[petsc-users] MatAssemblyEnd taking too long

Fri Aug 21 11:55:48 CDT 2020

I built petsc with mpich-3.3.2 on my MacBook Pro with Apple clang 11.0.3 and the test is finishing at my end. 

So, it appears that there is some issue with openmpi-4.0.1 on this machine. 

I will now build all my dependency toolchain with mpich and hopefully things will work for my application code. 

Thank you again for your help. 

Regards, 
Manav

> On Aug 20, 2020, at 10:45 PM, Junchao Zhang <junchao.zhang at gmail.com> wrote:
> 
> 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 <mailto: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 <mailto: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 <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 <mailto:jed at jedbrown.org>> wrote:
>> 
>> Matthew Knepley <knepley at gmail.com <mailto:knepley at gmail.com>> writes:
>> 
>>> On Thu, Aug 20, 2020 at 11:09 AM Manav Bhatia <bhatiamanav at gmail.com <mailto:bhatiamanav at gmail.com>> wrote:
>>> 
>>>> 
>>>> 
>>>> On Aug 20, 2020, at 8:31 AM, Stefano Zampini <stefano.zampini at gmail.com <mailto: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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