September 2021 - petsc-dev - mailman3.cels.anl.gov

Re: [petsc-dev] Cannot locate file: share/petsc/datafiles/matrices/small
by Antonio T. sagitter 12 Sep '21

12 Sep '21

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(a)gmail.com >> <mailto:[email protected]>> wrote: >> >> On Sun, Sep 12, 2021 at 2:49 PM Antonio T. sagitter >> <sagitter(a)fedoraproject.org <mailto:[email protected]>> 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(a)fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/

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Re: [petsc-dev] Cannot locate file: share/petsc/datafiles/matrices/small
by Junchao Zhang 12 Sep '21

12 Sep '21

An old issue with SF_Window is at https://gitlab.com/petsc/petsc/-/issues/555, though which is a different error. --Junchao Zhang On Sun, Sep 12, 2021 at 2:20 PM Junchao Zhang <junchao.zhang(a)gmail.com> wrote: > We met SF + Windows errors before. Stefano wrote the code, which I don't > think was worth doing. SF with MPI one-sided is hard to be correct (due to > shared memory programming), bad in performance, and no users use that. > I would suggest we just disable the test and feature? Stefano, what do > you think? > > --Junchao Zhang > > > On Sun, Sep 12, 2021 at 2:10 PM Pierre Jolivet <pierre(a)joliv.et> wrote: > >> >> On 12 Sep 2021, at 8:56 PM, Matthew Knepley <knepley(a)gmail.com> wrote: >> >> On Sun, Sep 12, 2021 at 2:49 PM Antonio T. sagitter < >> sagitter(a)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 >> >> Thanks, >> >> Matt >> >> >>> On 9/12/21 19:18, Antonio T. sagitter wrote: >>> > Okay. I will try to set correctly the DATAFILESPATH options. >>> > >>> > I see even this error: >>> > >>> > not ok >>> > vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create >>> # >>> > Error code: 68 >>> > >>> > # PetscSF Object: 4 MPI processes >>> > >>> > # type: window >>> > >>> > # [0] Number of roots=3, leaves=2, remote ranks=2 >>> > >>> > # [0] 0 <- (3,1) >>> > >>> > # [0] 1 <- (1,0) >>> > >>> > # [1] Number of roots=2, leaves=3, remote ranks=2 >>> > >>> > # [1] 0 <- (0,1) >>> > >>> > # [1] 1 <- (2,0) >>> > >>> > # [1] 2 <- (0,2) >>> > >>> > # [2] Number of roots=2, leaves=3, remote ranks=3 >>> > >>> > # [2] 0 <- (1,1) >>> > >>> > # [2] 1 <- (3,0) >>> > >>> > # [2] 2 <- (0,2) >>> > >>> > # [3] Number of roots=2, leaves=3, remote ranks=2 >>> > >>> > # [3] 0 <- (2,1) >>> > >>> > # [3] 1 <- (0,0) >>> > >>> > # [3] 2 <- (0,2) >>> > >>> > # [0] Roots referenced by my leaves, by rank >>> > >>> > # [0] 1: 1 edges >>> > >>> > # [0] 1 <- 0 >>> > >>> > # [0] 3: 1 edges >>> > >>> > # [0] 0 <- 1 >>> > >>> > # [1] Roots referenced by my leaves, by rank >>> > >>> > # [1] 0: 2 edges >>> > >>> > # [1] 0 <- 1 >>> > >>> > # [1] 2 <- 2 >>> > >>> > # [1] 2: 1 edges >>> > >>> > # [1] 1 <- 0 >>> > >>> > # [2] Roots referenced by my leaves, by rank >>> > >>> > # [2] 0: 1 edges >>> > >>> > # [2] 2 <- 2 >>> > >>> > # [2] 1: 1 edges >>> > >>> > # [2] 0 <- 1 >>> > >>> > # [2] 3: 1 edges >>> > >>> > # [2] 1 <- 0 >>> > >>> > # [3] Roots referenced by my leaves, by rank >>> > >>> > # [3] 0: 2 edges >>> > >>> > # [3] 1 <- 0 >>> > >>> > # [3] 2 <- 2 >>> > >>> > # [3] 2: 1 edges >>> > >>> > # [3] 0 <- 1 >>> > >>> > # current flavor=CREATE synchronization=FENCE MultiSF >>> sort=rank-order >>> > >>> > # current info=MPI_INFO_NULL >>> > >>> > # [buildhw-x86-09:1135574] *** An error occurred in MPI_Accumulate >>> > >>> > # [buildhw-x86-09:1135574] *** reported by process [3562602497,3] >>> > >>> > # [buildhw-x86-09:1135574] *** on win rdma window 4 >>> > >>> > # [buildhw-x86-09:1135574] *** MPI_ERR_RMA_RANGE: invalid RMA >>> address >>> > range >>> > >>> > # [buildhw-x86-09:1135574] *** MPI_ERRORS_ARE_FATAL (processes in >>> > this win will now abort, >>> > >>> > # [buildhw-x86-09:1135574] *** and potentially your MPI job) >>> > >>> > # [buildhw-x86-09.iad2.fedoraproject.org:1135567] 3 more processes >>> > have sent help message help-mpi-errors.txt / mpi_errors_are_fatal >>> > >>> > # [buildhw-x86-09.iad2.fedoraproject.org:1135567] Set MCA >>> parameter >>> > "orte_base_help_aggregate" to 0 to see all help / error messages >>> > >>> > Looks like an error related to OpenMPI-4*: >>> > https://github.com/open-mpi/ompi/issues/6374 >>> > >>> >>> -- >>> --- >>> Antonio Trande >>> Fedora Project >>> mailto: sagitter(a)fedoraproject.org >>> GPG key: 0x29FBC85D7A51CC2F >>> GPG key server: https://keyserver1.pgp.com/ >> >> >> >> -- >> 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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Re: [petsc-dev] Cannot locate file: share/petsc/datafiles/matrices/small
by Junchao Zhang 12 Sep '21

