A class which provides data and command access to Matlab from Epetra. More...
#include <EpetraExt_MatlabEngine.h>
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EpetraExt_MatlabEngine (const Epetra_Comm &Comm) | |
EpetraExt_MatlabEngine constructor which creates a MatlabEngine object with a connection to an instance of the application Matlab by starting a new Matlab process. | |
~EpetraExt_MatlabEngine () | |
EpetraExt_MatlabEngine destructor which closes the connection to Matlab which causes the Matlab process to also exit. | |
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int | EvalString (char *command, char *outputBuffer=NULL, int outputBufferSize=-1) |
Sends a command to Matlab. | |
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int | PutMultiVector (const Epetra_MultiVector &A, const char *variableName) |
Puts a copy of the serial or distributed MultiVector into the Matlab workspace. | |
int | PutRowMatrix (const Epetra_RowMatrix &A, const char *variableName, bool transA) |
Puts a copy of the serial or distributed RowMatrix into the Matlab workspace. | |
int | PutCrsGraph (const Epetra_CrsGraph &A, const char *variableName, bool transA) |
not implemented yet | |
int | PutSerialDenseMatrix (const Epetra_SerialDenseMatrix &A, const char *variableName, int proc=0) |
Puts a copy of the SerialDenseMatrix into the Matlab workspace. | |
int | PutIntSerialDenseMatrix (const Epetra_IntSerialDenseMatrix &A, const char *variableName, int proc=0) |
Puts a copy of the IntSerialDenseMatrix into the Matlab workspace. | |
int | PutBlockMap (const Epetra_BlockMap &blockMap, const char *variableName, bool transA) |
Puts a copy of the BlockMap or Map into the Matlab workspace. | |
int | PutIntoMatlab (const char *variableName, mxArray *matlabA) |
Puts a mxArray into Matlab. | |
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int | GetMultiVector (const char *variableName, Epetra_MultiVector &A) |
Puts a Matlab variable into a MultiVector. | |
int | GetSerialDenseMatrix (const char *variableName, Epetra_SerialDenseMatrix &A, int proc=0) |
Puts a Matlab variable into a SerialDenseMatrix on the specified PE. | |
int | GetIntSerialDenseMatrix (const char *variableName, Epetra_IntSerialDenseMatrix &A, int proc=0) |
Puts a Matlab variable into a IntSerialDenseMatrix on the specified PE. | |
int | GetCrsMatrix (const char *variableName, Epetra_CrsMatrix &A, bool getTrans) |
Puts a Matlab variable into a CrsMatrix. | |
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int | GetmxArrayDimensions (mxArray *matlabA, bool &isSparse, int &numRows, int &numCols, int &numNonZeros) |
Get general information about the mxArray. For internal use but can be used by an advanced user. | |
int | GetmxArray (const char *variableName, mxArray **matlabA) |
Get a mxArray from Matlab. For internal use but can be used by an advanced user. |
A class which provides data and command access to Matlab from Epetra.
The EpetraExt_MatlabEngine class allows Epetra data objects to be exported to Matlab and then operated on within Matlab using Matlab commands.
When an EpetraExt_MatlabEngine object is constructed a new instance of the application Matlab is started for EpetraExt_MatlabEngine to communicate with. All communication between EpetraExt_MatlabEngine and Matlab occurs on the root node (0) only. For parallel environments all objects are collected onto the root node before being put into Matlab. Object data is put into a mxArray which is then sent to the Matlab process. All objects passed to Matlab are copied into the Matlab memory space. So at the point when Matlab receives its copy of the data there is two copies of the mxArray in memory, one in the Epetra application and one in Matlab. Since Matlab has its own memory space the mxArray in the Epetra application should be deleted in order to free up memory space. All methods in EpetraExt_MatlabEngine that put Epetra objects into Matlab delete the temporary mxArray as soon as it is put into Matlab. If a user desires to create his/her own mxArray's and then send them to Matlab the method PutIntoMatlab can be used. It is important to note that PutIntoMatlab does NOT delete the mxArray it is passed. When the EpetraExt_MatlabEngine deconstructor is called the instance of Matlab that was started during construction of the EpetraExt_MatlabEngine object exits.
Error Codes
Build Instructions
These instructions can be found in the file Trilinos/packages/epetraext/doc/matlab.README.
Example Code
The following example code generates simple Epetra objects and then puts them into Matlab.
The point of this example is to illustrate the flow of calls when using EpetraExt_MatlabEngine. This example program can be found in the file Trilinos/packages/epetraext/example/matlab/cxx_main.cpp.
