[petsc-users] petsc on Cori Haswell

[Mark Adams]

Also, can anyone recommend a highly scalable test problem that Treb can run
with 64K cores?
Thanks,

On Wed, Apr 15, 2020 at 4:41 PM Mark Adams <mfadams at lbl.gov> wrote:

> 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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