12 Sep '21

We met SF + Windows errors before. Stefano wrote the code, which I don't think was worth doing. SF with MPI one-sided is hard to be correct (due to shared memory programming), bad in performance, and no users use that. I would suggest we just disable the test and feature? Stefano, what do you think? --Junchao Zhang On Sun, Sep 12, 2021 at 2:10 PM Pierre Jolivet <pierre(a)joliv.et> wrote: > > On 12 Sep 2021, at 8:56 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Sun, Sep 12, 2021 at 2:49 PM Antonio T. sagitter < > sagitter(a)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 > > Thanks, > > Matt > > >> On 9/12/21 19:18, Antonio T. sagitter wrote: >> > Okay. I will try to set correctly the DATAFILESPATH options. >> > >> > I see even this error: >> > >> > not ok >> > vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create >> # >> > Error code: 68 >> > >> > # PetscSF Object: 4 MPI processes >> > >> > # type: window >> > >> > # [0] Number of roots=3, leaves=2, remote ranks=2 >> > >> > # [0] 0 <- (3,1) >> > >> > # [0] 1 <- (1,0) >> > >> > # [1] Number of roots=2, leaves=3, remote ranks=2 >> > >> > # [1] 0 <- (0,1) >> > >> > # [1] 1 <- (2,0) >> > >> > # [1] 2 <- (0,2) >> > >> > # [2] Number of roots=2, leaves=3, remote ranks=3 >> > >> > # [2] 0 <- (1,1) >> > >> > # [2] 1 <- (3,0) >> > >> > # [2] 2 <- (0,2) >> > >> > # [3] Number of roots=2, leaves=3, remote ranks=2 >> > >> > # [3] 0 <- (2,1) >> > >> > # [3] 1 <- (0,0) >> > >> > # [3] 2 <- (0,2) >> > >> > # [0] Roots referenced by my leaves, by rank >> > >> > # [0] 1: 1 edges >> > >> > # [0] 1 <- 0 >> > >> > # [0] 3: 1 edges >> > >> > # [0] 0 <- 1 >> > >> > # [1] Roots referenced by my leaves, by rank >> > >> > # [1] 0: 2 edges >> > >> > # [1] 0 <- 1 >> > >> > # [1] 2 <- 2 >> > >> > # [1] 2: 1 edges >> > >> > # [1] 1 <- 0 >> > >> > # [2] Roots referenced by my leaves, by rank >> > >> > # [2] 0: 1 edges >> > >> > # [2] 2 <- 2 >> > >> > # [2] 1: 1 edges >> > >> > # [2] 0 <- 1 >> > >> > # [2] 3: 1 edges >> > >> > # [2] 1 <- 0 >> > >> > # [3] Roots referenced by my leaves, by rank >> > >> > # [3] 0: 2 edges >> > >> > # [3] 1 <- 0 >> > >> > # [3] 2 <- 2 >> > >> > # [3] 2: 1 edges >> > >> > # [3] 0 <- 1 >> > >> > # current flavor=CREATE synchronization=FENCE MultiSF >> sort=rank-order >> > >> > # current info=MPI_INFO_NULL >> > >> > # [buildhw-x86-09:1135574] *** An error occurred in MPI_Accumulate >> > >> > # [buildhw-x86-09:1135574] *** reported by process [3562602497,3] >> > >> > # [buildhw-x86-09:1135574] *** on win rdma window 4 >> > >> > # [buildhw-x86-09:1135574] *** MPI_ERR_RMA_RANGE: invalid RMA >> address >> > range >> > >> > # [buildhw-x86-09:1135574] *** MPI_ERRORS_ARE_FATAL (processes in >> > this win will now abort, >> > >> > # [buildhw-x86-09:1135574] *** and potentially your MPI job) >> > >> > # [buildhw-x86-09.iad2.fedoraproject.org:1135567] 3 more processes >> > have sent help message help-mpi-errors.txt / mpi_errors_are_fatal >> > >> > # [buildhw-x86-09.iad2.fedoraproject.org:1135567] Set MCA parameter >> > "orte_base_help_aggregate" to 0 to see all help / error messages >> > >> > Looks like an error related to OpenMPI-4*: >> > https://github.com/open-mpi/ompi/issues/6374 >> > >> >> -- >> --- >> Antonio Trande >> Fedora Project >> mailto: sagitter(a)fedoraproject.org >> GPG key: 0x29FBC85D7A51CC2F >> GPG key server: https://keyserver1.pgp.com/ > > > > -- > 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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Re: [petsc-dev] Cannot locate file: share/petsc/datafiles/matrices/small
by Pierre Jolivet 12 Sep '21