/*@HEADER // *********************************************************************** // // AztecOO: An Object-Oriented Aztec Linear Solver Package // Copyright (2002) Sandia Corporation // // Under terms of Contract DE-AC04-94AL85000, there is a non-exclusive // license for use of this work by or on behalf of the U.S. Government. // // This library is free software; you can redistribute it and/or modify // it under the terms of the GNU Lesser General Public License as // published by the Free Software Foundation; either version 2.1 of the // License, or (at your option) any later version. // // This library is distributed in the hope that it will be useful, but // WITHOUT ANY WARRANTY; without even the implied warranty of // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU // Lesser General Public License for more details. // // You should have received a copy of the GNU Lesser General Public // License along with this library; if not, write to the Free Software // Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 // USA // Questions? Contact Michael A. Heroux (maherou@sandia.gov) // // *********************************************************************** //@HEADER */ #include "AztecOO_config.h" #ifdef HAVE_MPI #include "mpi.h" #include "Epetra_MpiComm.h" #else #include "Epetra_SerialComm.h" #endif #include "Epetra_Map.h" #include "Epetra_Vector.h" #include "Epetra_CrsMatrix.h" #include "EpetraExt_OperatorOut.h" #include "EpetraExt_CrsMatrixIn.h" #include "AztecOO_Operator.h" #include "Epetra_InvOperator.h" #include <string> // prototypes int checkValues( double x, double y, string message = "", bool verbose = false) { if (fabs((x-y)/x) > 0.01) { return(1); if (verbose) cout << "********** " << message << " check failed.********** " << endl; } else { if (verbose) cout << message << " check OK." << endl; return(0); } } int main(int argc, char *argv[]) { #ifdef HAVE_MPI MPI_Init(&argc,&argv); Epetra_MpiComm comm (MPI_COMM_WORLD); #else Epetra_SerialComm comm; #endif int MyPID = comm.MyPID(); bool verbose = false; bool verbose1 = false; // Check if we should print results to standard out if (argc > 1) { if ((argv[1][0] == '-') && (argv[1][1] == 'v')) { verbose1 = true; if (MyPID==0) verbose = true; } } if (verbose1) cout << comm << endl; // Uncomment the next three lines to debug in mpi mode //int tmp; //if (MyPID==0) cin >> tmp; //comm.Barrier(); Epetra_CrsMatrix * A; EPETRA_CHK_ERR(EpetraExt::MatlabFileToCrsMatrix("A.dat", comm, A)); Epetra_Vector x(A->OperatorDomainMap()); Epetra_Vector b(A->OperatorRangeMap()); x.Random(); A->Apply(x,b); // Generate RHS from x Epetra_Vector xx(x); // Copy x to xx for later use Epetra_LinearProblem problem(A, &x, &b); // Construct a solver object for this problem AztecOO solver(problem); solver.SetAztecOption(AZ_precond, AZ_none); if (!verbose1) solver.SetAztecOption(AZ_output, AZ_none); solver.SetAztecOption(AZ_kspace, A->NumGlobalRows()); AztecOO_Operator AOpInv(&solver, A->NumGlobalRows()); Epetra_InvOperator AInvOp(&AOpInv); EPETRA_CHK_ERR(EpetraExt::OperatorToMatlabFile("Ainv.dat", AInvOp)); comm.Barrier(); Epetra_CrsMatrix * AInv; EPETRA_CHK_ERR(EpetraExt::MatlabFileToCrsMatrix("Ainv.dat", comm, AInv)); EPETRA_CHK_ERR(AInv->Apply(b,x)); EPETRA_CHK_ERR(x.Update(1.0, xx, -1.0)); double residual = 0.0; EPETRA_CHK_ERR(x.Norm2(&residual)); if (verbose) cout << "Norm of difference between computed x and exact x = " << residual << endl; int ierr = checkValues(residual,0.0,"Norm of difference between computed A1x1 and A1x1 from file", verbose); delete A; delete AInv; #ifdef HAVE_MPI MPI_Finalize() ; #endif return(ierr); }
Definition at line 102 of file EpetraExt_MatlabEngine.h.
EpetraExt::EpetraExt_MatlabEngine::EpetraExt_MatlabEngine | ( | const Epetra_Comm & | Comm | ) |
EpetraExt_MatlabEngine constructor which creates a MatlabEngine object with a connection to an instance of the application Matlab by starting a new Matlab process.
Comm | (In) An Epetra_Comm object. |
Definition at line 52 of file EpetraExt_MatlabEngine.cpp.
