[petsc-users] matcreate and assembly issue

[Matthew Knepley]

On Thu, Jun 11, 2020 at 12:52 PM Karl Lin <karl.linkui at gmail.com> wrote:

> Hi, Matthew
>
> Thanks for the suggestion, just did another run and here are some detailed
> stack traces, maybe will provide some more insight:
>  *** Process received signal ***
> Signal: Aborted (6)
> Signal code:  (-6)
> /lib64/libpthread.so.0(+0xf5f0)[0x2b56c46dc5f0]
>  [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2b56c5486337]
>  [ 2] /lib64/libc.so.6(abort+0x148)[0x2b56c5487a28]
>  [ 3] /libpetsc.so.3.10(PetscTraceBackErrorHandler+0xc4)[0x2b56c1e6a2d4]
>  [ 4] /libpetsc.so.3.10(PetscError+0x1b5)[0x2b56c1e69f65]
>  [ 5] /libpetsc.so.3.10(PetscCommBuildTwoSidedFReq+0x19f0)[0x2b56c1e03cf0]
>  [ 6] /libpetsc.so.3.10(+0x77db17)[0x2b56c2425b17]
>  [ 7] /libpetsc.so.3.10(+0x77a164)[0x2b56c2422164]
>  [ 8] /libpetsc.so.3.10(MatAssemblyBegin_MPIAIJ+0x36)[0x2b56c23912b6]
>  [ 9] /libpetsc.so.3.10(MatAssemblyBegin+0xca)[0x2b56c1feccda]
>
> By reconfiguring, you mean recompiling petsc with that option, correct?
>

Reconfiguring.

  Thanks,

    Matt


> Thank you.
>
> Karl
>
> On Thu, Jun 11, 2020 at 10:56 AM Matthew Knepley <knepley at gmail.com>
> wrote:
>
>> On Thu, Jun 11, 2020 at 11:51 AM Karl Lin <karl.linkui at gmail.com> wrote:
>>
>>> Hi, there
>>>
>>> We have written a program using Petsc to solve large sparse matrix
>>> system. It has been working fine for a while. Recently we encountered a
>>> problem when the size of the sparse matrix is larger than 10TB. We used
>>> several hundred nodes and 2200 processes. The program always crashes during
>>> MatAssemblyBegin.Upon a closer look, there seems to be something unusual.
>>> We have a little memory check during loading the matrix to keep track of
>>> rss. The printout of rss in the log shows normal increase up to rank 2160,
>>> i.e., if we load in a portion of matrix that is 1GB, after MatSetValues for
>>> that portion, rss will increase roughly about that number. From rank 2161
>>> onwards, the rss in every rank doesn't increase after matrix loaded. Then
>>> comes MatAssemblyBegin, the program crashed on rank 2160.
>>>
>>> Is there a upper limit on the number of processes Petsc can handle?
>>> or is there a upper limit in terms of the size of the matrix petsc can
>>> handle? Thank you very much for any info.
>>>
>>
>> It sounds like you overflowed int somewhere. We try and check for this,
>> but catching every place is hard. Try reconfiguring with
>>
>>   --with-64-bit-indices
>>
>>   Thanks,
>>
>>      Matt
>>
>>
>>> Regards,
>>>
>>> Karl
>>>
>>
>>
>> --
>> 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/>
>>
>

-- 
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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