12 Sep '21

> On 12 Sep 2021, at 8:56 PM, Matthew Knepley <knepley(a)gmail.com> wrote: > > On Sun, Sep 12, 2021 at 2:49 PM Antonio T. sagitter <sagitter(a)fedoraproject.org <mailto:[email protected]>> 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 > Thanks, > > Matt > > On 9/12/21 19:18, Antonio T. sagitter wrote: > > Okay. I will try to set correctly the DATAFILESPATH options. > > > > I see even this error: > > > > not ok > > vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create # > > Error code: 68 > > > > # PetscSF Object: 4 MPI processes > > > > # type: window > > > > # [0] Number of roots=3, leaves=2, remote ranks=2 > > > > # [0] 0 <- (3,1) > > > > # [0] 1 <- (1,0) > > > > # [1] Number of roots=2, leaves=3, remote ranks=2 > > > > # [1] 0 <- (0,1) > > > > # [1] 1 <- (2,0) > > > > # [1] 2 <- (0,2) > > > > # [2] Number of roots=2, leaves=3, remote ranks=3 > > > > # [2] 0 <- (1,1) > > > > # [2] 1 <- (3,0) > > > > # [2] 2 <- (0,2) > > > > # [3] Number of roots=2, leaves=3, remote ranks=2 > > > > # [3] 0 <- (2,1) > > > > # [3] 1 <- (0,0) > > > > # [3] 2 <- (0,2) > > > > # [0] Roots referenced by my leaves, by rank > > > > # [0] 1: 1 edges > > > > # [0] 1 <- 0 > > > > # [0] 3: 1 edges > > > > # [0] 0 <- 1 > > > > # [1] Roots referenced by my leaves, by rank > > > > # [1] 0: 2 edges > > > > # [1] 0 <- 1 > > > > # [1] 2 <- 2 > > > > # [1] 2: 1 edges > > > > # [1] 1 <- 0 > > > > # [2] Roots referenced by my leaves, by rank > > > > # [2] 0: 1 edges > > > > # [2] 2 <- 2 > > > > # [2] 1: 1 edges > > > > # [2] 0 <- 1 > > > > # [2] 3: 1 edges > > > > # [2] 1 <- 0 > > > > # [3] Roots referenced by my leaves, by rank > > > > # [3] 0: 2 edges > > > > # [3] 1 <- 0 > > > > # [3] 2 <- 2 > > > > # [3] 2: 1 edges > > > > # [3] 0 <- 1 > > > > # current flavor=CREATE synchronization=FENCE MultiSF sort=rank-order > > > > # current info=MPI_INFO_NULL > > > > # [buildhw-x86-09:1135574] *** An error occurred in MPI_Accumulate > > > > # [buildhw-x86-09:1135574] *** reported by process [3562602497,3] > > > > # [buildhw-x86-09:1135574] *** on win rdma window 4 > > > > # [buildhw-x86-09:1135574] *** MPI_ERR_RMA_RANGE: invalid RMA address > > range > > > > # [buildhw-x86-09:1135574] *** MPI_ERRORS_ARE_FATAL (processes in > > this win will now abort, > > > > # [buildhw-x86-09:1135574] *** and potentially your MPI job) > > > > # [buildhw-x86-09.iad2.fedoraproject.org:1135567 <http://buildhw-x86-09.iad2.fedoraproject.org:1135567>] 3 more processes > > have sent help message help-mpi-errors.txt / mpi_errors_are_fatal > > > > # [buildhw-x86-09.iad2.fedoraproject.org:1135567 <http://buildhw-x86-09.iad2.fedoraproject.org:1135567>] Set MCA parameter > > "orte_base_help_aggregate" to 0 to see all help / error messages > > > > Looks like an error related to OpenMPI-4*: > > https://github.com/open-mpi/ompi/issues/6374 <https://github.com/open-mpi/ompi/issues/6374> > > > > -- > --- > Antonio Trande > Fedora Project > mailto: sagitter(a)fedoraproject.org <mailto:[email protected]> > GPG key: 0x29FBC85D7A51CC2F > GPG key server: https://keyserver1.pgp.com/ <https://keyserver1.pgp.com/> > > -- > 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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Re: [petsc-dev] Cannot locate file: share/petsc/datafiles/matrices/small
by Matthew Knepley 12 Sep '21

