[petsc-users] petsc on Cori Haswell

[Matthew Knepley]

On Wed, Apr 15, 2020 at 5:10 PM Junchao Zhang <junchao.zhang at 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 <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
>>>
>>>

-- 
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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