[petsc-dev] Cannot locate file: share/petsc/datafiles/matrices/small

Junchao Zhang junchao.zhang at gmail.com
Tue Sep 14 10:10:57 CDT 2021 

MPI one-sided is tricky and needs careful synchronization (like OpenMP).
An incorrect code could work in one interface but fail in another.

--Junchao Zhang


On Tue, Sep 14, 2021 at 10:01 AM Barry Smith <bsmith at petsc.dev> wrote:

>
>    It sounds reproducible and related to using a particular versions of
> OpenMPI and even particular interfaces.
>
>   Barry
>
>    On Tue, Sep 14, 2021 at 2:35 AM Stefano Zampini <
> stefano.zampini at gmail.com> wrote:
>>
>> I can reproduce it even with OpenMPI 4.1.1 on a different machine (Ubuntu
>> 18 + AMD milan + clang from AOCC)  and it is definitely an OpenMPI bug in
>> the vader BTL If I use tcp, everything runs smooth
>>
>>
>>
>>
> On Sep 14, 2021, at 10:54 AM, Junchao Zhang <junchao.zhang at gmail.com>
> wrote:
>
> Without a standalone & valid mpi example to reproduce the error, we are
> not assured to say it is an OpenMPI bug.
>
> --Junchao Zhang
>
>
> On Tue, Sep 14, 2021 at 6:17 AM Matthew Knepley <knepley at gmail.com> wrote:
>
>> Okay, we have to send this to OpenMPI. Volunteers?
>>
>> Maybe we should note this in the FAQ, or installation, so we remember how
>> to fix it if someone else asks?
>>
>>   Thanks,
>>
>>      Matt
>>
>> On Tue, Sep 14, 2021 at 2:35 AM Stefano Zampini <
>> stefano.zampini at gmail.com> wrote:
>>
>>> I can reproduce it even with OpenMPI 4.1.1 on a different machine
>>> (Ubuntu 18 + AMD milan + clang from AOCC)  and it is definitely an OpenMPI
>>> bug in the vader BTL If I use tcp, everything runs smooth
>>>
>>> zampins at kanary:~/Devel/petsc$ cat
>>> /home/zampins/local/etc/openmpi-mca-params.conf | grep btl
>>> btl = tcp,self
>>> zampins at kanary:~/Devel/petsc$ make -f gmakefile.test
>>> vec_is_sf_tutorials-ex1_4
>>> Using MAKEFLAGS:
>>>         TEST arch-debug/tests/counts/vec_is_sf_tutorials-ex1_4.counts
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-dynamic
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-dynamic
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-allocate
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-allocate
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-create
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-create
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-dynamic
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-dynamic
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-allocate
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-allocate
>>>  ok vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-create
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-create
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-dynamic
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-dynamic
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-allocate
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-allocate
>>>
>>>
>>> zampins at kanary:~/Devel/petsc$ cat
>>> /home/zampins/local/etc/openmpi-mca-params.conf | grep btl
>>> btl = vader,tcp,self
>>> zampins at kanary:~/Devel/petsc$ make -f gmakefile.test
>>> vec_is_sf_tutorials-ex1_4
>>> Using MAKEFLAGS:
>>>         TEST arch-debug/tests/counts/vec_is_sf_tutorials-ex1_4.counts
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create
>>> not ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create
>>> # Error code: 1
>>> # 43,46c43,46
>>> # < [0] 0: 4001 2000 2002 3002 4002
>>> # < [1] 0: 1001 3000
>>> # < [2] 0: 2001 4000
>>> # < [3] 0: 3001 1000
>>> # ---
>>> # > [0] 0: 2002 2146435072 2 2146435072 38736240
>>> # > [1] 0: 3000 2146435072
>>> # > [2] 0: 2001 2146435072
>>> # > [3] 0: 3001 2146435072
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-dynamic
>>> not ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-dynamic
>>> # Error code: 1
>>> # 43,46c43,46
>>> # < [0] 0: 4001 2000 2002 3002 4002
>>> # < [1] 0: 1001 3000
>>> # < [2] 0: 2001 4000
>>> # < [3] 0: 3001 1000
>>> # ---
>>> # > [0] 0: 2002 2146435072 2 2146435072 0
>>> # > [1] 0: 3000 2146435072
>>> # > [2] 0: 2001 2146435072
>>> # > [3] 0: 3001 2146435072
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-allocate
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-allocate
>>> # retrying
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-create
>>> not ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-create #
>>> Error code: 98
>>> # [1]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> # [1]PETSC ERROR: General MPI error
>>> # [1]PETSC ERROR: MPI error 6 MPI_ERR_RANK: invalid rank
>>> # [1]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>> shooting.