12 Sep '21

On Sun, Sep 12, 2021 at 2:49 PM Antonio T. sagitter < sagitter(a)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? Thanks, Matt > On 9/12/21 19:18, Antonio T. sagitter wrote: > > Okay. I will try to set correctly the DATAFILESPATH options. > > > > I see even this error: > > > > not ok > > vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create # > > Error code: 68 > > > > # PetscSF Object: 4 MPI processes > > > > # type: window > > > > # [0] Number of roots=3, leaves=2, remote ranks=2 > > > > # [0] 0 <- (3,1) > > > > # [0] 1 <- (1,0) > > > > # [1] Number of roots=2, leaves=3, remote ranks=2 > > > > # [1] 0 <- (0,1) > > > > # [1] 1 <- (2,0) > > > > # [1] 2 <- (0,2) > > > > # [2] Number of roots=2, leaves=3, remote ranks=3 > > > > # [2] 0 <- (1,1) > > > > # [2] 1 <- (3,0) > > > > # [2] 2 <- (0,2) > > > > # [3] Number of roots=2, leaves=3, remote ranks=2 > > > > # [3] 0 <- (2,1) > > > > # [3] 1 <- (0,0) > > > > # [3] 2 <- (0,2) > > > > # [0] Roots referenced by my leaves, by rank > > > > # [0] 1: 1 edges > > > > # [0] 1 <- 0 > > > > # [0] 3: 1 edges > > > > # [0] 0 <- 1 > > > > # [1] Roots referenced by my leaves, by rank > > > > # [1] 0: 2 edges > > > > # [1] 0 <- 1 > > > > # [1] 2 <- 2 > > > > # [1] 2: 1 edges > > > > # [1] 1 <- 0 > > > > # [2] Roots referenced by my leaves, by rank > > > > # [2] 0: 1 edges > > > > # [2] 2 <- 2 > > > > # [2] 1: 1 edges > > > > # [2] 0 <- 1 > > > > # [2] 3: 1 edges > > > > # [2] 1 <- 0 > > > > # [3] Roots referenced by my leaves, by rank > > > > # [3] 0: 2 edges > > > > # [3] 1 <- 0 > > > > # [3] 2 <- 2 > > > > # [3] 2: 1 edges > > > > # [3] 0 <- 1 > > > > # current flavor=CREATE synchronization=FENCE MultiSF > sort=rank-order > > > > # current info=MPI_INFO_NULL > > > > # [buildhw-x86-09:1135574] *** An error occurred in MPI_Accumulate > > > > # [buildhw-x86-09:1135574] *** reported by process [3562602497,3] > > > > # [buildhw-x86-09:1135574] *** on win rdma window 4 > > > > # [buildhw-x86-09:1135574] *** MPI_ERR_RMA_RANGE: invalid RMA address > > range > > > > # [buildhw-x86-09:1135574] *** MPI_ERRORS_ARE_FATAL (processes in > > this win will now abort, > > > > # [buildhw-x86-09:1135574] *** and potentially your MPI job) > > > > # [buildhw-x86-09.iad2.fedoraproject.org:1135567] 3 more processes > > have sent help message help-mpi-errors.txt / mpi_errors_are_fatal > > > > # [buildhw-x86-09.iad2.fedoraproject.org:1135567] Set MCA parameter > > "orte_base_help_aggregate" to 0 to see all help / error messages > > > > Looks like an error related to OpenMPI-4*: > > https://github.com/open-mpi/ompi/issues/6374 > > > > -- > --- > Antonio Trande > Fedora Project > mailto: sagitter(a)fedoraproject.org > GPG key: 0x29FBC85D7A51CC2F > GPG key server: https://keyserver1.pgp.com/ -- 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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Re: [petsc-dev] Cannot locate file: share/petsc/datafiles/matrices/small
by Antonio T. sagitter 12 Sep '21

12 Sep '21

Those attached are configure.log/make.log from a MPI build in Fedora 34 x86_64 where the error below occurred. On 9/12/21 19:18, Antonio T. sagitter wrote: > Okay. I will try to set correctly the DATAFILESPATH options. > > I see even this error: > > not ok > vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create # > Error code: 68 > > # PetscSF Object: 4 MPI processes > > # type: window > > # [0] Number of roots=3, leaves=2, remote ranks=2 > > # [0] 0 <- (3,1) > > # [0] 1 <- (1,0) > > # [1] Number of roots=2, leaves=3, remote ranks=2 > > # [1] 0 <- (0,1) > > # [1] 1 <- (2,0) > > # [1] 2 <- (0,2) > > # [2] Number of roots=2, leaves=3, remote ranks=3 > > # [2] 0 <- (1,1) > > # [2] 1 <- (3,0) > > # [2] 2 <- (0,2) > > # [3] Number of roots=2, leaves=3, remote ranks=2 > > # [3] 0 <- (2,1) > > # [3] 1 <- (0,0) > > # [3] 2 <- (0,2) > > # [0] Roots referenced by my leaves, by rank > > # [0] 1: 1 edges > > # [0] 1 <- 0 > > # [0] 3: 1 edges > > # [0] 0 <- 1 > > # [1] Roots referenced by my leaves, by rank > > # [1] 0: 2 edges > > # [1] 0 <- 1 > > # [1] 2 <- 2 > > # [1] 2: 1 edges > > # [1] 1 <- 0 > > # [2] Roots referenced by my leaves, by rank > > # [2] 0: 1 edges > > # [2] 2 <- 2 > > # [2] 1: 1 edges > > # [2] 0 <- 1 > > # [2] 3: 1 edges > > # [2] 1 <- 0 > > # [3] Roots referenced by my leaves, by rank > > # [3] 0: 2 edges > > # [3] 1 <- 0 > > # [3] 2 <- 2 > > # [3] 2: 1 edges > > # [3] 0 <- 1 > > # current flavor=CREATE synchronization=FENCE MultiSF sort=rank-order > > # current info=MPI_INFO_NULL > > # [buildhw-x86-09:1135574] *** An error occurred in MPI_Accumulate > > # [buildhw-x86-09:1135574] *** reported by process [3562602497,3] > > # [buildhw-x86-09:1135574] *** on win rdma window 4 > > # [buildhw-x86-09:1135574] *** MPI_ERR_RMA_RANGE: invalid RMA address > range > > # [buildhw-x86-09:1135574] *** MPI_ERRORS_ARE_FATAL (processes in > this win will now abort, > > # [buildhw-x86-09:1135574] *** and potentially your MPI job) > > # [buildhw-x86-09.iad2.fedoraproject.org:1135567] 3 more processes > have sent help message help-mpi-errors.txt / mpi_errors_are_fatal > > # [buildhw-x86-09.iad2.fedoraproject.org:1135567] Set MCA parameter > "orte_base_help_aggregate" to 0 to see all help / error messages > > Looks like an error related to OpenMPI-4*: > https://github.com/open-mpi/ompi/issues/6374 > -- --- Antonio Trande Fedora Project mailto: sagitter(a)fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/

