Using MATLAB with PETSc

There are three basic ways to use MATLAB with PETSc:

  1. (Dumping Data for MATLAB) dumping files to be read into MATLAB,

  2. (Sending Data to an Interactive MATLAB Session) automatically sending data from a running PETSc program to a MATLAB process where you may interactively type MATLAB commands (or run scripts), and

  3. (Using the MATLAB Compute Engine) automatically sending data back and forth between PETSc and MATLAB where MATLAB commands are issued not interactively but from a script or the PETSc program (this uses the MATLAB Engine).

Dumping Data for MATLAB

Dumping ASCII MATLAB data

One can dump PETSc matrices and vectors to the screen in an ASCII format that MATLAB can read in directly. This is done with the command line options -vec_view ::ascii_matlab or -mat_view ::ascii_matlab. To write a a file, use -vec_view :filename.m:ascii_matlab or -mat_view :filename.m:ascii_matlab.

This causes the PETSc program to print the vectors and matrices every time VecAssemblyEnd() or MatAssemblyEnd() are called. To provide finer control over when and what vectors and matrices are dumped one can use the VecView() and MatView() functions with a viewer type of ASCII (see PetscViewerASCIIOpen(), PETSC_VIEWER_STDOUT_WORLD, PETSC_VIEWER_STDOUT_SELF, or PETSC_VIEWER_STDOUT_(MPI_Comm)). Before calling the viewer set the output type with, for example,

PetscViewerPushFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_MATLAB);
VecView(A,PETSC_VIEWER_STDOUT_WORLD);
PetscViewerPopFormat(PETSC_VIEWER_STDOUT_WORLD);

The name of each PETSc variable printed for MATLAB may be set with

PetscObjectSetName((PetscObject)A,"name");

If no name is specified, the object is given a default name using PetscObjectName().

Dumping Binary Data for MATLAB

One can also read PETSc binary files (see Viewers: Looking at PETSc Objects) directly into MATLAB via the scripts available in $PETSC_DIR/share/matlab. This requires less disk space and is recommended for all but the smallest data sizes. One can also use

PetscViewerPushFormat(viewer,PETSC_VIEWER_BINARY_MATLAB)

to dump both a PETSc binary file and a corresponding .info file which PetscReadBinaryMatlab.m will use to format the binary file in more complex cases, such as using a DMDA. For an example, see DM Tutorial ex7. In MATLAB (R2015b), one may then generate a useful structure. For example:

setenv('PETSC_DIR','~/petsc');
setenv('PETSC_ARCH','arch-darwin-double-debug');
addpath('~/petsc/share/petsc/matlab');
gridData=PetscReadBinaryMatlab('output_file');

Sending Data to an Interactive MATLAB Session

One creates a viewer to MATLAB via

PetscViewerSocketOpen(MPI_Comm,char *machine,int port,PetscViewer *v);

(port is usually set to PETSC_DEFAULT; use NULL for the machine if the MATLAB interactive session is running on the same machine as the PETSc program) and then sends matrices or vectors via

VecView(Vec A,v);
MatView(Mat B,v);

See Viewers: Looking at PETSc Objects for more on PETSc viewers. One may start the MATLAB program manually or use the PETSc command PetscStartMatlab(MPI_Comm,char *machine,char *script,FILE **fp); where machine and script may be NULL. It is also possible to start your PETSc program from MATLAB via launch().

To receive the objects in MATLAB, make sure that ${PETSC_DIR}/${PETSC_ARCH}/lib/petsc/matlab and ${PETSC_DIR}/share/petsc/matlab are in the MATLAB path. Use p = PetscOpenSocket(); (or p = PetscOpenSocket(portnum) if you provided a port number in your call to PetscViewerSocketOpen()), and then a = PetscBinaryRead(p); returns the object passed from PETSc. PetscBinaryRead() may be called any number of times. Each call should correspond on the PETSc side with viewing a single vector or matrix. close() closes the connection from MATLAB. On the PETSc side, one should destroy the viewer object with PetscViewerDestroy().

For an example, which includes sending data back to PETSc, see Vec Tutorial ex42 and the associated .m file.

Using the MATLAB Compute Engine

One creates access to the MATLAB engine via

PetscMatlabEngineCreate(MPI_Comm comm,char *machine,PetscMatlabEngine *e);

where machine is the name of the machine hosting MATLAB (NULL may be used for localhost). One can send objects to MATLAB via

PetscMatlabEnginePut(PetscMatlabEngine e,PetscObject obj);

One can get objects via

PetscMatlabEngineGet(PetscMatlabEngine e,PetscObject obj);

Similarly, one can send arrays via

PetscMatlabEnginePutArray(PetscMatlabEngine e,int m,int n,PetscScalar *array,char *name);

and get them back via

PetscMatlabEngineGetArray(PetscMatlabEngine e,int m,int n,PetscScalar *array,char *name);

One cannot use MATLAB interactively in this mode but one can send MATLAB commands via

PetscMatlabEngineEvaluate(PetscMatlabEngine,"format",...);

where format has the usual printf() format. For example,

PetscMatlabEngineEvaluate(PetscMatlabEngine,"x = \%g *y + z;",avalue);

The name of each PETSc variable passed to MATLAB may be set with

PetscObjectSetName((PetscObject)A,"name");

Text responses can be returned from MATLAB via

PetscMatlabEngineGetOutput(PetscMatlabEngine,char **);

or

PetscMatlabEnginedPrintOutput(PetscMatlabEngine,FILE*).

There is a short-cut to starting the MATLAB engine with PETSC_MATLAB_ENGINE_(MPI_Comm).