[petsc-users] Various Questions Regarding PETSC
Mohammed Mostafa
mo7ammedmostafa at gmail.com
Sat Jul 13 11:20:11 CDT 2019
I am sorry but I don’t see what you mean by small times
Although mat assembly is relatively smaller
The cost of mat set values is still significant
The same can be said for vec assembly
Combined vec/mat assembly and matsetvalues constitute about 50% of the
total cost of matrix construction
So is this problem of my matrix setup/ preallocation
Or is this a hardware issue, for whatever reason the copy is overly slow
The code was run on a single node
Or is this function call overhead since matsetvalues is being called 1M
times inside the for loop ( 170k times in each process)
Thanks, Kamra
On Sun, Jul 14, 2019 at 12:41 AM Matthew Knepley <knepley at gmail.com> wrote:
> On Sat, Jul 13, 2019 at 9:56 AM Mohammed Mostafa <
> mo7ammedmostafa at gmail.com> wrote:
>
>> Hello Matt,
>>
>> I revised my code and changed the way I create the rhs vector,
>> previosly I was using vecCreateGhost just in case I need the ghost
>> values, but for now I changed that to
>> vecCreateMPI(.......)
>> So maybe that was the cause of the scatter
>> I am attaching with this email a new log output
>>
>
> Okay, the times are now very small. How does it scale up?
>
> Thanks,
>
> Matt
>
>
>> Also regarding how I fill my petsc matrix,
>> In my code I fill a temp CSR format matrix becasue otherwise I would need
>> "MatSetValue" to fill the petsc mat element by element
>> which is not recommmeded in the petsc manual and probably very expensive
>> due to function call overhead
>> *So after I create my matrix in CSR format, I fill the PETSC mat A as
>> follows*
>>
>>> for (i = 0; i < nMatRows; i++) {
>>> cffset = CSR_iptr[i];
>>> row_index = row_gIndex[i];
>>> nj = Eqn_nj[i];
>>> MatSetValues(PhiEqnSolver.A, 1, &row_index, nj, CSR_jptr + offset,
>>> CSR_vptr + offset, INSERT_VALUES);
>>> }
>>>
>> *After That*
>>
>>> VecAssemblyBegin(RHS);
>>> VecAssemblyEnd(RHS);
>>>
>>> MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
>>> MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
>>>
>>
>> *I don't believe , I am doing anything special, if possible I would like
>> to set the whole csr matrix at once in one command.*
>> *I took a look at the code for MatSetValues, if I am understanding it
>> correctly(hopefully) I think I could do it, maybe modify it or create a new
>> routine entirely for this pupose.*
>>
>> *i.e. MatSetValuesFromCSR(.....)*
>> *Or is there a particular reason why it has to be this way*
>>
>> I also tried ksp ex3 but I slightly tweaked it to add a logging stage
>> around the assembly and MatSetValues and I am attaching the modified
>> example here as well.
>> Although in this example the matrix stash is not empty ( means
>> off-processor values are being set ) but the timing values for roughly the
>> same matrix size , the command I used is
>> mpirun -np 6 ./mod_ksp_ex3 -m 1000 -log_view -info
>>
>>
>> Regards,
>> Kamra
>>
>> On Sat, Jul 13, 2019 at 1:43 PM Matthew Knepley <knepley at gmail.com>
>> wrote:
>>
>>> On Fri, Jul 12, 2019 at 10:51 PM Mohammed Mostafa <
>>> mo7ammedmostafa at gmail.com> wrote:
>>>
>>>> Hello Matt,
>>>> Attached is the dumped entire log output using -log_view and -info.
>>>>
>>>
>>> In matrix construction, it looks like you have a mixture of load
>>> imbalance (see the imbalance in the Begin events)
>>> and lots of Scatter messages in your assembly. We turn off
>>> MatSetValues() logging by default since it is usually
>>> called many times, but you can explicitly turn it back on if you want. I
>>> don't think that is the problem here. Its easy
>>> to see from examples (say SNES ex5) that it is not the major time sink.
>>> What is the Scatter doing?
>>>
>>> Thanks,
>>>
>>> Matt
>>>
>>>
>>>> Thanks,
>>>> Kamra
>>>>
>>>> On Fri, Jul 12, 2019 at 9:23 PM Matthew Knepley <knepley at gmail.com>
>>>> wrote:
>>>>
>>>>> On Fri, Jul 12, 2019 at 5:19 AM Mohammed Mostafa via petsc-users <
>>>>> petsc-users at mcs.anl.gov> wrote:
>>>>>
>>>>>> Hello all,
>>>>>> I have a few question regarding Petsc,
>>>>>>
>>>>>
>>>>> Please send the entire output of a run with all the logging turned on,
>>>>> using -log_view and -info.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> Matt
>>>>>
>>>>>
>>>>>> Question 1:
>>>>>> For the profiling , is it possible to only show the user defined log
>>>>>> events in the breakdown of each stage in Log-view.