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Re: [petsc-dev] Cannot locate file: share/petsc/datafiles/matrices/small
by Pierre Jolivet 12 Sep '21

12 Sep '21

Could you please forward configure.log to petsc-maint(a)mcs.anl.gov <mailto:[email protected]>? It’ll help the SF people figure out if it’s a false positive or if something needs fixing. Thanks, Pierre > On 12 Sep 2021, at 7:33 PM, Antonio T. sagitter <sagitter(a)fedoraproject.org> wrote: > > On 9/12/21 19:29, Pierre Jolivet wrote: >> In your configure.log, I see --with-mpi=0, so I’m surprised this is even running, and even more surprised that you are encountering OpenMPI errors. >> Is this from a different build? > > Yes, sorry. This is another build with MPI. > >> Thanks, >> Pierre >>> On 12 Sep 2021, at 7:18 PM, Antonio T. sagitter <sagitter(a)fedoraproject.org> wrote: >>> >>> Okay. I will try to set correctly the DATAFILESPATH options. >>> >>> I see even this error: >>> >>> not ok vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create # Error code: 68 >>> >>> # PetscSF Object: 4 MPI processes >>> >>> # type: window >>> >>> # [0] Number of roots=3, leaves=2, remote ranks=2 >>> >>> # [0] 0 <- (3,1) >>> >>> # [0] 1 <- (1,0) >>> >>> # [1] Number of roots=2, leaves=3, remote ranks=2 >>> >>> # [1] 0 <- (0,1) >>> >>> # [1] 1 <- (2,0) >>> >>> # [1] 2 <- (0,2) >>> >>> # [2] Number of roots=2, leaves=3, remote ranks=3 >>> >>> # [2] 0 <- (1,1) >>> >>> # [2] 1 <- (3,0) >>> >>> # [2] 2 <- (0,2) >>> >>> # [3] Number of roots=2, leaves=3, remote ranks=2 >>> >>> # [3] 0 <- (2,1) >>> >>> # [3] 1 <- (0,0) >>> >>> # [3] 2 <- (0,2) >>> >>> # [0] Roots referenced by my leaves, by rank >>> >>> # [0] 1: 1 edges >>> >>> # [0] 1 <- 0 >>> >>> # [0] 3: 1 edges >>> >>> # [0] 0 <- 1 >>> >>> # [1] Roots referenced by my leaves, by rank >>> >>> # [1] 0: 2 edges >>> >>> # [1] 0 <- 1 >>> >>> # [1] 2 <- 2 >>> >>> # [1] 2: 1 edges >>> >>> # [1] 1 <- 0 >>> >>> # [2] Roots referenced by my leaves, by rank >>> >>> # [2] 0: 1 edges >>> >>> # [2] 2 <- 2 >>> >>> # [2] 1: 1 edges >>> >>> # [2] 0 <- 1 >>> >>> # [2] 3: 1 edges >>> >>> # [2] 1 <- 0 >>> >>> # [3] Roots referenced by my leaves, by rank >>> >>> # [3] 0: 2 edges >>> >>> # [3] 1 <- 0 >>> >>> # [3] 2 <- 2 >>> >>> # [3] 2: 1 edges >>> >>> # [3] 0 <- 1 >>> >>> # current flavor=CREATE synchronization=FENCE MultiSF sort=rank-order >>> >>> # current info=MPI_INFO_NULL >>> >>> # [buildhw-x86-09:1135574] *** An error occurred in MPI_Accumulate >>> >>> # [buildhw-x86-09:1135574] *** reported by process [3562602497,3] >>> >>> # [buildhw-x86-09:1135574] *** on win rdma window 4 >>> >>> # [buildhw-x86-09:1135574] *** MPI_ERR_RMA_RANGE: invalid RMA address range >>> >>> # [buildhw-x86-09:1135574] *** MPI_ERRORS_ARE_FATAL (processes in this win will now abort, >>> >>> # [buildhw-x86-09:1135574] *** and potentially your MPI job) >>> >>> # [buildhw-x86-09.iad2.fedoraproject.org:1135567] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal >>> >>> # [buildhw-x86-09.iad2.fedoraproject.org:1135567] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages >>> >>> Looks like an error related to OpenMPI-4*: >>> https://github.com/open-mpi/ompi/issues/6374 >>> >>> Thank you. >>> >>> On 9/12/21 18:09, Pierre Jolivet wrote: >>>> Hello, >>>> Did you copy the files from https://gitlab.com/petsc/datafiles <https://gitlab.com/petsc/datafiles> before the make check? >>>> cfd.1.10 is not part of https://gitlab.com/petsc/petsc <https://gitlab.com/petsc/petsc>, so you either need to copy the files from the datafiles repository, or remove the --DATAFILESPATH=/home/sagitter/rpmbuild/BUILD/petsc-3.15.4/petsc-3.15.4/share/petsc/datafiles configure option. >>>> Thanks, >>>> Pierre >>>>> On 12 Sep 2021, at 6:02 PM, Antonio T. sagitter <sagitter(a)fedoraproject.org <mailto:[email protected]>> wrote: >>>>> >>>>> Hi all. >>>>> >>>>> This error is repeated when the tests are compiled in PETSc-3.15.4 compilation: >>>>> https://paste.in/MhdNjf <https://paste.in/MhdNjf> >>>>> >>>>> This happens in Fedora 34 x86_64 with gcc-11.2.1 >>>>> >>>>> make.log and configure.log are attached >>>>> -- >>>>> --- >>>>> Antonio Trande >>>>> Fedora Project >>>>> mailto: sagitter(a)fedoraproject.org >>>>> GPG key: 0x29FBC85D7A51CC2F >>>>> GPG key server: https://keyserver1.pgp.com/ >>>>> <make_configure.zip><OpenPGP_0x29FBC85D7A51CC2F.asc> >>> >>> -- >>> --- >>> Antonio Trande >>> Fedora Project >>> mailto: sagitter(a)fedoraproject.org >>> GPG key: 0x29FBC85D7A51CC2F >>> GPG key server: https://keyserver1.pgp.com/ > > -- > --- > Antonio Trande > Fedora Project > mailto: sagitter(a)fedoraproject.org > GPG key: 0x29FBC85D7A51CC2F > GPG key server: https://keyserver1.pgp.com/

