[petsc-users] Matrix and vector type selection & memory allocation for efficient matrix import?
Zou, Ling
ling.zou at inl.gov
Fri Apr 20 15:28:30 CDT 2018
Mat, is this book you recommended?
https://www.amazon.com/Using-MPI-Programming-Message-Passing-Engineering/dp/0262527391/ref=pd_lpo_sbs_14_img_0?_encoding=UTF8&psc=1&refRID=EYCV0H0J5EQ9M0GDKWFT
Thanks,
Ling
On Fri, Apr 20, 2018 at 2:17 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Fri, Apr 20, 2018 at 4:07 PM, Klaus Burkart <k_burkart at yahoo.com>
> wrote:
>
>> Sorry, I don't understand you:
>>
>> The example says:
>>
>> Step 1: Create the gobal matrix
>>
>> MatCreate(...,&A); // no problem
>>
>> Step 2: Make it a parallel matrix
>>
>> MatSetType(A,MATMPIAIJ); // no problem
>>
>> Step 3: Define the size of the global matrix and the number of rows per
>> process IF this number is the same for all processes
>>
>> MatSetSizes(A, N,n,N,N); In the example, I have the problem with n
>> which is 3 or 2 depending on the process but I can only set n to 3 or 2 so
>> it will be the wrong for at least one process
>>
>
> 1) Get the book "Using MPI" just like I suggested. It explains this part
> of parallel programming that you do not understand.
>
> 2) Suppose we have two processes P0 and P1. Here are the call made on both
> processes for a matrix with 5 rows split 3, 2:
>
> P0: MatSetSizes(A, 3, 3, 5, 5);
> P1: MatSetSizes(A, 2, 2, 5, 5);
>
> See how different processes give different numbers to the routine? This is
> what SPMD programming is all about.
>
> Thanks,
>
> Matt
>
>
>> Step 4: Preallocate memory for the d_nnz and o_nnz values which are
>> different for each row (for each n)
>>
>> MatMPIAIJSetPreallocation(A,0,d_nnz[n],0,o_nnz[n]); // How to do
>> this repeatedly for all processes especially when using PETEC_DECIDE for n
>> and m as shown in many examples in which case I don't even know the n per
>> process
>>
>> I have to retrieve the relevant values (content and structure) from an
>> application and I absolutely don't understand how to enter the exact same
>> matrix structure as shown in the example (only much larger) into PETSc
>> using the retrieved data?
>>
>> How would assign the d_nnz and o_nnz values of a global matrix on a 32
>> core workstation to the 32 processes using MatMPIAIJSetPreallocation(A,0,d_nnz[n],0,o_nnz[n]);?
>> (Which means in my case assigning 64 arrays with different content
>> containing the d_nnz and o_nnz values for the 32 processes)
>>
>> Would I use a for loop - but then how to get hold of the individual
>> processes? Same for Step 3?
>>
>> I don't get the underlying idea about how to create a parallel matrix
>> structure in PETSc - don't get me wrong I understand the layout "simply"
>> not how to enter more than one local matrix it into PETSc.
>>
>> Klaus
>>
>> Am Freitag, 20. April 2018, 19:52:11 MESZ hat Matthew Knepley <
>> knepley at gmail.com> Folgendes geschrieben:
>>
>>
>> On Fri, Apr 20, 2018 at 1:30 PM, Klaus Burkart <k_burkart at yahoo.com>
>> wrote:
>>
>> In my case N=M but n for process 0, 1, 2, 3,... no_processes-1 can be
>> different from the nth process like in the example where the nth
>> process=Proc2 and has only two rows while all other processes have three
>> rows:
>>
>>
>> Yes.
>>
>>
>> Example from the PETSc webpage mentioned before:
>>
>> 1 2 0 | 0 3 0 | 0 4
>> Proc0 0 5 6 | 7 0 0 | 8 0
>> 9 0 10 | 11 0 0 | 12 0
>> ------------------------------ -------
>> 13 0 14 | 15 16 17 | 0 0
>> Proc1 0 18 0 | 19 20 21 | 0 0
>> 0 0 0 | 22 23 0 | 24 0
>> ------------------------------ -------
>> Proc2 25 26 27 | 0 0 28 | 29 0
>> 30 0 0 | 31 32 33 | 0 34
>>
>> and I need to enter different values for d_nnz and o_nnz for each row
>> somewhere too
>>
>> proc0: d_nnz = [2,2,2] and o_nnz = [2,2,2]
>> proc1: d_nnz = [3,3,2] and o_nnz = [2,1,1]
>> proc2: d_nnz = [1,1] and o_nnz = [4,4]
>>
>> Each process only sets d_nnz and o_nnz for its LOCAL rows. Thus, it is
>> exactly as shown above. Proc1 sets values
>> only for rows 3-5.
