[petsc-users] Matrix and vector type selection & memory allocation for efficient matrix import?
Zou, Ling
ling.zou at inl.gov
Fri Apr 20 15:40:05 CDT 2018
Thanks, will take a look.
Ling
On Fri, Apr 20, 2018 at 2:37 PM, Matthew Knepley <knepley at gmail.com> wrote:
> On Fri, Apr 20, 2018 at 4:28 PM, Zou, Ling <ling.zou at inl.gov> wrote:
>
>> 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
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.amazon.com_Using-2DMPI-2DProgramming-2DMessage-2DPassing-2DEngineering_dp_0262527391_ref-3Dpd-5Flpo-5Fsbs-5F14-5Fimg-5F0-3F-5Fencoding-3DUTF8-26psc-3D1-26refRID-3DEYCV0H0J5EQ9M0GDKWFT&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=kuHHom1yjd94zUrBWecnYg&m=H9gBslMxj0ZFfVMySdiTBJp6ymHNjzk8VK7mkOWd8lg&s=rsHq3ROt1GBcoAGrwdFt9gWLJnuBGA2MSiXpbb4TJnM&e=>
>>
>
> Yep. I think its the best one, although Victor's book is also nice
>
> http://pages.tacc.utexas.edu/~eijkhout/istc/istc.html
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__pages.tacc.utexas.edu_-7Eeijkhout_istc_istc.html&d=DwMFaQ&c=54IZrppPQZKX9mLzcGdPfFD1hxrcB__aEkJFOKJFd00&r=kuHHom1yjd94zUrBWecnYg&m=H9gBslMxj0ZFfVMySdiTBJp6ymHNjzk8VK7mkOWd8lg&s=WezGrH6e-K8-ONnhfYR_SL_SR_UPDSRRIMkOku8-i10&e=>
>
> Matt
>
>
>> 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=>
>>>
>>
>>
>
>
> --
> 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=H9gBslMxj0ZFfVMySdiTBJp6ymHNjzk8VK7mkOWd8lg&s=4yIdrwQym0G30_P7yZEh2HNhqU0E3wlkpQwsgH9rvhg&e=>
>
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