to the right place.
>
> Barry
>
>
>
>
> On Nov 28, 2023, at 6:44 PM, Amneet Bhalla <mail2amneet at gmail.com> wrote:
>
>
> Hi Folks,
>
> I am using MatZeroRows() to set Dirichlet boundary conditions. This works
> fine for the serial run and the solver produces correct results (verified
> through analytical solution). However, when I run the case in parallel, the
> simulation gets stuck at MatZeroRows(). My understanding is that this
> function needs to be called after the MatAssemblyBegin{End}() has been
> called, and should be called by all processors. Here is that bit of the
> code which calls MatZeroRows() after the matrix has been assembled
>
>
> https://github.com/IBAMR/IBAMR/blob/amneetb/acoustically-driven-flows/src/acoustic_streaming/AcousticStreamingPETScMatUtilities.cpp#L724-L801
>
> I ran the parallel code (on 3 processors) in the debugger
> (-start_in_debugger). Below is the call stack from the processor that gets
> stuck
>
> amneetb at APSB-MBP-16:~$ lldb -p 4307
> (lldb) process attach --pid 4307
> Process 4307 stopped
> * thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGSTOP
> frame #0: 0x000000018a2d750c libsystem_kernel.dylib`__semwait_signal
> + 8
> libsystem_kernel.dylib`:
> -> 0x18a2d750c <+8>: b.lo 0x18a2d752c ; <+40>
> 0x18a2d7510 <+12>: pacibsp
> 0x18a2d7514 <+16>: stp x29, x30, [sp, #-0x10]!
> 0x18a2d7518 <+20>: mov x29, sp
> Target 0: (fo_acoustic_streaming_solver_2d) stopped.
> Executable module set to
> "/Users/amneetb/Softwares/IBAMR-Git/objs-dbg/tests/IBTK/fo_acoustic_streaming_solver_2d".
> Architecture set to: arm64-apple-macosx-.
> (lldb) cont
> Process 4307 resuming
> Process 4307 stopped
> * thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGSTOP
> frame #0: 0x0000000109d281b8
> libpmpi.12.dylib`MPIDI_POSIX_mpi_barrier_release_gather + 400
> libpmpi.12.dylib`MPIDI_POSIX_mpi_barrier_release_gather:
> -> 0x109d281b8 <+400>: ldr w9, [x24]
> 0x109d281bc <+404>: cmp w8, w9
> 0x109d281c0 <+408>: b.lt 0x109d281a0 ; <+376>
> 0x109d281c4 <+412>: bl 0x109d28e64 ;
> MPID_Progress_test
> Target 0: (fo_acoustic_streaming_solver_2d) stopped.
> (lldb) bt
> * thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGSTOP
> * frame #0: 0x0000000109d281b8
> libpmpi.12.dylib`MPIDI_POSIX_mpi_barrier_release_gather + 400
> frame #1: 0x0000000109d27d14 libpmpi.12.dylib`MPIDI_SHM_mpi_barrier +
> 224
> frame #2: 0x0000000109d27b60
> libpmpi.12.dylib`MPIDI_Barrier_intra_composition_alpha + 44
> frame #3: 0x0000000109d0d490 libpmpi.12.dylib`MPIR_Barrier + 900
> frame #4: 0x000000010224d030 libmpi.12.dylib`MPI_Barrier + 684
> frame #5: 0x00000001045ea638
> libpetsc.3.17.dylib`PetscCommDuplicate(comm_in=-2080374782,
> comm_out=0x000000010300bcb0, first_tag=0x000000010300bce4) at tagm.c:235:5
> frame #6: 0x00000001045f2910
> libpetsc.3.17.dylib`PetscHeaderCreate_Private(h=0x000000010300bc70,
> classid=1211227, class_name="PetscSF", descr="Star Forest",
> mansec="PetscSF", comm=-2080374782,
> destroy=(libpetsc.3.17.dylib`PetscSFDestroy at sf.c:224),
> view=(libpetsc.3.17.dylib`PetscSFView at sf.c:841)) at inherit.c:62:3
> frame #7: 0x00000001049cf820
> libpetsc.3.17.dylib`PetscSFCreate(comm=-2080374782, sf=0x000000016f911a50)
> at sf.c:62:3
> frame #8: 0x0000000104cd3024
> libpetsc.3.17.dylib`MatZeroRowsMapLocal_Private(A=0x00000001170c1270, N=1,
> rows=0x000000016f912cb4, nr=0x000000016f911df8, olrows=0x000000016f911e00)
> at zerorows.c:36:5
> frame #9: 0x000000010504ea50
> libpetsc.3.17.dylib`MatZeroRows_MPIAIJ(A=0x00000001170c1270, N=1,
> rows=0x000000016f912cb4, diag=1, x=0x0000000000000000,
> b=0x0000000000000000) at mpiaij.c:768:3
> frame #10: 0x0000000104d95fac
> libpetsc.3.17.dylib`MatZeroRows(mat=0x00000001170c1270, numRows=1,
> rows=0x000000016f912cb4, diag=1, x=0x0000000000000000,
> b=0x0000000000000000) at matrix.c:5935:3
> frame #11: 0x000000010067d320
> fo_acoustic_streaming_solver_2d`IBAMR::AcousticStreamingPETScMatUtilities::constructPatchLevelFOAcousticStreamingOp(mat=0x000000016f91c178,
> omega=1, sound_speed=1, rho_idx=3, mu_idx=2, lambda_idx=4,
> u_bc_coefs=0x000000016f91c3a8, data_time=NaN, num_dofs_per_proc=size=3,
> u_dof_index_idx=27, p_dof_index_idx=28,
> patch_level=Pointer<SAMRAI::hier::PatchLevel<2> > @ 0x000000016f914ed0,
> mu_interp_type=VC_HARMONIC_INTERP) at
> AcousticStreamingPETScMatUtilities.cpp:794:36
> frame #12: 0x0000000100694bdc
> fo_acoustic_streaming_solver_2d`IBAMR::FOAcousticStreamingPETScLevelSolver::initializeSolverStateSpecialized(this=0x000000016f91c028,
> x=0x000000016f91d788, (null)=0x000000016f91d690) at
> FOAcousticStreamingPETScLevelSolver.cpp:149:5
> frame #13: 0x000000010083232c
> fo_acoustic_streaming_solver_2d`IBTK::PETScLevelSolver::initializeSolverState(this=0x000000016f91c028,
> x=0x000000016f91d788, b=0x000000016f91d690) at PETScLevelSolver.cpp:340:5
> frame #14: 0x00000001004eb230
> fo_acoustic_streaming_solver_2d`main(argc=11, argv=0x000000016f91f460) at
> fo_acoustic_streaming_solver.cpp:400:22
> frame #15: 0x0000000189fbbf28 dyld`start + 2236
>
>
> Any suggestions on how to avoid this barrier? Here are all MAT options I
> am using (in the debug mode), if that is helpful:
>
>
> https://github.com/IBAMR/IBAMR/blob/amneetb/acoustically-driven-flows/src/acoustic_streaming/AcousticStreamingPETScMatUtilities.cpp#L453-L458
>
> Thanks,
> --
> --Amneet
>
>
>
>
>
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