>>> # [1]PETSC ERROR: Petsc Development GIT revision:
>>> v3.15.4-783-g168bb9f76b  GIT Date: 2021-09-13 14:01:22 +0000
>>> # [1]PETSC ERROR: ../ex1 on a arch-debug named kanary.kaust.edu.sa by
>>> zampins Tue Sep 14 09:31:42 2021
>>> # [1]PETSC ERROR: [2]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> # [2]PETSC ERROR: General MPI error
>>> # [2]PETSC ERROR: MPI error 6 MPI_ERR_RANK: invalid rank
>>> # [2]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>> shooting.
>>> # [2]PETSC ERROR: Petsc Development GIT revision:
>>> v3.15.4-783-g168bb9f76b  GIT Date: 2021-09-13 14:01:22 +0000
>>> # [2]PETSC ERROR: ../ex1 on a arch-debug named kanary.kaust.edu.sa by
>>> zampins Tue Sep 14 09:31:42 2021
>>> # [2]PETSC ERROR: Configure options
>>> --with-cc=/home/zampins/local/bin/mpicc --with-cxx-dialect=c++14
>>> --with-cxx=/home/zampins/local/bin/mpicxx --with-debugging=1
>>> --with-fc=/home/zampins/local/bin/mpifort --with-fortran-bindings=0
>>> --with-hip-dir=/opt/rocm --with-hip=1
>>> --with-hypre-dir=/home/zampins/local-petsc
>>> --with-kokkos-dir=/home/zampins/local-petsc
>>> --with-kokkos-kernels-dir=/home/zampins/local-petsc
>>> --with-blaslapack-include=/home/zampins/local-aocl/aocc/3.0-6/include
>>> --with-blaslapack-lib="[/home/zampins/local-aocl/aocc/3.0-6/lib/liblapacke.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libflame.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libblis-mt.a]"
>>> HIPFLAGS=--amdgpu-target=gfx908
>>> HIPPPFLAGS=-I/home/zampins/local-petsc/include PETSC_ARCH=arch-debug
>>> # [2]PETSC ERROR: #1 PetscSFGetGroups() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:1166
>>> # [2]PETSC ERROR: #2 PetscSFSetUp_Window() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/impls/window/sfwindow.c:708
>>> # [2]PETSC ERROR: #3 PetscSFSetUp() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:318
>>> # [2]PETSC ERROR: #4 main() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/tutorials/ex1.c:172
>>> # [2]PETSC ERROR: PETSc Option Table entries:
>>> # [2]PETSC ERROR: -sf_type window
>>> # [2]PETSC ERROR: -sf_window_flavor create
>>> # [2]PETSC ERROR: -sf_window_sync active
>>> # [2]PETSC ERROR: -test_gather
>>> # [2]PETSC ERROR: ----------------End of Error Message -------send
>>> entire error message to petsc-maint at mcs.anl.gov----------
>>> # [3]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> # [3]PETSC ERROR: General MPI error
>>> # [3]PETSC ERROR: MPI error 6 MPI_ERR_RANK: invalid rank
>>> # [3]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>> shooting.
