Using MATLAB with PETSc — PETSc 3.17.4 documentation

# 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 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/petsc/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

    PetscMatlabEnginePrintOutput(PetscMatlabEngine,FILE*).

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

If you are running PETSc on a cluster (or machine) that does not have a license for MATLAB, you might able to run MATLAB on the `head node` of the cluster or some other machine accessible to the cluster using the `-matlab_engine_host hostname` option.

## Licensing the MATLAB Compute Engine on a cluster

To activate MATLAB on head node which does not have access to the internet. (see also: https://www.mathworks.com/matlabcentral/answers/259627-how-do-i-activate-matlab-or-other-mathworks-products-without-an-internet-connection)

First ssh into the head node using the command: ssh node_name

Obtain the Host Id using the command: ip addr | grep ether (More details found on: http://www.mathworks.com/matlabcentral/answers/101892) You will see something like this: link/ether xx:xx:xx:xx:xx:xx ABC yy:yy:yy:yy:yy:yy Note the value: xx:xx:xx:xx:xx:xx

Login to your MathWorks Account from a computer which has internet access. You will see the available license that your account has. Select a license from the list.

Then, select Install and Activate option and select the Activate to Retrieve License File option.

Enter the information and click Continue.

An option to download the License file will appear. Download it and copy the license file to the cluster (your home directory). Now, launch MATLAB where you have sshed into your head node.

Select the Activate manually without the internet option and click Next >. Browse and locate the license file.

MATLAB is activated and ready to use.