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Re: [petsc-dev] Cannot locate file: share/petsc/datafiles/matrices/small
by Antonio T. sagitter 12 Sep '21

12 Sep '21

On 9/12/21 19:29, Pierre Jolivet wrote: > In your configure.log, I see --with-mpi=0, so I’m surprised this is even running, and even more surprised that you are encountering OpenMPI errors. > Is this from a different build? > Yes, sorry. This is another build with MPI. > Thanks, > Pierre > >> On 12 Sep 2021, at 7:18 PM, Antonio T. sagitter <sagitter(a)fedoraproject.org> wrote: >> >> Okay. I will try to set correctly the DATAFILESPATH options. >> >> I see even this error: >> >> not ok vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create # Error code: 68 >> >> # PetscSF Object: 4 MPI processes >> >> # type: window >> >> # [0] Number of roots=3, leaves=2, remote ranks=2 >> >> # [0] 0 <- (3,1) >> >> # [0] 1 <- (1,0) >> >> # [1] Number of roots=2, leaves=3, remote ranks=2 >> >> # [1] 0 <- (0,1) >> >> # [1] 1 <- (2,0) >> >> # [1] 2 <- (0,2) >> >> # [2] Number of roots=2, leaves=3, remote ranks=3 >> >> # [2] 0 <- (1,1) >> >> # [2] 1 <- (3,0) >> >> # [2] 2 <- (0,2) >> >> # [3] Number of roots=2, leaves=3, remote ranks=2 >> >> # [3] 0 <- (2,1) >> >> # [3] 1 <- (0,0) >> >> # [3] 2 <- (0,2) >> >> # [0] Roots referenced by my leaves, by rank >> >> # [0] 1: 1 edges >> >> # [0] 1 <- 0 >> >> # [0] 3: 1 edges >> >> # [0] 0 <- 1 >> >> # [1] Roots referenced by my leaves, by rank >> >> # [1] 0: 2 edges >> >> # [1] 0 <- 1 >> >> # [1] 2 <- 2 >> >> # [1] 2: 1 edges >> >> # [1] 1 <- 0 >> >> # [2] Roots referenced by my leaves, by rank >> >> # [2] 0: 1 edges >> >> # [2] 2 <- 2 >> >> # [2] 1: 1 edges >> >> # [2] 0 <- 1 >> >> # [2] 3: 1 edges >> >> # [2] 1 <- 0 >> >> # [3] Roots referenced by my leaves, by rank >> >> # [3] 0: 2 edges >> >> # [3] 1 <- 0 >> >> # [3] 2 <- 2 >> >> # [3] 2: 1 edges >> >> # [3] 0 <- 1 >> >> # current flavor=CREATE synchronization=FENCE MultiSF sort=rank-order >> >> # current info=MPI_INFO_NULL >> >> # [buildhw-x86-09:1135574] *** An error occurred in MPI_Accumulate >> >> # [buildhw-x86-09:1135574] *** reported by process [3562602497,3] >> >> # [buildhw-x86-09:1135574] *** on win rdma window 4 >> >> # [buildhw-x86-09:1135574] *** MPI_ERR_RMA_RANGE: invalid RMA address range >> >> # [buildhw-x86-09:1135574] *** MPI_ERRORS_ARE_FATAL (processes in this win will now abort, >> >> # [buildhw-x86-09:1135574] *** and potentially your MPI job) >> >> # [buildhw-x86-09.iad2.fedoraproject.org:1135567] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal >> >> # [buildhw-x86-09.iad2.fedoraproject.org:1135567] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages >> >> Looks like an error related to OpenMPI-4*: >> https://github.com/open-mpi/ompi/issues/6374 >> >> Thank you. >> >> On 9/12/21 18:09, Pierre Jolivet wrote: >>> Hello, >>> Did you copy the files from https://gitlab.com/petsc/datafiles <https://gitlab.com/petsc/datafiles> before the make check? >>> cfd.1.10 is not part of https://gitlab.com/petsc/petsc <https://gitlab.com/petsc/petsc>, so you either need to copy the files from the datafiles repository, or remove the --DATAFILESPATH=/home/sagitter/rpmbuild/BUILD/petsc-3.15.4/petsc-3.15.4/share/petsc/datafiles configure option. >>> Thanks, >>> Pierre >>>> On 12 Sep 2021, at 6:02 PM, Antonio T. sagitter <sagitter(a)fedoraproject.org <mailto:[email protected]>> wrote: >>>> >>>> Hi all. >>>> >>>> This error is repeated when the tests are compiled in PETSc-3.15.4 compilation: >>>> https://paste.in/MhdNjf <https://paste.in/MhdNjf> >>>> >>>> This happens in Fedora 34 x86_64 with gcc-11.2.1 >>>> >>>> make.log and configure.log are attached >>>> -- >>>> --- >>>> Antonio Trande >>>> Fedora Project >>>> mailto: sagitter(a)fedoraproject.org >>>> GPG key: 0x29FBC85D7A51CC2F >>>> GPG key server: https://keyserver1.pgp.com/ >>>> <make_configure.zip><OpenPGP_0x29FBC85D7A51CC2F.asc> >> >> -- >> --- >> Antonio Trande >> Fedora Project >> mailto: sagitter(a)fedoraproject.org >> GPG key: 0x29FBC85D7A51CC2F >> GPG key server: https://keyserver1.pgp.com/ > -- --- Antonio Trande Fedora Project mailto: sagitter(a)fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/

