[Pytrilinos-users] Re: [Trilinos-Users] Epetra python interface

[Bill Spotz]

Maxsim,

Looking through the Epetra documentation, I do not see a C++  
implementation of precisely what you are asking for.  This means that  
swig (the Simple Wrapper Interface Generator that creates the  
PyTrilinos code) will not automatically generate such a method.

However, your efficiency argument makes sense, so I should add this  
method.  I will file a feature request with Bugzilla and have it out  
with the next release, which I believe is planned for August.  I'll  
add it to CrsMatrix so that FECrsMatrix inherits it.

On Jun 1, 2007, at 8:51 AM, maxsimg at nist.gov wrote:

> I have gotten the methods there to work now, but I still have some  
> questions.
>
> For example, to do something like set all of the entries above the  
> diagonal, I
> would have to manually iterate through all the rows in the matrix,  
> in Python,
> doing calls to InsertGlobalValues for each row - and that is  
> inefficient, since
> doing the looping in python has very large overhead costs. I have  
> been able to
> set a submatrix of the sparse matrix to a pre-made dense matrix -  
> however, I
> don't think this helps in the situation where I want to set, say,  
> all of the
> elements on the diagonal. I was wondering whether there would be  
> some way of
> passing in, say, a vector of row indices i, a vector of column  
> indices j, and a
> vector of values V, all of the same length, to then have the value  
> of the matrix
> elements in positions (i_k, j_k) set to V_k. This would allow the  
> iteration to
> be done efficiently in the underlying c++ code instead of having it  
> done
> explicitly in python, avoiding the performance penalty. Is there  
> some way of
> doing this? Or some other way of inserting values that would  
> prevent the need
> for explicit Python looping? (Either for summing into, replacing,  
> or inserting
> values - the interfaces available seem consistent.)
>
> -Maxsim Gibiansky
>
> Quoting Bill Spotz <wfspotz at sandia.gov>:
>
>> Maxsim,
>>
>> I provided the wrappers for Epetra.FECrsMatrix, but haven't tested it
>> much yet.  However, the auto-generated documentation seems useful:
>>
>> $ python
>> Python 2.5.1 (r251:54863, May 27 2007, 17:33:37)
>> [GCC 4.0.1 (Apple Computer, Inc. build 5363)] on darwin
>> Type "help", "copyright", "credits" or "license" for more  
>> information.
>>>>> from PyTrilinos import Epetra
>>>>> help(Epetra.FECrsMatrix.SumIntoGlobalValues)
>>
>> Help on method SumIntoGlobalValues in module Epetra:
>>
>> SumIntoGlobalValues(*args) unbound Epetra.FECrsMatrix method
>>      SumIntoGlobalValues(self, int GlobalRow, int NumEntries, double
>> Values, int Indices) -> int
>>      SumIntoGlobalValues(self, int row, PyObject values, PyObject
>> indices) -> int
>>      SumIntoGlobalValues(self, int numIndices, int indices, double
>> values, int format=COLUMN_MAJOR) -> int
>>      SumIntoGlobalValues(self, int numIndices, int indices, double
>> values) -> int
>>      SumIntoGlobalValues(self, int numRows, int rows, int numCols,
>> int cols, double values,
>>          int format=COLUMN_MAJOR) -> int
>>      SumIntoGlobalValues(self, int numRows, int rows, int numCols,
>> int cols, double values) -> int
>>      SumIntoGlobalValues(self, int numIndices, int indices, double
>> values, int format=ROW_MAJOR) -> int
>>      SumIntoGlobalValues(self, int numIndices, int indices, double
>> values) -> int
>>      SumIntoGlobalValues(self, int numRows, int rows, int numCols,
>> int cols, double values,
>>          int format=ROW_MAJOR) -> int
>>      SumIntoGlobalValues(self, int numRows, int rows, int numCols,
>> int cols, double values) -> int
>>      SumIntoGlobalValues(self, Epetra_IntSerialDenseVector indices,
>> Epetra_SerialDenseMatrix values,
>>          int format=COLUMN_MAJOR) -> int
>>      SumIntoGlobalValues(self, Epetra_IntSerialDenseVector indices,
>> Epetra_SerialDenseMatrix values) -> int
>>      SumIntoGlobalValues(self, Epetra_IntSerialDenseVector rows,
>> Epetra_IntSerialDenseVector cols,
>>          Epetra_SerialDenseMatrix values,
>>          int format=COLUMN_MAJOR) -> int
>>      SumIntoGlobalValues(self, Epetra_IntSerialDenseVector rows,
>> Epetra_IntSerialDenseVector cols,
>>          Epetra_SerialDenseMatrix values) -> int
>>
>>
>> The last four calling signatures may be of interest to you since they
>> use serial dense vectors and matrices to specify more complicated
>> assignment operations.
>>
>> On May 30, 2007, at 2:28 PM, maxsimg at nist.gov wrote:
>>
>>> Hello everyone,
>>>
>>> I am trying to populate an epetra sparse matrix, using the python
>>> interfaces
>>> available through PyTrilinos. Ideally, I would like to specify a
>>> list of row
>>> indices, column indices, and values to insert (or sum into) the
>>> matrix. I've
>>> tried to use some of the overloaded forms of InsertGlobalValues and
>>> SumIntoGlobalValues, but some of the ones that I have tried give me
>>> "NotImplementedError: Wrong number of arguments for overloaded
>>> function
>>> 'FECrsMatrix_SumIntoGlobalValues'" and others don't support
>>> inserting into
>>> multiple rows, so I'm not sure what to use and how. Would someone
>>> be able to
>>> suggest what is a good way to populate a matrix through the
>>> available python
>>> wrappers?
>>>
>>> Ideally, I'd like to do something like
>>>
>>> theMatrix.putGlobalValues(values, i, j)
>>>
>>> where i is a list of indices and j is a list of indices, where the
>>> lengths of
>>> i,j, and values are the same.
>>>
>>> -Maxsim Gibiansky
>>
>> ** Bill Spotz                                              **
>> ** Sandia National Laboratories  Voice: (505)845-0170      **
>> ** P.O. Box 5800                 Fax:   (505)284-5451      **
>> ** Albuquerque, NM 87185-0370    Email: wfspotz at sandia.gov **
>>
>>
>>
>>
>
>
>
>
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** Bill Spotz                                              **
** Sandia National Laboratories  Voice: (505)845-0170      **
** P.O. Box 5800                 Fax:   (505)284-5451      **
** Albuquerque, NM 87185-0370    Email: wfspotz at sandia.gov **