>>> # [3]PETSC ERROR: Petsc Development GIT revision:
>>> v3.15.4-783-g168bb9f76b  GIT Date: 2021-09-13 14:01:22 +0000
>>> # [3]PETSC ERROR: ../ex1 on a arch-debug named kanary.kaust.edu.sa by
>>> zampins Tue Sep 14 09:31:42 2021
>>> # [3]PETSC ERROR: Configure options
>>> --with-cc=/home/zampins/local/bin/mpicc --with-cxx-dialect=c++14
>>> --with-cxx=/home/zampins/local/bin/mpicxx --with-debugging=1
>>> --with-fc=/home/zampins/local/bin/mpifort --with-fortran-bindings=0
>>> --with-hip-dir=/opt/rocm --with-hip=1
>>> --with-hypre-dir=/home/zampins/local-petsc
>>> --with-kokkos-dir=/home/zampins/local-petsc
>>> --with-kokkos-kernels-dir=/home/zampins/local-petsc
>>> --with-blaslapack-include=/home/zampins/local-aocl/aocc/3.0-6/include
>>> --with-blaslapack-lib="[/home/zampins/local-aocl/aocc/3.0-6/lib/liblapacke.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libflame.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libblis-mt.a]"
>>> HIPFLAGS=--amdgpu-target=gfx908
>>> HIPPPFLAGS=-I/home/zampins/local-petsc/include PETSC_ARCH=arch-debug
>>> # [3]PETSC ERROR: #1 PetscSFGetGroups() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:1166
>>> # [3]PETSC ERROR: #2 PetscSFSetUp_Window() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/impls/window/sfwindow.c:708
>>> # [3]PETSC ERROR: #3 PetscSFSetUp() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:318
>>> # [3]PETSC ERROR: #4 main() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/tutorials/ex1.c:172
>>> # [3]PETSC ERROR: PETSc Option Table entries:
>>> # [3]PETSC ERROR: -sf_type window
>>> # [3]PETSC ERROR: -sf_window_flavor create
>>> # [3]PETSC ERROR: Configure options
>>> --with-cc=/home/zampins/local/bin/mpicc --with-cxx-dialect=c++14
>>> --with-cxx=/home/zampins/local/bin/mpicxx --with-debugging=1
>>> --with-fc=/home/zampins/local/bin/mpifort --with-fortran-bindings=0
>>> --with-hip-dir=/opt/rocm --with-hip=1
>>> --with-hypre-dir=/home/zampins/local-petsc
>>> --with-kokkos-dir=/home/zampins/local-petsc
>>> --with-kokkos-kernels-dir=/home/zampins/local-petsc
>>> --with-blaslapack-include=/home/zampins/local-aocl/aocc/3.0-6/include
>>> --with-blaslapack-lib="[/home/zampins/local-aocl/aocc/3.0-6/lib/liblapacke.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libflame.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libblis-mt.a]"
>>> HIPFLAGS=--amdgpu-target=gfx908
>>> HIPPPFLAGS=-I/home/zampins/local-petsc/include PETSC_ARCH=arch-debug
>>> # [1]PETSC ERROR: #1 PetscSFGetGroups() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:1166
>>> # [1]PETSC ERROR: #2 PetscSFSetUp_Window() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/impls/window/sfwindow.c:708
>>> # [1]PETSC ERROR: #3 PetscSFSetUp() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:318
>>> # [1]PETSC ERROR: #4 main() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/tutorials/ex1.c:172
>>> # [1]PETSC ERROR: PETSc Option Table entries:
>>> # [1]PETSC ERROR: -sf_type window
>>> # [1]PETSC ERROR: -sf_window_flavor create
>>> # [1]PETSC ERROR: -sf_window_sync active
>>> # [1]PETSC ERROR: -test_gather
>>> # [1]PETSC ERROR: ----------------End of Error Message -------send
>>> entire error message to petsc-maint at mcs.anl.gov----------
>>> # -sf_window_sync active
>>> # [3]PETSC ERROR: -test_gather
>>> # [3]PETSC ERROR: ----------------End of Error Message -------send
>>> entire error message to petsc-maint at mcs.anl.gov----------
>>> #
>>> --------------------------------------------------------------------------
>>> # MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
>>> # with errorcode 98.
>>> #
>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> # You may or may not see output from other processes, depending on
>>> # exactly when Open MPI kills them.
>>> #
>>> --------------------------------------------------------------------------
>>> # [kanary.kaust.edu.sa:115527] 2 more processes have sent help message
>>> help-mpi-api.txt / mpi-abort
>>> # [kanary.kaust.edu.sa:115527] Set MCA parameter
>>> "orte_base_help_aggregate" to 0 to see all help / error messages
>>>  ok vec_is_sf_tutorials-ex1_4 # SKIP Command failed so no diff
>>> # retrying
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-dynamic
>>> not ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-dynamic #
>>> Error code: 98
>>> # [1]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> # [1]PETSC ERROR: General MPI error
>>> # [1]PETSC ERROR: MPI error 6 MPI_ERR_RANK: invalid rank
>>> # [1]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>> shooting.
