[petsc-users] [Ext] Re: matcreate and assembly issue

Thu Jul 2 23:40:28 CDT 2020

Karl,

Are you taking into account that every "integer" index might be 64 bits instead of 32 bits, depending on the PETSc configuration / compilation choices for PetscInt?

Ernesto.

From: petsc-users [mailto:petsc-users-bounces at mcs.anl.gov] On Behalf Of Junchao Zhang
Sent: Thursday, July 2, 2020 11:21 PM
To: Karl Lin <karl.linkui at gmail.com>
Cc: PETSc users list <petsc-users at mcs.anl.gov>
Subject: [Ext] Re: [petsc-users] matcreate and assembly issue

Is it because indices for the nonzeros also need memory?
--Junchao Zhang

On Thu, Jul 2, 2020 at 10:04 PM Karl Lin <karl.linkui at gmail.com<mailto:karl.linkui at gmail.com>> wrote:
Hi, Matthew

Thanks for the reply. However, I don't really get why additional malloc would double the memory footprint. If I know there is only 1GB matrix being loaded, there shouldn't be 2GB memory occupied even if Petsc needs to allocate more space.

regards,

Karl

On Thu, Jul 2, 2020 at 8:10 PM Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>> wrote:
On Thu, Jul 2, 2020 at 7:30 PM Karl Lin <karl.linkui at gmail.com<mailto:karl.linkui at gmail.com>> wrote:
Hi, Matt

Thanks for the tip last time. We just encountered another issue with large data sets. This time the behavior is the opposite from last time. The data is 13.5TB, the total number of matrix columns is 2.4 billion. Our program crashed during matrix loading due to memory overflow in one node. As said before, 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 in many nodes, i.e., if we load in a portion of the matrix that is 1GB, after MatSetValues for that portion, rss will increase roughly about 1GB. On the node that has memory overflow, the rss increased by 2GB after only 1GB of matrix is loaded through MatSetValues. We are very puzzled by this. What could make the memory footprint twice as much as needed? Thanks in advance for any insight.

The only way I can imagine this happening is that you have not preallocated correctly, so that some values are causing additional mallocs.

  Thanks,

     Matt

Regards,

Karl

On Thu, Jun 11, 2020 at 12:00 PM Matthew Knepley <knepley at gmail.com<mailto:knepley at gmail.com>> wrote:
On Thu, Jun 11, 2020 at 12:52 PM Karl Lin <karl.linkui at gmail.com<mailto: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<mailto:knepley at gmail.com>> wrote:
On Thu, Jun 11, 2020 at 11:51 AM Karl Lin <karl.linkui at gmail.com<mailto: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

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--
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

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--
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/<https://urldefense.com/v3/__http:/www.cse.buffalo.edu/*knepley/__;fg!!Kjv0uj3L4nM6H-I!1KBn92fUc-8pAvJy257WTFoHD80IUf6u5iIhyL_vrliEm3psAK4KAJFCdygnPA$>

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