>>>>>> I tried deactivating all ClassIDs, MAT,VEC, PC, KSP,PC,
>>>>>> PetscLogEventExcludeClass(MAT_CLASSID);
>>>>>> PetscLogEventExcludeClass(VEC_CLASSID);
>>>>>> PetscLogEventExcludeClass(KSP_CLASSID);
>>>>>> PetscLogEventExcludeClass(PC_CLASSID);
>>>>>> which should "Deactivates event logging for a PETSc object class in
>>>>>> every stage" according to the manual.
>>>>>> however I still see them in the stage breakdown
>>>>>> --- Event Stage 1: Matrix Construction
>>>>>>
>>>>>> BuildTwoSidedF 4 1.0 2.7364e-02 2.4 0.00e+00 0.0 0.0e+00
>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 18 0 0 0 0 0
>>>>>> VecSet 1 1.0 4.5300e-06 2.4 0.00e+00 0.0 0.0e+00
>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>> VecAssemblyBegin 2 1.0 2.7344e-02 2.4 0.00e+00 0.0 0.0e+00
>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 18 0 0 0 0 0
>>>>>> VecAssemblyEnd 2 1.0 8.3447e-06 1.5 0.00e+00 0.0 0.0e+00
>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>> VecScatterBegin 2 1.0 7.5102e-05 1.7 0.00e+00 0.0 3.6e+01
>>>>>> 2.1e+03 0.0e+00 0 0 3 0 0 0 0 50 80 0 0
>>>>>> VecScatterEnd 2 1.0 3.5286e-05 2.2 0.00e+00 0.0 0.0e+00
>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>> MatAssemblyBegin 2 1.0 8.8930e-05 1.9 0.00e+00 0.0 0.0e+00
>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 0 0 0 0 0 0
>>>>>> MatAssemblyEnd 2 1.0 1.3566e-02 1.1 0.00e+00 0.0 3.6e+01
>>>>>> 5.3e+02 8.0e+00 0 0 3 0 6 10 0 50 20100 0
>>>>>> AssembleMats 2 1.0 3.9774e-02 1.7 0.00e+00 0.0 7.2e+01
>>>>>> 1.3e+03 8.0e+00 0 0 7 0 6 28 0100100100 0 # USER EVENT
>>>>>> myMatSetValues 2 1.0 2.6931e-02 1.2 0.00e+00 0.0 0.0e+00
>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 19 0 0 0 0 0 # USER EVENT
>>>>>> setNativeMat 1 1.0 3.5613e-02 1.3 0.00e+00 0.0 0.0e+00
>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 24 0 0 0 0 0 # USER EVENT
>>>>>> setNativeMatII 1 1.0 4.7023e-02 1.5 0.00e+00 0.0 0.0e+00
>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 28 0 0 0 0 0 # USER EVENT
>>>>>> callScheme 1 1.0 2.2333e-03 1.2 0.00e+00 0.0 0.0e+00
>>>>>> 0.0e+00 0.0e+00 0 0 0 0 0 2 0 0 0 0 0 # USER EVENT
>>>>>>
>>>>>> Also is possible to clear the logs so that I can write a separate
>>>>>> profiling output file for each timestep ( since I am solving a transient
>>>>>> problem and I want to know the change in performance as time goes by )
>>>>>>
>>>>>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>> Question 2:
>>>>>> Regarding MatSetValues
>>>>>> Right now, I writing a finite volume code, due to algorithm
>>>>>> requirement I have to write the matrix into local native format ( array of
>>>>>> arrays) and then loop through rows and use MatSetValues to set the elements
>>>>>> in "Mat A"
>>>>>> MatSetValues(A, 1, &row, nj, j_index, coefvalues, INSERT_VALUES);
>>>>>> but it is very slow and it is killing my performance
>>>>>> although the matrix was properly set using
>>>>>> MatCreateAIJ(PETSC_COMM_WORLD, this->local_size, this->local_size,
>>>>>> PETSC_DETERMINE,
>>>>>> PETSC_DETERMINE, -1, d_nnz, -1, o_nnz, &A);
>>>>>> with d_nnz,and o_nnz properly assigned so no mallocs occur during
>>>>>> matsetvalues and all inserted values are local so no off-processor values
>>>>>> So my question is it possible to set multiple rows at once hopefully
>>>>>> all, I checked the manual and MatSetValues can only set dense matrix block
>>>>>> because it seems that row by row is expensive
>>>>>> Or perhaps is it possible to copy all rows to the underlying matrix
>>>>>> data, as I mentioned all values are local and no off-processor values (
>>>>>> stash is 0 )
>>>>>> [0] VecAssemblyBegin_MPI_BTS(): Stash has 0 entries, uses 0 mallocs.
>>>>>> [0] VecAssemblyBegin_MPI_BTS(): Block-Stash has 0 entries, uses 0
>>>>>> mallocs.
>>>>>> [0] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
>>>>>> [1] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
>>>>>> [2] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
>>>>>> [3] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
>>>>>> [4] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
>>>>>> [5] MatAssemblyBegin_MPIAIJ(): Stash has 0 entries, uses 0 mallocs.