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Re: [petsc-dev] Cannot locate file: share/petsc/datafiles/matrices/small
by Pierre Jolivet 12 Sep '21

12 Sep '21

In your configure.log, I see --with-mpi=0, so I’m surprised this is even running, and even more surprised that you are encountering OpenMPI errors. Is this from a different build? Thanks, Pierre > On 12 Sep 2021, at 7:18 PM, Antonio T. sagitter <sagitter(a)fedoraproject.org> wrote: > > Okay. I will try to set correctly the DATAFILESPATH options. > > I see even this error: > > not ok vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create # Error code: 68 > > # PetscSF Object: 4 MPI processes > > # type: window > > # [0] Number of roots=3, leaves=2, remote ranks=2 > > # [0] 0 <- (3,1) > > # [0] 1 <- (1,0) > > # [1] Number of roots=2, leaves=3, remote ranks=2 > > # [1] 0 <- (0,1) > > # [1] 1 <- (2,0) > > # [1] 2 <- (0,2) > > # [2] Number of roots=2, leaves=3, remote ranks=3 > > # [2] 0 <- (1,1) > > # [2] 1 <- (3,0) > > # [2] 2 <- (0,2) > > # [3] Number of roots=2, leaves=3, remote ranks=2 > > # [3] 0 <- (2,1) > > # [3] 1 <- (0,0) > > # [3] 2 <- (0,2) > > # [0] Roots referenced by my leaves, by rank > > # [0] 1: 1 edges > > # [0] 1 <- 0 > > # [0] 3: 1 edges > > # [0] 0 <- 1 > > # [1] Roots referenced by my leaves, by rank > > # [1] 0: 2 edges > > # [1] 0 <- 1 > > # [1] 2 <- 2 > > # [1] 2: 1 edges > > # [1] 1 <- 0 > > # [2] Roots referenced by my leaves, by rank > > # [2] 0: 1 edges > > # [2] 2 <- 2 > > # [2] 1: 1 edges > > # [2] 0 <- 1 > > # [2] 3: 1 edges > > # [2] 1 <- 0 > > # [3] Roots referenced by my leaves, by rank > > # [3] 0: 2 edges > > # [3] 1 <- 0 > > # [3] 2 <- 2 > > # [3] 2: 1 edges > > # [3] 0 <- 1 > > # current flavor=CREATE synchronization=FENCE MultiSF sort=rank-order > > # current info=MPI_INFO_NULL > > # [buildhw-x86-09:1135574] *** An error occurred in MPI_Accumulate > > # [buildhw-x86-09:1135574] *** reported by process [3562602497,3] > > # [buildhw-x86-09:1135574] *** on win rdma window 4 > > # [buildhw-x86-09:1135574] *** MPI_ERR_RMA_RANGE: invalid RMA address range > > # [buildhw-x86-09:1135574] *** MPI_ERRORS_ARE_FATAL (processes in this win will now abort, > > # [buildhw-x86-09:1135574] *** and potentially your MPI job) > > # [buildhw-x86-09.iad2.fedoraproject.org:1135567] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal > > # [buildhw-x86-09.iad2.fedoraproject.org:1135567] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages > > Looks like an error related to OpenMPI-4*: > https://github.com/open-mpi/ompi/issues/6374 > > Thank you. > > On 9/12/21 18:09, Pierre Jolivet wrote: >> Hello, >> Did you copy the files from https://gitlab.com/petsc/datafiles <https://gitlab.com/petsc/datafiles> before the make check? >> cfd.1.10 is not part of https://gitlab.com/petsc/petsc <https://gitlab.com/petsc/petsc>, so you either need to copy the files from the datafiles repository, or remove the --DATAFILESPATH=/home/sagitter/rpmbuild/BUILD/petsc-3.15.4/petsc-3.15.4/share/petsc/datafiles configure option. >> Thanks, >> Pierre >>> On 12 Sep 2021, at 6:02 PM, Antonio T. sagitter <sagitter(a)fedoraproject.org <mailto:[email protected]>> wrote: >>> >>> Hi all. >>> >>> This error is repeated when the tests are compiled in PETSc-3.15.4 compilation: >>> https://paste.in/MhdNjf <https://paste.in/MhdNjf> >>> >>> This happens in Fedora 34 x86_64 with gcc-11.2.1 >>> >>> make.log and configure.log are attached >>> -- >>> --- >>> Antonio Trande >>> Fedora Project >>> mailto: sagitter(a)fedoraproject.org >>> GPG key: 0x29FBC85D7A51CC2F >>> GPG key server: https://keyserver1.pgp.com/ >>> <make_configure.zip><OpenPGP_0x29FBC85D7A51CC2F.asc> > > -- > --- > Antonio Trande > Fedora Project > mailto: sagitter(a)fedoraproject.org > GPG key: 0x29FBC85D7A51CC2F > GPG key server: https://keyserver1.pgp.com/

