[petsc-users] petsc on Cori Haswell

[Mark Adams]

Whoops, this is actually Cori-KNL.

On Wed, Apr 15, 2020 at 4:33 PM Mark Adams <mfadams at 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 <dptrebotich at lbl.gov>
> Date: Wed, Apr 15, 2020 at 4:20 PM
> Subject: Re: petsc on Cori Haswell
> To: Mark Adams <mfadams at 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
>
>
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