>>>>>> [2] MatAssemblyEnd_SeqAIJ(): Matrix size: 186064 X 186064; storage
>>>>>> space: 0 unneeded,743028 used
>>>>>> [1] MatAssemblyEnd_SeqAIJ(): Matrix size: 186062 X 186062; storage
>>>>>> space: 0 unneeded,742972 used
>>>>>> [1] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [1] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 4
>>>>>> [1] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 0)/(num_localrows 186062) < 0.6. Do not use CompressedRow routines.
>>>>>> [2] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [2] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 4
>>>>>> [2] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 0)/(num_localrows 186064) < 0.6. Do not use CompressedRow routines.
>>>>>> [4] MatAssemblyEnd_SeqAIJ(): Matrix size: 186063 X 186063; storage
>>>>>> space: 0 unneeded,743093 used
>>>>>> [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 186062 X 186062; storage
>>>>>> space: 0 unneeded,743036 used
>>>>>> [4] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [4] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 4
>>>>>> [4] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 0)/(num_localrows 186063) < 0.6. Do not use CompressedRow routines.
>>>>>> [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [5] MatAssemblyEnd_SeqAIJ(): Matrix size: 186062 X 186062; storage
>>>>>> space: 0 unneeded,742938 used
>>>>>> [5] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [5] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 4
>>>>>> [5] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 0)/(num_localrows 186062) < 0.6. Do not use CompressedRow routines.
>>>>>> [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 4
>>>>>> [0] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 0)/(num_localrows 186062) < 0.6. Do not use CompressedRow routines.
>>>>>> [3] MatAssemblyEnd_SeqAIJ(): Matrix size: 186063 X 186063; storage
>>>>>> space: 0 unneeded,743049 used
>>>>>> [3] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [3] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 4
>>>>>> [3] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 0)/(num_localrows 186063) < 0.6. Do not use CompressedRow routines.
>>>>>> [2] MatAssemblyEnd_SeqAIJ(): Matrix size: 186064 X 685; storage
>>>>>> space: 0 unneeded,685 used
>>>>>> [4] MatAssemblyEnd_SeqAIJ(): Matrix size: 186063 X 649; storage
>>>>>> space: 0 unneeded,649 used
>>>>>> [4] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [4] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
>>>>>> [4] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 185414)/(num_localrows 186063) > 0.6. Use CompressedRow routines.
>>>>>> [2] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [2] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
>>>>>> [2] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 185379)/(num_localrows 186064) > 0.6. Use CompressedRow routines.
>>>>>> [1] MatAssemblyEnd_SeqAIJ(): Matrix size: 186062 X 1011; storage
>>>>>> space: 0 unneeded,1011 used
>>>>>> [5] MatAssemblyEnd_SeqAIJ(): Matrix size: 186062 X 1137; storage
>>>>>> space: 0 unneeded,1137 used
>>>>>> [5] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [5] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
>>>>>> [5] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 184925)/(num_localrows 186062) > 0.6. Use CompressedRow routines.
>>>>>> [1] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [1] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
>>>>>> [3] MatAssemblyEnd_SeqAIJ(): Matrix size: 186063 X 658; storage
>>>>>> space: 0 unneeded,658 used
>>>>>> [0] MatAssemblyEnd_SeqAIJ(): Matrix size: 186062 X 648; storage
>>>>>> space: 0 unneeded,648 used
>>>>>> [1] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 185051)/(num_localrows 186062) > 0.6. Use CompressedRow routines.
>>>>>> [0] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [0] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
>>>>>> [0] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 185414)/(num_localrows 186062) > 0.6. Use CompressedRow routines.
>>>>>> [3] MatAssemblyEnd_SeqAIJ(): Number of mallocs during MatSetValues()
>>>>>> is 0
>>>>>> [3] MatAssemblyEnd_SeqAIJ(): Maximum nonzeros in any row is 1
>>>>>> [3] MatCheckCompressedRow(): Found the ratio (num_zerorows
>>>>>> 185405)/(num_localrows 186063) > 0.6. Use CompressedRow routines.
>>>>>>
>>>>>>
>>>>>> ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>>>>>> Question 3:
>>>>>> If all matrix and vector inserted data are local, what part of the
>>>>>> vec/mat assembly consumes time because matsetvalues and matassembly consume
>>>>>> more time than matrix builder
>>>>>> Also this is not just for the first time MAT_FINAL_ASSEMBLY
>>>>>>
>>>>>>
>>>>>> For context the matrix in the above is nearly 1Mx1M partitioned over
>>>>>> six processes and it was NOT built using DM
>>>>>>
>>>>>> Finally the configure options are:
>>>>>>
>>>>>> Configure options:
>>>>>> PETSC_ARCH=release3 -with-debugging=0 COPTFLAGS="-O3 -march=native
>>>>>> -mtune=native" CXXOPTFLAGS="-O3 -march=native -mtune=native" FOPTFLAGS="-O3
>>>>>> -march=native -mtune=native" --with-cc=mpicc --with-cxx=mpicxx
>>>>>> --with-fc=mpif90 --download-metis --download-hypre
>>>>>>
>>>>>> Sorry for such long question and thanks in advance
>>>>>> Thanks
>>>>>> M. Kamra
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> 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/>
>>>>>
>>>>
>>>
>>> --
>>> 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/>
>>>
>>
>
> --
> 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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