>>
>> Thanks,
>>
>> Matt
>>
>>
>> I simply can't identify the function(s) used to set the values for n,
>> d_nnz and o_nnz for the individual local matrices allocated to all the
>> processes if n isn't the same for all processes and d_nnz and o_nnz are
>> different for each local matrix?
>>
>> Approach described on the PETSc webpage:
>>
>> MatCreate <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mcs.anl.gov_petsc_petsc-2Dcurrent_docs_manualpages_Mat_MatCreate.html-23MatCreate&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=kuHHom1yjd94zUrBWecnYg&m=N7Qj9HPi7_sDdfpeUPyFGoLWR95huadKQYfwt6HFZTg&s=fuaWHR03gK4mnNvFfFyicLPfKIaRobbPAKA7KvdbbQM&e=>(...,&A);
>>
>>
>>
>> MatSetType <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mcs.anl.gov_petsc_petsc-2Dcurrent_docs_manualpages_Mat_MatSetType.html-23MatSetType&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=kuHHom1yjd94zUrBWecnYg&m=N7Qj9HPi7_sDdfpeUPyFGoLWR95huadKQYfwt6HFZTg&s=Kh5W-9DyiSe82fN1OgujmDWs-IijI441g7ujXZGreiY&e=>(A,MATMPIAIJ <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mcs.anl.gov_petsc_petsc-2Dcurrent_docs_manualpages_Mat_MATMPIAIJ.html-23MATMPIAIJ&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=kuHHom1yjd94zUrBWecnYg&m=N7Qj9HPi7_sDdfpeUPyFGoLWR95huadKQYfwt6HFZTg&s=CpJmovpIlWJ4se4dYFhIrakh2Hve3t62RiWMcpRtL54&e=>);
>>
>>
>>
>> MatSetSizes <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mcs.anl.gov_petsc_petsc-2Dcurrent_docs_manualpages_Mat_MatSetSizes.html-23MatSetSizes&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=kuHHom1yjd94zUrBWecnYg&m=N7Qj9HPi7_sDdfpeUPyFGoLWR95huadKQYfwt6HFZTg&s=rdrEy7Pg8fLeMoQveCRqUHzi3IpOfCjvBGB-gFL73Ws&e=>(A, m,n,M,N); // for the example above using this function would set the no. of rows for Proc2 to 3 but it's 2
>>
>>
>>
>>
>> MatMPIAIJSetPreallocation <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mcs.anl.gov_petsc_petsc-2Dcurrent_docs_manualpages_Mat_MatMPIAIJSetPreallocation.html-23MatMPIAIJSetPreallocation&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=kuHHom1yjd94zUrBWecnYg&m=N7Qj9HPi7_sDdfpeUPyFGoLWR95huadKQYfwt6HFZTg&s=RsveZcVp1senr6bpfVWoVoin2d28-0D1000viYN2aqA&e=>(A,.. .); // this function can be used to set values for ONE local matrix only
>>
>>
>>
>> In addition to that I don't know which functions to use to preallocate
>> memory for ALL local matrices when each of them has different values for
>> d_nnz and o_nnz.
>>
>> I other words, what's the code for the 3 process example above? (entering
>> the matrix structure and allocating memory)
>>
>> Klaus
>>
>> Am Freitag, 20. April 2018, 17:13:26 MESZ hat Smith, Barry F. <
>> bsmith at mcs.anl.gov> Folgendes geschrieben:
>>
>>
>>
>> For square matrices almost always n is the same as m. On different
>> processes m can be different. You get to decide what makes sense for each
>> processes what its m should be.
>>
>> Barry
>>
>>
>> > On Apr 20, 2018, at 10:05 AM, Klaus Burkart <k_burkart at yahoo.com>
>> wrote:
>> >
>> > I think I understood the matrix structure for parallel computation with
>> the rows, diagonal (d) and off-diagonal (o) structure, where I have
>> problems is how to do the setup including memory allocation in PETSc:
>> >
>> > Lets assume, I use a 16 core workstation (=16 processes) and the number
>> of nonzeros varies in each row for both d and o and the number of rows
>> assigned to each process differs too - at least for the nth process.
>> >
>> > Looking at the manual and http://www.mcs.anl.gov/petsc/
>> petsc-current/docs/ manualpages/Mat/MatCreateAIJ. html#MatCreateAIJ,
>> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.mcs.anl.gov_petsc_petsc-2Dcurrent_docs_manualpages_Mat_MatCreateAIJ.html-23MatCreateAIJ-2C&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=kuHHom1yjd94zUrBWecnYg&m=N7Qj9HPi7_sDdfpeUPyFGoLWR95huadKQYfwt6HFZTg&s=-_yf6zmL3d2iNa4ipS2vN3X9L0S7LxolfdXQI12_u7c&e=>I
>> don't understand how to enter a global matrix when n is NOT the same for
>> each process as e.g. in MatSetSizes(A, m,n,M,N); n and m are integers, not
>> arrays?
