On Wed, Apr 15, 2020 at 5:10 PM Junchao Zhang <junchao.zh...@gmail.com> wrote:
> Was there a petsc error stack? > 1) SNES ex5 is a highly scalable problem. Just give it large enough m and n. 2) Junchao, it looks like MPI_Init() is failing, which I believe comes before we install our signal handler to get us the stack. Thanks, Matt > --Junchao Zhang > > > On Wed, Apr 15, 2020 at 3:41 PM Mark Adams <mfad...@lbl.gov> wrote: > >> Whoops, this is actually Cori-KNL. >> >> On Wed, Apr 15, 2020 at 4:33 PM Mark Adams <mfad...@lbl.gov> wrote: >> >>> We have a problem when going from 32K to 64K cores on Cori-haswell. >>> Does Anyone have any thoughts? >>> Thanks, >>> Mark >>> >>> ---------- Forwarded message --------- >>> From: David Trebotich <dptrebot...@lbl.gov> >>> Date: Wed, Apr 15, 2020 at 4:20 PM >>> Subject: Re: petsc on Cori Haswell >>> To: Mark Adams <mfad...@lbl.gov> >>> >>> >>> Hey Mark- >>> I am running into some issues that I am convinced are from the PETSc >>> build. I am able to build and run on up to 32K cores. At 64K I start >>> getting stuff like below (looks like two issues: pmi stuff and MPI_Init). I >>> have been working with Brian Freisen to see if it's a NERSC problem. At >>> this point I build without PETSc and then run native gmg in Chombo and have >>> no problems. The problems only come with building with PETSc, and at larger >>> concurrencies. The only thing that has changed is that this is a new PETSc >>> installation. Perhaps something changed in the PETSc version you built from >>> previously? Thanks for the help. >>> Treb >>> >>> Mon Apr 13 17:49:45 2020: [PE_101955]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=33, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_101958]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=33, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_101958]:_pmi_init:_pmi_mmap_init returned >>> -1 >>> Mon Apr 13 17:49:45 2020: [PE_101979]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=33, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_101979]:_pmi_init:_pmi_mmap_init returned >>> -1 >>> Mon Apr 13 17:49:45 2020: [PE_82712]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=28, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_17868]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=32, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_97918]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=33, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_17869]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=32, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_17869]:_pmi_init:_pmi_mmap_init returned -1 >>> Mon Apr 13 17:49:45 2020: [PE_110562]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=27, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_110562]:_pmi_init:_pmi_mmap_init returned >>> -1 >>> Mon Apr 13 17:49:45 2020: [PE_110563]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=27, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_27899]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=38, pes_this_node=64, timeout=180 secs >>> [Mon Apr 13 17:49:45 2020] [c7-4c1s6n0] Fatal error in MPI_Init: Other >>> MPI error, error stack: >>> MPIR_Init_thread(537): >>> MPID_Init(246).......: channel initialization failed >>> MPID_Init(647).......: PMI2 init failed: 1 >>> Attempting to use an MPI routine before initializing MPICH >>> [Mon Apr 13 17:49:45 2020] [c7-4c1s6n0] Fatal error in MPI_Init: Other >>> MPI error, error stack: >>> MPIR_Init_thread(537): >>> MPID_Init(246).......: channel initialization failed >>> MPID_Init(647).......: PMI2 init failed: 1 >>> Attempting to use an MPI routine before initializing MPICH >>> Mon Apr 13 17:49:45 2020: [PE_71961]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=35, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_71961]:_pmi_init:_pmi_mmap_init returned -1 >>> Mon Apr 13 17:49:45 2020: [PE_71962]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=35, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_64329]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=32, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_64335]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=32, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_64335]:_pmi_init:_pmi_mmap_init returned -1 >>> [Mon Apr 13 17:49:45 2020] [c6-1c2s5n2] Fatal error in MPI_Init: Other >>> MPI error, error stack: >>> MPIR_Init_thread(537): >>> MPID_Init(246).......: channel initialization failed >>> MPID_Init(647).......: PMI2 init failed: 1 >>> Attempting to use an MPI routine before initializing MPICH >>> [Mon Apr 13 17:49:45 2020] [c9-4c2s13n2] Fatal error in MPI_Init: Other >>> MPI error, error stack: >>> MPIR_Init_thread(537): >>> MPID_Init(246).......: channel initialization failed >>> MPID_Init(647).......: PMI2 init failed: 1 >>> Attempting to use an MPI routine before initializing MPICH >>> Mon Apr 13 17:49:45 2020: [PE_71960]:_pmi_mmap_tmp: Warning bootstrap >>> barrier failed: num_syncd=35, pes_this_node=64, timeout=180 secs >>> Mon Apr 13 17:49:45 2020: [PE_71960]:_pmi_init:_pmi_mmap_init returned -1 >>> [Mon Apr 13 17:49:45 2020] [c6-3c2s9n1] Fatal error in MPI_Init: Other >>> MPI error, error stack: >>> MPIR_Init_thread(537): >>> MPID_Init(246).......: channel initialization failed >>> >>> -- 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/>