[petsc-users] [Ext] Re: matcreate and assembly issue
Matthew Knepley
knepley at gmail.com
Fri Jul 3 10:57:21 CDT 2020
On Fri, Jul 3, 2020 at 11:38 AM Karl Lin <karl.linkui at gmail.com> wrote:
> Hi, Barry
>
> Thanks for the explanation. Following your tip, I have a guess. We use
> MatCreateAIJ to create the matrix, I believe this call will preallocate as
> well. Before this call we figure out the number of nonzeros per row for all
> rows and put those number in an array, say numNonZero. We pass numNonZero
> as d_nnz and o_nnz to MatCreateAIJ call, so essentially we preallocate
> twice as much as needed. For the process that double the memory footprint
> and crashed, there are a lot of values in both the diagonal and
> off-diagonal part for the process, so the temporary space gets filled up
> for both diagonal and off-diagonal parts of the matrix, also there are
> unused temporary space until MatAssembly, so gradually fill up the
> preallocated space which doubles the memory footprint. Once MatAssembly is
> done, the unused temporary space gets squeezed out, we return the correct
> memory footprint of the matrix. But before MatAssembly, large amount of
> unused temporary space needs to be kept because of the diagonal and
> off-diagonal pattern of the input. Would you say this is a plausible
> explanation? thank you.
>
Yes. We find that it takes a very small amount of time to just loop over
the insertion twice, the first time counting the nonzeros. We built
something to do this for you:
https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/MatPreallocatorPreallocate.html
Thanks,
Matt
> Regards,
>
> Karl
>
> On Fri, Jul 3, 2020 at 9:50 AM Barry Smith <bsmith at petsc.dev> wrote:
>
>>
>> Karl,
>>
>> If a particular process is receiving values with MatSetValues() that
>> belong to a different process it needs to allocate temporary space for
>> those values. If there are many values destined for a different process
>> this space can be arbitrarily large. The values are not pass to the final
>> owning process until the MatAssemblyBegin/End calls.
>>
>> If you have not preallocated enough room the matrix actually makes a
>> complete copy of itself with extra space for additional values, copies the
>> values over and then deletes the old matrix this the memory use can double
>> when the preallocation is not correct.
>>
>>
>> Barry
>>
>>
>> On Jul 3, 2020, at 9:44 AM, Karl Lin <karl.linkui at gmail.com> wrote:
>>
>> Yes, I did. The memory check for rss computes the memory footprint of
>> column index using size of unsigned long long instead of int.
>>
>> For Junchao, I wonder if keeping track of which loaded columns are owned
>> by the current process and which loaded columns are not owned also needs
>> some memory storage. Just a wild thought.
>>
>> On Thu, Jul 2, 2020 at 11:40 PM Ernesto Prudencio <EPrudencio at slb.com>
>> wrote:
>>
>>> 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 <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 <karl.linkui at gmail.com>> Cc: PETSc users list
>>> <petsc-users at mcs.anl.gov <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 <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 <knepley at gmail.com>> wrote: On
>>> Thu, Jul 2, 2020 at 7:30 PM Karl Lin <karl.linkui at gmail.com
>>> <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 <knepley at gmail.com>> wrote: On Thu, Jun 11, 2020
>>> at 12:52 PM Karl Lin <karl.linkui at gmail.com <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 <knepley at gmail.com>>
>>> wrote: On Thu, Jun 11, 2020 at 11:51 AM Karl Lin <karl.linkui at gmail.com
>>> <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/
>>> <https://urldefense.com/v3/__http:/www.cse.buffalo.edu/*knepley/__;fg!!Kjv0uj3L4nM6H-I!1KBn92fUc-8pAvJy257WTFoHD80IUf6u5iIhyL_vrliEm3psAK4KAJFCdygnPA$>
>>> -- What most experimenters take for granted before they begin their
>>> experiments is infinitely more interesting than any results to which their
>>> experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/
>>> <https://urldefense.com/v3/__http:/www.cse.buffalo.edu/*knepley/__;fg!!Kjv0uj3L4nM6H-I!1KBn92fUc-8pAvJy257WTFoHD80IUf6u5iIhyL_vrliEm3psAK4KAJFCdygnPA$>
>>> -- 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$>
>>> Schlumberger-Private *
>>>
>>
>>
--
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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