>> >
>> > MatCreate(...,&A);
>> >
>> > MatSetType(A,MATMPIAIJ);
>> >
>> > MatSetSizes(A, m,n,M,N); // seems to assume n and m are the same for
>> each process which isn't even the case in the example on the page mentioned
>> above?!
>> >
>> > MatMPIAIJSetPreallocation(A,.. .);
>> >
>> >
>> > How can I enter the parallel global-local matrix structure?
>> >
>> > How can the memory preallocation be done?
>> >
>> > Klaus
>> >
>> > Am Donnerstag, 19. April 2018, 01:47:59 MESZ hat Smith, Barry F. <
>> bsmith at mcs.anl.gov> Folgendes geschrieben:
>> >
>> >
>> >
>> >
>> > > On Apr 18, 2018, at 4:42 PM, k_burkart at yahoo.com wrote:
>> > >
>> > > So, practically speaking, l should invent routines to decompose the
>> matrix e.g. into a block matrix structure to be able to make real use of
>> PETSc ie. be able to solve a linear system using more than one process/core?
>> >
>> > To really use PETSc efficiently/effectively you need to generate your
>> matrix in parallel.
>> >
>> > Barry
>> >
>> > >
>> > > Klaus
>> > >
>> > > Von meinem Huawei-Mobiltelefon gesendet
>> > >
>> > >
>> > > -------- Originalnachricht --------
>> > > Betreff: Re: [petsc-users] Matrix and vector type selection & memory
>> allocation for efficient matrix import?
>> > > Von: "Smith, Barry F."
>> > > An: Klaus Burkart
>> > > Cc: PETSc Users List
>> > >
>> > >
>> > >
>> > > If you can only generate the nonzero allocation sequentially you can
>> only solve sequentially which means your matrix is MATSEQAIJ and your
>> vector is VECSEQ and your communicator is PETSC_COMM_SELF.
>> > >
>> > > If you pass and array for nnz, what you pass for nz is irrelevant,
>> you might as well pass 0.
>> > >
>> > > Barry
>> > >
>> > >
>> > > > On Apr 18, 2018, at 10:48 AM, Klaus Burkart wrote:
>> > > >
>> > > > More questions about matrix and vector type selection for my
>> application:
>> > > >
>> > > > My starting point is a huge sparse matrix which can be symmetric or
>> asymmetric and a rhs vector. There's no defined local or block structure at
>> all, just row and column indices and the values and an array style rhs
>> vector together describing the entire linear system to be solved. With
>> quite some effort, I should be able to create an array nnz[N] containing
>> the number of nonzeros per row in the global matrix for memory allocation
>> which would leave me with MatSeqAIJSetPreallocation(M, 0, nnz); as the only
>> option for efficient memory allocation ie. a MATSEQAIJ matrix and VECSEQ. I
>> assume here, that 0 indicates different numbers of nonzero values in each
>> row, the exact number being stored in the nnz array. Regarding this detail
>> but one example assume a constant number of nz per row so I am not sure
>> whether I should write 0 or NULL for nz?
>> > > >
>> > > > I started with:
>> > > >
>> > > > MatCreate(PETSC_COMM_WORLD, &M);
>> > > > MatSetSizes(M, PETSC_DECIDE, PETSC_DECIDE, N, N);
>> > > > MatSetFromOptions(M);
>> > > >
>> > > > taken from a paper and assume, the latter would set the matrix type
>> to MATSEQAIJ which might conflict with PETSC_COMM_WORLD. Maybe
>> decompositioning took place at an earlier stage and the authors of the
>> paper were able to retrieve the local data and structure.
>> > > >
>> > > > What type of matrix and vector should I use for my application e.g.
>> MATSEQAIJ and VECSEQ to be able to use MatSeqAIJSetPreallocation(M, 0,
>> nnz); for efficient memory allocation?
>> > > >
>>
>> > > > In this case, where would the decompositioning / MPI process
>> allocation take place?
>> > >
>>
>>
>>
>>
>> --
>> 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.proofpoint.com/v2/url?u=http-3A__www.caam.rice.edu_-7Emk51_&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=kuHHom1yjd94zUrBWecnYg&m=N7Qj9HPi7_sDdfpeUPyFGoLWR95huadKQYfwt6HFZTg&s=X1XTDkxAzSG3ajhCqaTWt8j4MtmpP7m1h8PAUX0xslA&e=>
>>
>>
>
>
> --
> 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.proofpoint.com/v2/url?u=http-3A__www.caam.rice.edu_-7Emk51_&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=kuHHom1yjd94zUrBWecnYg&m=N7Qj9HPi7_sDdfpeUPyFGoLWR95huadKQYfwt6HFZTg&s=X1XTDkxAzSG3ajhCqaTWt8j4MtmpP7m1h8PAUX0xslA&e=>
>
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