>>> # [1]PETSC ERROR: Petsc Development GIT revision:
>>> v3.15.4-783-g168bb9f76b  GIT Date: 2021-09-13 14:01:22 +0000
>>> # [1]PETSC ERROR: ../ex1 on a arch-debug named kanary.kaust.edu.sa by
>>> zampins Tue Sep 14 09:31:45 2021
>>> # [1]PETSC ERROR: Configure options
>>> --with-cc=/home/zampins/local/bin/mpicc --with-cxx-dialect=c++14
>>> --with-cxx=/home/zampins/local/bin/mpicxx --with-debugging=1
>>> --with-fc=/home/zampins/local/bin/mpifort --with-fortran-bindings=0
>>> --with-hip-dir=/opt/rocm --with-hip=1
>>> --with-hypre-dir=/home/zampins/local-petsc
>>> --with-kokkos-dir=/home/zampins/local-petsc
>>> --with-kokkos-kernels-dir=/home/zampins/local-petsc
>>> --with-blaslapack-include=/home/zampins/local-aocl/aocc/3.0-6/include
>>> --with-blaslapack-lib="[/home/zampins/local-aocl/aocc/3.0-6/lib/liblapacke.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libflame.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libblis-mt.a]"
>>> HIPFLAGS=--amdgpu-target=gfx908
>>> HIPPPFLAGS=-I/home/zampins/local-petsc/include PETSC_ARCH=arch-debug
>>> # [1]PETSC ERROR: #1 PetscSFGetGroups() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:1166
>>> # [1]PETSC ERROR: #2 PetscSFSetUp_Window() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/impls/window/sfwindow.c:708
>>> # [1]PETSC ERROR: #3 PetscSFSetUp() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:318
>>> # [1]PETSC ERROR: #4 main() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/tutorials/ex1.c:172
>>> # [1]PETSC ERROR: PETSc Option Table entries:
>>> # [1]PETSC ERROR: -sf_type window
>>> # [1]PETSC ERROR: [2]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> # [2]PETSC ERROR: General MPI error
>>> # [2]PETSC ERROR: MPI error 6 MPI_ERR_RANK: invalid rank
>>> # [2]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>> shooting.
>>> # [2]PETSC ERROR: Petsc Development GIT revision:
>>> v3.15.4-783-g168bb9f76b  GIT Date: 2021-09-13 14:01:22 +0000
>>> # [2]PETSC ERROR: ../ex1 on a arch-debug named kanary.kaust.edu.sa by
>>> zampins Tue Sep 14 09:31:45 2021
>>> # [2]PETSC ERROR: Configure options
>>> --with-cc=/home/zampins/local/bin/mpicc --with-cxx-dialect=c++14
>>> --with-cxx=/home/zampins/local/bin/mpicxx --with-debugging=1
>>> --with-fc=/home/zampins/local/bin/mpifort --with-fortran-bindings=0
>>> --with-hip-dir=/opt/rocm --with-hip=1
>>> --with-hypre-dir=/home/zampins/local-petsc
>>> --with-kokkos-dir=/home/zampins/local-petsc
>>> --with-kokkos-kernels-dir=/home/zampins/local-petsc
>>> --with-blaslapack-include=/home/zampins/local-aocl/aocc/3.0-6/include
>>> --with-blaslapack-lib="[/home/zampins/local-aocl/aocc/3.0-6/lib/liblapacke.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libflame.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libblis-mt.a]"
>>> HIPFLAGS=--amdgpu-target=gfx908
>>> HIPPPFLAGS=-I/home/zampins/local-petsc/include PETSC_ARCH=arch-debug
>>> # [2]PETSC ERROR: #1 PetscSFGetGroups() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:1166
>>> # [2]PETSC ERROR: #2 PetscSFSetUp_Window() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/impls/window/sfwindow.c:708
>>> # [2]PETSC ERROR: #3 PetscSFSetUp() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:318
>>> # [2]PETSC ERROR: #4 main() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/tutorials/ex1.c:172
>>> # [2]PETSC ERROR: PETSc Option Table entries:
>>> # [2]PETSC ERROR: -sf_type window
>>> # [2]PETSC ERROR: -sf_window_flavor dynamic
>>> # [2]PETSC ERROR: -sf_window_sync active
>>> # [2]PETSC ERROR: -test_gather
>>> # [2]PETSC ERROR: ----------------End of Error Message -------send
>>> entire error message to petsc-maint at mcs.anl.gov----------
>>> # [3]PETSC ERROR: --------------------- Error Message
>>> --------------------------------------------------------------
>>> # [3]PETSC ERROR: General MPI error
>>> # [3]PETSC ERROR: MPI error 6 MPI_ERR_RANK: invalid rank
>>> # [3]PETSC ERROR: See https://petsc.org/release/faq/ for trouble
>>> shooting.
