[petsc-users] (no subject)

[Ji Zhang]

Thanks for your warm help. Could you please show me some necessary
functions or a simple demo code?


Wayne

On Fri, Sep 16, 2016 at 10:32 AM, Barry Smith <bsmith at mcs.anl.gov> wrote:

>
>   You should create your small m_ij matrices as just dense two dimensional
> arrays and then set them into the big M matrix. Do not create the small
> dense matrices as PETSc matrices.
>
>   Barry
>
>
> > On Sep 15, 2016, at 9:21 PM, Ji Zhang <gotofd at gmail.com> wrote:
> >
> > I'm so apologize for the ambiguity. Let me clarify it.
> >
> > I'm trying to simulation interactions among different bodies. Now I have
> calculated the interaction between two of them and stored in the sub-matrix
> m_ij. What I want to do is to consider the whole interaction and construct
> all sub-matrices m_ij into a big matrix M, just like this, imaging the
> problem contain 3 bodies,
> >
> >          [  m11  m12  m13  ]
> >  M =  |  m21  m22  m23  |   ,
> >          [  m31  m32  m33  ]
> >
> > The system is huge that I have to use MPI and a lot of cups. A mcve code
> is showing below, and I'm using a python wrap of PETSc, however, their
> grammar is similar.
> >
> > import numpy as np
> > from petsc4py import PETSc
> >
> > mSizes = (5, 8, 6)
> > mij = []
> >
> > # create sub-matrices mij
> > for i in range(len(mSizes)):
> >     for j in range(len(mSizes)):
> >         temp_m = PETSc.Mat().create(comm=PETSc.COMM_WORLD)
> >         temp_m.setSizes(((None, mSizes[i]), (None, mSizes[j])))
> >         temp_m.setType('mpidense')
> >         temp_m.setFromOptions()
> >         temp_m.setUp()
> >         temp_m[:, :] = np.random.random_sample((mSizes[i], mSizes[j]))
> >         temp_m.assemble()
> >         mij.append(temp_m)
> >
> > # Now we have four sub-matrices. I would like to construct them into a
> big matrix M.
> > M = PETSc.Mat().create(comm=PETSc.COMM_WORLD)
> > M.setSizes(((None, np.sum(mSizes)), (None, np.sum(mSizes))))
> > M.setType('mpidense')
> > M.setFromOptions()
> > M.setUp()
> > mLocations = np.insert(np.cumsum(mSizes), 0, 0)    # mLocations = [0,
> mSizes]
> > for i in range(len(mSizes)):
> >     for j in range(len(mSizes)):
> >         M[mLocations[i]:mLocations[i+1], mLocations[j]:mLocations[j+1]]
> = mij[i*len(mSizes)+j][:, :]
> > M.assemble()
> >
> > Thanks.
> >
> >
> > 2016-09-16
> > Best,
> > Regards,
> > Zhang Ji
> > Beijing Computational Science Research Center
> > E-mail: gotofd at gmail.com
> >
> >
> >
> >
> >
> > Wayne
> >
> > On Thu, Sep 15, 2016 at 8:58 PM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Thu, Sep 15, 2016 at 4:23 AM, Ji Zhang <gotofd at gmail.com> wrote:
> > Thanks Matt. It works well for signal core. But is there any solution if
> I need a MPI program?
> >
> > It unclear what the stuff below would mean in parallel.
> >
> > If you want to assemble several blocks of a parallel matrix that looks
> like serial matrices, then use
> >
> >   http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/Mat/
> MatGetLocalSubMatrix.html
> >
> >   Thanks,
> >
> >      Matt
> >
> > Thanks.
> >
> > Wayne
> >
> > On Tue, Sep 13, 2016 at 9:30 AM, Matthew Knepley <knepley at gmail.com>
> wrote:
> > On Mon, Sep 12, 2016 at 8:24 PM, Ji Zhang <gotofd at gmail.com> wrote:
> > Dear all,
> >
> > I'm using petsc4py and now face some problems.
> > I have a number of small petsc dense matrices mij, and I want to
> construct them to a big matrix M like this:
> >
> >          [  m11  m12  m13  ]
> >     M =  |  m21  m22  m23  |   ,
> >          [  m31  m32  m33  ]
> > How could I do it effectively?
> >
> > Now I'm using the code below:
> >
> >     # get indexes of matrix mij
> >     index1_begin, index1_end = getindex_i( )
> >     index2_begin, index2_end = getindex_j( )
> >     M[index1_begin:index1_end, index2_begin:index2_end] = mij[:, :]
> > which report such error messages:
> >
> >     petsc4py.PETSc.Error: error code 56
> >     [0] MatGetValues() line 1818 in /home/zhangji/PycharmProjects/
> petsc-petsc-31a1859eaff6/src/mat/interface/matrix.c
> >     [0] MatGetValues_MPIDense() line 154 in
> /home/zhangji/PycharmProjects/petsc-petsc-31a1859eaff6/src/
> mat/impls/dense/mpi/mpidense.c
> >
> > Make M a sequential dense matrix.
> >
> >    Matt
> >
> >     [0] No support for this operation for this object type
> >     [0] Only local values currently supported
> >
> > Thanks.
> >
> >
> > 2016-09-13
> > Best,
> > Regards,
> > Zhang Ji
> > Beijing Computational Science Research Center
> > E-mail: gotofd at gmail.com
> >
> >
> >
> >
> >
> > --
> > 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
> >
> >
> >
> >
> > --
> > 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
> >
>
>
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