[petsc-users] MatAssemblyEnd taking too long

[Junchao Zhang]

Manav,
 I downloaded your petsc_mat.tgz but could not reproduce the problem, on
both Linux and Mac. I used the petsc commit id df0e4300 you mentioned.
 On Linux, I have openmpi-4.0.2 + gcc-8.3.0, and petsc is configured
--with-debugging --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpifort
--COPTFLAGS="-g -O0" --FOPTFLAGS="-g -O0" --CXXOPTFLAGS="-g -O0"
--PETSC_ARCH=linux-host-dbg
 On Mac, I have mpich-3.3.1 + clang-11.0.0-apple, and petsc is
configured --with-debugging=1 --with-cc=mpicc --with-cxx=mpicxx
--with-fc=mpifort --with-ctable=0 COPTFLAGS="-O0 -g" CXXOPTFLAGS="-O0 -g"
PETSC_ARCH=mac-clang-dbg

mpirun -n 8 ./test
rank: 1 : stdout.processor.1
rank: 4 : stdout.processor.4
rank: 0 : stdout.processor.0
rank: 5 : stdout.processor.5
rank: 6 : stdout.processor.6
rank: 7 : stdout.processor.7
rank: 3 : stdout.processor.3
rank: 2 : stdout.processor.2
rank: 1 : Beginning reading nnz...
rank: 4 : Beginning reading nnz...
rank: 0 : Beginning reading nnz...
rank: 5 : Beginning reading nnz...
rank: 7 : Beginning reading nnz...
rank: 2 : Beginning reading nnz...
rank: 3 : Beginning reading nnz...
rank: 6 : Beginning reading nnz...
rank: 5 : Finished reading nnz
rank: 5 : Beginning mat preallocation...
rank: 3 : Finished reading nnz
rank: 3 : Beginning mat preallocation...
rank: 4 : Finished reading nnz
rank: 4 : Beginning mat preallocation...
rank: 7 : Finished reading nnz
rank: 7 : Beginning mat preallocation...
rank: 1 : Finished reading nnz
rank: 1 : Beginning mat preallocation...
rank: 0 : Finished reading nnz
rank: 0 : Beginning mat preallocation...
rank: 2 : Finished reading nnz
rank: 2 : Beginning mat preallocation...
rank: 6 : Finished reading nnz
rank: 6 : Beginning mat preallocation...
rank: 5 : Finished preallocation
rank: 5 : Beginning reading and setting matrix values...
rank: 1 : Finished preallocation
rank: 1 : Beginning reading and setting matrix values...
rank: 7 : Finished preallocation
rank: 7 : Beginning reading and setting matrix values...
rank: 2 : Finished preallocation
rank: 2 : Beginning reading and setting matrix values...
rank: 4 : Finished preallocation
rank: 4 : Beginning reading and setting matrix values...
rank: 0 : Finished preallocation
rank: 0 : Beginning reading and setting matrix values...
rank: 3 : Finished preallocation
rank: 3 : Beginning reading and setting matrix values...
rank: 6 : Finished preallocation
rank: 6 : Beginning reading and setting matrix values...
rank: 1 : Finished reading and setting matrix values
rank: 1 : Beginning mat assembly...
rank: 5 : Finished reading and setting matrix values
rank: 5 : Beginning mat assembly...
rank: 4 : Finished reading and setting matrix values
rank: 4 : Beginning mat assembly...
rank: 2 : Finished reading and setting matrix values
rank: 2 : Beginning mat assembly...
rank: 3 : Finished reading and setting matrix values
rank: 3 : Beginning mat assembly...
rank: 7 : Finished reading and setting matrix values
rank: 7 : Beginning mat assembly...
rank: 6 : Finished reading and setting matrix values
rank: 6 : Beginning mat assembly...
rank: 0 : Finished reading and setting matrix values
rank: 0 : Beginning mat assembly...
rank: 1 : Finished mat assembly
rank: 3 : Finished mat assembly
rank: 7 : Finished mat assembly
rank: 0 : Finished mat assembly
rank: 5 : Finished mat assembly
rank: 2 : Finished mat assembly
rank: 4 : Finished mat assembly
rank: 6 : Finished mat assembly

--Junchao Zhang


On Thu, Aug 20, 2020 at 5:29 PM Junchao Zhang <junchao.zhang at gmail.com>
wrote:

> I will have a look and report back to you. Thanks.
> --Junchao Zhang
>
>
> On Thu, Aug 20, 2020 at 5:23 PM Manav Bhatia <bhatiamanav at gmail.com>
> wrote:
>
>> I have created a standalone test that demonstrates the problem at my end.
>> I have stored the indices, etc.  from my problem in a text file for each
>> rank, which I use to initialize the matrix.
>> Please note that the test is specifically for 8 ranks.
>>
>> The .tgz file is on my google drive:
>> https://drive.google.com/file/d/1R-WjS36av3maXX3pUyiR3ndGAxteTVj-/view?usp=sharing
>>
>>
>> This contains a README file with instructions on running. Please note
>> that the work directory needs the index files.
>>
>> Please let me know if I can provide any further information.
>>
>> Thank you all for your help.
>>
>> Regards,
>> Manav
>>
>> On Aug 20, 2020, at 12:54 PM, Jed Brown <jed at jedbrown.org> wrote:
>>
>> Matthew Knepley <knepley at gmail.com> writes:
>>
>> On Thu, Aug 20, 2020 at 11:09 AM Manav Bhatia <bhatiamanav at gmail.com>
>> wrote:
>>
>>
>>
>> On Aug 20, 2020, at 8:31 AM, Stefano Zampini <stefano.zampini at gmail.com>
>> wrote:
>>
>> Can you add a MPI_Barrier before
>>
>> ierr = MatAssemblyBegin(aij->A,mode);CHKERRQ(ierr);
>>
>>
>> With a MPI_Barrier before this function call:
>> —  three of the processes have already hit this barrier,
>> —  the other 5 are inside MatStashScatterGetMesg_Private ->
>> MatStashScatterGetMesg_BTS -> MPI_Waitsome(2 processes)/MPI_Waitall(3
>> processes)
>>
>>
>> This is not itself evidence of inconsistent state.  You can use
>>
>>  -build_twosided allreduce
>>
>> to avoid the nonblocking sparse algorithm.
>>
>>
>> Okay, you should run this with -matstash_legacy just to make sure it is
>> not
>> a bug in your MPI implementation. But it looks like
>> there is inconsistency in the parallel state. This can happen because we
>> have a bug, or it could be that you called a collective
>> operation on a subset of the processes. Is there any way you could cut
>> down
>> the example (say put all 1s in the matrix, etc) so
>> that you could give it to us to run?
>>
>>
>>
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