[petsc-users] matcreate and assembly issue

[Satish Balay]

On Thu, 11 Jun 2020, Karl Lin 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?

yes. you can use a different PETSC_ARCH for this build - so that both builds are usable [by just switching PETSC_ARCH from your appliation makefile]

Satish

> 
> 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/>
> >
>