I want to know who called MPI_Init(). Petsc or Chombo? --Junchao Zhang
On Wed, Apr 15, 2020 at 4:13 PM Matthew Knepley <knep...@gmail.com> wrote: > 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/> >