EpetraExt::EpetraExt_MatlabEngine::~EpetraExt_MatlabEngine | ( | void | ) |
EpetraExt_MatlabEngine destructor which closes the connection to Matlab which causes the Matlab process to also exit.
Definition at line 60 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::EvalString | ( | char * | command, | |
char * | outputBuffer = NULL , |
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int | outputBufferSize = -1 | |||
) |
Sends a command to Matlab.
Any command that can normally be typed in at the Matlab command line can be passed in to EvalString(char* command). Commands such as 'help desk', 'edit', and 'plot(MATRIX)' will pop up an interactive window.
command | (In) the matlab command to run | |
outputBuffer | (Out) (Optional) a user preallocated buffer for Matlab text output | |
outputBufferSize | (In) (Optional) the size of the outputBuffer |
Definition at line 68 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::PutMultiVector | ( | const Epetra_MultiVector & | A, | |
const char * | variableName | |||
) |
Puts a copy of the serial or distributed MultiVector into the Matlab workspace.
A | (In) the Epetra_MultiVector to put into Matlab | |
variableName | (In) the variable name in the Matlab workspace of the Matlab double array (matrix) that will contain the values of the MultiVector |
Definition at line 85 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::PutRowMatrix | ( | const Epetra_RowMatrix & | A, | |
const char * | variableName, | |||
bool | transA | |||
) |
Puts a copy of the serial or distributed RowMatrix into the Matlab workspace.
A | (In) the Epetra_RowMatrix to put into Matlab | |
variableName | (In) the variable name in the Matlab workspace of the Matlab sparse double array (matrix) that will contain the values of the RowMatrix | |
transA | (In) if true then the transpose of A is put into Matlab NOTE: It is faster to put the transpose of A into Matlab since Matlab stores matrices in column-major form whereas Epetra stores them in row-major form. |
Definition at line 109 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::PutCrsGraph | ( | const Epetra_CrsGraph & | A, | |
const char * | variableName, | |||
bool | transA | |||
) |
not implemented yet
Definition at line 157 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::PutSerialDenseMatrix | ( | const Epetra_SerialDenseMatrix & | A, | |
const char * | variableName, | |||
int | proc = 0 | |||
) |
Puts a copy of the SerialDenseMatrix into the Matlab workspace.
A | (In) the Epetra_SerialDenseMatrix to put into Matlab | |
variableName | (In) the variable name in the Matlab workspace of the Matlab double array (matrix) that will contain the values of the SerialDenseMatrix | |
proc | (In) for serial environment set to 0 for a parallel environment set to the process ID that owns the SerialDenseMatrix |
Definition at line 162 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::PutIntSerialDenseMatrix | ( | const Epetra_IntSerialDenseMatrix & | A, | |
const char * | variableName, | |||
int | proc = 0 | |||
) |
Puts a copy of the IntSerialDenseMatrix into the Matlab workspace.
A | (In) the Epetra_IntSerialDenseMatrix to put into Matlab | |
variableName | (In) the variable name in the Matlab workspace of the Matlab double array (matrix) that will contain the values of the IntSerialDenseMatrix | |
proc | (In) for serial environment set to 0 for a parallel environment set to the process ID that owns the IntSerialDenseMatrix |
Definition at line 222 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::PutBlockMap | ( | const Epetra_BlockMap & | blockMap, | |
const char * | variableName, | |||
bool | transA | |||
) |
Puts a copy of the BlockMap or Map into the Matlab workspace.
blockMap | (In) the Epetra_BlockMap to put into Matlab | |
variableName | (In) the variable name in the Matlab workspace of the Matlab sparse double array (matrix) that will contain the values of the BlockMap | |
transA | (In) if true then the transpose of blockMap is put into Matlab NOTE: It is faster to put the transpose of blockMap into Matlab since Matlab stores matrices in column-major form whereas Epetra stores them in row-major form. |
Definition at line 326 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::PutIntoMatlab | ( | const char * | variableName, | |
mxArray * | matlabA | |||
) |
Puts a mxArray into Matlab.