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Re: [petsc-dev] Cannot locate file: share/petsc/datafiles/matrices/small
by Antonio T. sagitter 12 Sep '21

12 Sep '21

Okay. I will try to set correctly the DATAFILESPATH options. I see even this error: not ok vec_is_sf_tutorials-ex1_4+sf_window_sync-fence_sf_window_flavor-create # Error code: 68 # PetscSF Object: 4 MPI processes # type: window # [0] Number of roots=3, leaves=2, remote ranks=2 # [0] 0 <- (3,1) # [0] 1 <- (1,0) # [1] Number of roots=2, leaves=3, remote ranks=2 # [1] 0 <- (0,1) # [1] 1 <- (2,0) # [1] 2 <- (0,2) # [2] Number of roots=2, leaves=3, remote ranks=3 # [2] 0 <- (1,1) # [2] 1 <- (3,0) # [2] 2 <- (0,2) # [3] Number of roots=2, leaves=3, remote ranks=2 # [3] 0 <- (2,1) # [3] 1 <- (0,0) # [3] 2 <- (0,2) # [0] Roots referenced by my leaves, by rank # [0] 1: 1 edges # [0] 1 <- 0 # [0] 3: 1 edges # [0] 0 <- 1 # [1] Roots referenced by my leaves, by rank # [1] 0: 2 edges # [1] 0 <- 1 # [1] 2 <- 2 # [1] 2: 1 edges # [1] 1 <- 0 # [2] Roots referenced by my leaves, by rank # [2] 0: 1 edges # [2] 2 <- 2 # [2] 1: 1 edges # [2] 0 <- 1 # [2] 3: 1 edges # [2] 1 <- 0 # [3] Roots referenced by my leaves, by rank # [3] 0: 2 edges # [3] 1 <- 0 # [3] 2 <- 2 # [3] 2: 1 edges # [3] 0 <- 1 # current flavor=CREATE synchronization=FENCE MultiSF sort=rank-order # current info=MPI_INFO_NULL # [buildhw-x86-09:1135574] *** An error occurred in MPI_Accumulate # [buildhw-x86-09:1135574] *** reported by process [3562602497,3] # [buildhw-x86-09:1135574] *** on win rdma window 4 # [buildhw-x86-09:1135574] *** MPI_ERR_RMA_RANGE: invalid RMA address range # [buildhw-x86-09:1135574] *** MPI_ERRORS_ARE_FATAL (processes in this win will now abort, # [buildhw-x86-09:1135574] *** and potentially your MPI job) # [buildhw-x86-09.iad2.fedoraproject.org:1135567] 3 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal # [buildhw-x86-09.iad2.fedoraproject.org:1135567] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages Looks like an error related to OpenMPI-4*: https://github.com/open-mpi/ompi/issues/6374 Thank you. On 9/12/21 18:09, Pierre Jolivet wrote: > Hello, > Did you copy the files from https://gitlab.com/petsc/datafiles > <https://gitlab.com/petsc/datafiles> before the make check? > cfd.1.10 is not part of https://gitlab.com/petsc/petsc > <https://gitlab.com/petsc/petsc>, so you either need to copy the files > from the datafiles repository, or remove > the --DATAFILESPATH=/home/sagitter/rpmbuild/BUILD/petsc-3.15.4/petsc-3.15.4/share/petsc/datafiles > configure option. > > Thanks, > Pierre > >> On 12 Sep 2021, at 6:02 PM, Antonio T. sagitter >> <sagitter(a)fedoraproject.org <mailto:[email protected]>> wrote: >> >> Hi all. >> >> This error is repeated when the tests are compiled in PETSc-3.15.4 >> compilation: >> https://paste.in/MhdNjf <https://paste.in/MhdNjf> >> >> This happens in Fedora 34 x86_64 with gcc-11.2.1 >> >> make.log and configure.log are attached >> -- >> --- >> Antonio Trande >> Fedora Project >> mailto: sagitter(a)fedoraproject.org >> GPG key: 0x29FBC85D7A51CC2F >> GPG key server: https://keyserver1.pgp.com/ >> <make_configure.zip><OpenPGP_0x29FBC85D7A51CC2F.asc> > -- --- Antonio Trande Fedora Project mailto: sagitter(a)fedoraproject.org GPG key: 0x29FBC85D7A51CC2F GPG key server: https://keyserver1.pgp.com/

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