>>> # [3]PETSC ERROR: Petsc Development GIT revision:
>>> v3.15.4-783-g168bb9f76b  GIT Date: 2021-09-13 14:01:22 +0000
>>> # [3]PETSC ERROR: ../ex1 on a arch-debug named kanary.kaust.edu.sa by
>>> zampins Tue Sep 14 09:31:45 2021
>>> # [3]PETSC ERROR: Configure options
>>> --with-cc=/home/zampins/local/bin/mpicc --with-cxx-dialect=c++14
>>> --with-cxx=/home/zampins/local/bin/mpicxx --with-debugging=1
>>> --with-fc=/home/zampins/local/bin/mpifort --with-fortran-bindings=0
>>> --with-hip-dir=/opt/rocm --with-hip=1
>>> --with-hypre-dir=/home/zampins/local-petsc
>>> --with-kokkos-dir=/home/zampins/local-petsc
>>> --with-kokkos-kernels-dir=/home/zampins/local-petsc
>>> --with-blaslapack-include=/home/zampins/local-aocl/aocc/3.0-6/include
>>> --with-blaslapack-lib="[/home/zampins/local-aocl/aocc/3.0-6/lib/liblapacke.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libflame.a,/home/zampins/local-aocl/aocc/3.0-6/lib/libblis-mt.a]"
>>> HIPFLAGS=--amdgpu-target=gfx908
>>> HIPPPFLAGS=-I/home/zampins/local-petsc/include PETSC_ARCH=arch-debug
>>> # [3]PETSC ERROR: #1 PetscSFGetGroups() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:1166
>>> # [3]PETSC ERROR: #2 PetscSFSetUp_Window() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/impls/window/sfwindow.c:708
>>> # [3]PETSC ERROR: #3 PetscSFSetUp() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/interface/sf.c:318
>>> # [3]PETSC ERROR: #4 main() at
>>> /home/zampins/Devel/petsc/src/vec/is/sf/tutorials/ex1.c:172
>>> # [3]PETSC ERROR: PETSc Option Table entries:
>>> # [3]PETSC ERROR: -sf_type window
>>> # [3]PETSC ERROR: -sf_window_flavor dynamic
>>> # [3]PETSC ERROR: -sf_window_sync active
>>> # [3]PETSC ERROR: -test_gather
>>> # [3]PETSC ERROR: ----------------End of Error Message -------send
>>> entire error message to petsc-maint at mcs.anl.gov----------
>>> # -sf_window_flavor dynamic
>>> # [1]PETSC ERROR: -sf_window_sync active
>>> # [1]PETSC ERROR: -test_gather
>>> # [1]PETSC ERROR: ----------------End of Error Message -------send
>>> entire error message to petsc-maint at mcs.anl.gov----------
>>> #
>>> --------------------------------------------------------------------------
>>> # MPI_ABORT was invoked on rank 3 in communicator MPI_COMM_WORLD
>>> # with errorcode 98.
>>> #
>>> # NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
>>> # You may or may not see output from other processes, depending on
>>> # exactly when Open MPI kills them.