The Matlab provided C library provides mxArray which is used to construct and fill a Matlab object before sending it to Matlab to be put into the Matlab workspace. The mxArray is copied into the Matlab memory space and is not needed after it has been passed to Matlab. mxArrays should be destroyed using mxDestoryArray(mxArray) when they are no longer needed by the C/C++ program using them. Objects in Matlab must be destroyed using EvalString(char* command) and the appropriate Matlab command to destroy the object. EpetraExt::MatlabEngine uses PutIntoMatlab to pass all mxArrays it generates into Matlab. However, a user can create, fill, and put his/her own mxArrays into Matlab using this method. To create a mxArray mex.h must be included. For more information on how to use mxArrays see Matlab's documentation (type helpdesk at the Matlab command prompt) and see the External API Reference section.
variableName | (In) the name for the mxArray once it has been put into the Matlab workspace | |
matlabA | (In) the mxArray to put into the Matlab workspace |
Definition at line 366 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::GetMultiVector | ( | const char * | variableName, | |
Epetra_MultiVector & | A | |||
) |
Puts a Matlab variable into a MultiVector.
The values from the Matlab variable are exported to the MultiVector using an export object. Therefore the MultiVector must be prepared by the user just like any MultiVector would be before calling an export.
variableName | (In) the name of the Matlab variable to be put into the given MultiVector | |
A | (In) the MultiVector to put the Matlab variable values into |
Definition at line 381 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::GetSerialDenseMatrix | ( | const char * | variableName, | |
Epetra_SerialDenseMatrix & | A, | |||
int | proc = 0 | |||
) |
Puts a Matlab variable into a SerialDenseMatrix on the specified PE.
The SerialDenseMatrix must be constructed by the user and have the proper amount of space to hold the values that will be copied from the given Matlab variable.
variableName | (In) the name of the Matlab variable to be put into the given SerialDenseMatrix | |
A | (In) the SerialDenseMatrix to put the Matlab variable values into | |
proc | (In) the PE that will own the SerialDenseMatrix |
Definition at line 422 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::GetIntSerialDenseMatrix | ( | const char * | variableName, | |
Epetra_IntSerialDenseMatrix & | A, | |||
int | proc = 0 | |||
) |
Puts a Matlab variable into a IntSerialDenseMatrix on the specified PE.
The IntSerialDenseMatrix must be constructed by the user and have the proper amount of space to hold the values that will be copied from the given Matlab variable.
variableName | (In) the name of the Matlab variable to be put into the given IntSerialDenseMatrix | |
A | (In) the IntSerialDenseMatrix to put the Matlab variable values into | |
proc | (In) the PE that will own the IntSerialDenseMatrix |
Definition at line 447 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::GetCrsMatrix | ( | const char * | variableName, | |
Epetra_CrsMatrix & | A, | |||
bool | getTrans | |||
) |
Puts a Matlab variable into a CrsMatrix.
The values from the Matlab variable are exported to the CrsMatrix using an export object. Therefore the CrsMatrix must be prepared by the user just like any CrsMatrix would be before calling an export.
variableName | (In) the name of the Matlab variable to be put into the given CrsMatrix | |
A | (In) the CrsMatrix to put the Matlab variable values into | |
getTrans | (In) if false then a temporary Matlab variable is created TRANS_variableName if true then the transpose of A copied from Matlab NOTE: It is faster to copy the transpose of A from Matlab since Matlab stores matrices in column-major form whereas Epetra stores them in row-major form. |
Definition at line 478 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::GetmxArrayDimensions | ( | mxArray * | matlabA, | |
bool & | isSparse, | |||
int & | numRows, | |||
int & | numCols, | |||
int & | numNonZeros | |||
) |
Get general information about the mxArray. For internal use but can be used by an advanced user.
Makes several Matlab function calls on the mxArray in order to determine the number of rows, columns, nonzeros, and whether or not the mxArray is sparse.
matlabA | (In) the mxArray to get information about | |
isSparse | (Out) true if the mxArray is sparse | |
numRows | (Out) the number of rows in the mxArray | |
numCols | (Out) the number of columns in the mxArray | |
numNonZeros | (Out) the number of nonzeros in the mxArray |
Definition at line 563 of file EpetraExt_MatlabEngine.cpp.
int EpetraExt::EpetraExt_MatlabEngine::GetmxArray | ( | const char * | variableName, | |
mxArray ** | matlabA | |||
) |
Get a mxArray from Matlab. For internal use but can be used by an advanced user.
Calls the Matlab provided engGetVariable function which copies the specified variable from the Matlab workspace into a mxArray. Hence any changes to mxArray will not show up in Matlab, and any changes to the Matlab variable in Matlab will not show up in the mxArray. When finished with the mxArray mxDestroyArray should be called on the mxArray. Matlab appears to perform a copy to a new mxArray each time engGetVariable is called.
variableName | (In) the mxArray to get from the Matlab workspace | |
matlabA | (Out) a pointer to a mxArray* to put the mxArray that engGetVariable returns |
Definition at line 586 of file EpetraExt_MatlabEngine.cpp.