>>> #
>>> --------------------------------------------------------------------------
>>> # [kanary.kaust.edu.sa:115572] 2 more processes have sent help message
>>> help-mpi-api.txt / mpi-abort
>>> # [kanary.kaust.edu.sa:115572] Set MCA parameter
>>> "orte_base_help_aggregate" to 0 to see all help / error messages
>>>  ok vec_is_sf_tutorials-ex1_4 # SKIP Command failed so no diff
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-allocate
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-active_sf_window_flavor-allocate
>>>  ok vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-create
>>> not ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-create
>>> # Error code: 1
>>> # 43,46c43,46
>>> # < [0] 0: 4001 2000 2002 3002 4002
>>> # < [1] 0: 1001 3000
>>> # < [2] 0: 2001 4000
>>> # < [3] 0: 3001 1000
>>> # ---
>>> # > [0] 0: 4002 2146435072 2 2146435072 34619728
>>> # > [1] 0: 3000 2146435072
>>> # > [2] 0: 4000 2146435072
>>> # > [3] 0: 3001 2146435072
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-dynamic
>>> not ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-dynamic
>>> # Error code: 1
>>> # 43,46c43,46
>>> # < [0] 0: 4001 2000 2002 3002 4002
>>> # < [1] 0: 1001 3000
>>> # < [2] 0: 2001 4000
>>> # < [3] 0: 3001 1000
>>> # ---
>>> # > [0] 0: 4002 2146435072 2 2146435072 0
>>> # > [1] 0: 3000 2146435072
>>> # > [2] 0: 4000 2146435072
>>> # > [3] 0: 3001 2146435072
>>>  ok
>>> vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-allocate
>>>  ok
>>> diff-vec_is_sf_tutorials-ex1_4+sf_window_sync-lock_sf_window_flavor-allocate
>>>
>>>
>>>
>>> Il giorno mar 14 set 2021 alle ore 07:44 Stefano Zampini <
>>> stefano.zampini at gmail.com> ha scritto:
>>>
>>>> I'll see if I can reproduce
>>>>
>>>> Il Mar 14 Set 2021, 06:58 Junchao Zhang <junchao.zhang at gmail.com> ha
>>>> scritto:
>>>>
>>>>> Hi, Stefano,
>>>>>    Ping you again to see if you want to resolve this problem before
>>>>> petsc-3.16
>>>>>
>>>>> --Junchao Zhang
>>>>>
>>>>>
>>>>> On Sun, Sep 12, 2021 at 3:06 PM Antonio T. sagitter <
>>>>> sagitter at fedoraproject.org> wrote:
>>>>>
>>>>>> Unfortunately, it's not possible. I must use the OpenMPI provided by
>>>>>> Fedora build-system (these rpm builds of PETSc are for Fedora's
>>>>>> repositories), downloading external software is not permitted.
>>>>>>
>>>>>> On 9/12/21 21:10, Pierre Jolivet wrote:
>>>>>> >
>>>>>> >> On 12 Sep 2021, at 8:56 PM, Matthew Knepley <knepley at gmail.com
>>>>>> >> <mailto:knepley at gmail.com>> wrote:
>>>>>> >>
>>>>>> >> On Sun, Sep 12, 2021 at 2:49 PM Antonio T. sagitter
>>>>>> >> <sagitter at fedoraproject.org <mailto:sagitter at fedoraproject.org>>
>>>>>> wrote:
>>>>>> >>
>>>>>> >>     Those attached are configure.log/make.log from a MPI build in
>>>>>> >>     Fedora 34
>>>>>> >>     x86_64 where the error below occurred.
>>>>>> >>
>>>>>> >>
>>>>>> >> This is OpenMPI 4.1.0. Is that the only MPI you build? My first
>>>>>> >> inclination is that this is an MPI implementation bug.
>>>>>> >>
>>>>>> >> Junchao, do we have an OpenMPI build in the CI?
>>>>>> >
>>>>>> > config/examples/arch-ci-linux-cuda-double-64idx.py:
>>>>>> >   '--download-openmpi=1',
>>>>>> > config/examples/arch-ci-linux-pkgs-dbg-ftn-interfaces.py:
>>>>>> >   '--download-openmpi=1',
>>>>>> > config/examples/arch-ci-linux-pkgs-opt.py:  '--download-openmpi=1',
>>>>>> >
>>>>>> > config/BuildSystem/config/packages/OpenMPI.py uses version 4.1.0 as
>>>>>> well.
>>>>>> > I’m not sure PETSc is to blame here Antonio. You may want to try to
>>>>>> > ditch the OpenMPI shipped by your packet manager and try
>>>>>> > --download-openmpi as well, just for a quick sanity check.
>>>>>> >
>>>>>> > Thanks,
>>>>>> > Pierre
>>>>>> >
>>>>>>
>>>>>> --
>>>>>> ---
>>>>>> Antonio Trande
>>>>>> Fedora Project
>>>>>> mailto: sagitter at fedoraproject.org
>>>>>> GPG key: 0x29FBC85D7A51CC2F
>>>>>> GPG key server: https://keyserver1.pgp.com/
>>>>>>
>>>>>
>>>
>>> --
>>> Stefano
>>>
>>
>>
>> --
>> 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/
>> <http://www.cse.buffalo.edu/~knepley/>
>>
>
>
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