Actual source code: vmatlab.c
1: #include <petsc/private/viewerimpl.h>
2: #include <mat.h>
4: typedef struct {
5: MATFile *ep;
6: PetscMPIInt rank;
7: PetscFileMode btype;
8: } PetscViewer_Matlab;
10: /*@C
11: PetscViewerMatlabPutArray - Puts an array into the `PETSCVIEWERMATLAB` viewer.
13: Not Collective, only processor zero saves `array`
15: Input Parameters:
16: + mfile - the viewer
17: . m - the first dimensions of `array`
18: . n - the second dimensions of `array`
19: . array - the array (represented in one dimension)
20: - name - the MATLAB name of `array`
22: Level: advanced
24: Note:
25: Only writes `array` values on processor 0.
27: .seealso: `PETSCVIEWERMATLAB`, `PetscViewerMatlabGetArray()`
28: @*/
29: PetscErrorCode PetscViewerMatlabPutArray(PetscViewer mfile, int m, int n, const PetscScalar *array, const char *name)
30: {
31: PetscViewer_Matlab *ml;
32: mxArray *mat;
34: PetscFunctionBegin;
35: PetscCheck(mfile, PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Null argument: probably PETSC_VIEWER_MATLAB_() failed");
36: ml = (PetscViewer_Matlab *)mfile->data;
37: if (!ml->rank) {
38: PetscCall(PetscInfo(mfile, "Putting MATLAB array %s\n", name));
39: #if !defined(PETSC_USE_COMPLEX)
40: mat = mxCreateDoubleMatrix(m, n, mxREAL);
41: #else
42: mat = mxCreateDoubleMatrix(m, n, mxCOMPLEX);
43: #endif
44: PetscCall(PetscArraycpy(mxGetPr(mat), array, m * n));
45: matPutVariable(ml->ep, name, mat);
47: PetscCall(PetscInfo(mfile, "Put MATLAB array %s\n", name));
48: }
49: PetscFunctionReturn(PETSC_SUCCESS);
50: }
52: PetscErrorCode PetscViewerMatlabPutVariable(PetscViewer viewer, const char *name, void *mat)
53: {
54: PetscViewer_Matlab *ml = (PetscViewer_Matlab *)viewer->data;
56: PetscFunctionBegin;
57: matPutVariable(ml->ep, name, (mxArray *)mat);
58: PetscFunctionReturn(PETSC_SUCCESS);
59: }
61: /*@C
62: PetscViewerMatlabGetArray - Gets a variable from a `PETSCVIEWERMATLAB` viewer into an array
64: Not Collective; only processor zero reads in the array
66: Input Parameters:
67: + mfile - the MATLAB file viewer
68: . m - the first dimensions of `array`
69: . n - the second dimensions of `array`
70: . array - the array (represented in one dimension), must of be length `m` * `n`
71: - name - the MATLAB name of `array`
73: Level: advanced
75: Note:
76: Only reads in `array` values on processor 0.
78: .seealso: `PETSCVIEWERMATLAB`, `PetscViewerMatlabPutArray()`
79: @*/
80: PetscErrorCode PetscViewerMatlabGetArray(PetscViewer mfile, int m, int n, PetscScalar *array, const char *name)
81: {
82: PetscViewer_Matlab *ml;
83: mxArray *mat;
85: PetscFunctionBegin;
86: PetscCheck(mfile, PETSC_COMM_SELF, PETSC_ERR_ARG_NULL, "Null argument: probably PETSC_VIEWER_MATLAB_() failed");
87: ml = (PetscViewer_Matlab *)mfile->data;
88: if (!ml->rank) {
89: PetscCall(PetscInfo(mfile, "Getting MATLAB array %s\n", name));
90: mat = matGetVariable(ml->ep, name);
91: PetscCheck(mat, PETSC_COMM_SELF, PETSC_ERR_LIB, "Unable to get array %s from matlab", name);
92: PetscCall(PetscArraycpy(array, mxGetPr(mat), m * n));
93: PetscCall(PetscInfo(mfile, "Got MATLAB array %s\n", name));
94: }
95: PetscFunctionReturn(PETSC_SUCCESS);
96: }
98: static PetscErrorCode PetscViewerFileSetMode_Matlab(PetscViewer viewer, PetscFileMode type)
99: {
100: PetscViewer_Matlab *vmatlab = (PetscViewer_Matlab *)viewer->data;
102: PetscFunctionBegin;
103: vmatlab->btype = type;
104: PetscFunctionReturn(PETSC_SUCCESS);
105: }
107: /*
108: Actually opens the file
109: */
110: static PetscErrorCode PetscViewerFileSetName_Matlab(PetscViewer viewer, const char name[])
111: {
112: PetscViewer_Matlab *vmatlab = (PetscViewer_Matlab *)viewer->data;
113: PetscFileMode type = vmatlab->btype;
115: PetscFunctionBegin;
116: PetscCheck(type != (PetscFileMode)-1, PETSC_COMM_SELF, PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
117: if (vmatlab->ep) matClose(vmatlab->ep);
119: /* only first processor opens file */
120: if (!vmatlab->rank) {
121: if (type == FILE_MODE_READ) vmatlab->ep = matOpen(name, "r");
122: else if (type == FILE_MODE_WRITE) vmatlab->ep = matOpen(name, "w");
123: else {
124: PetscCheck(type != FILE_MODE_UNDEFINED, PetscObjectComm((PetscObject)viewer), PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
125: SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_SUP, "Unsupported file mode %s", PetscFileModes[type]);
126: }
127: }
128: PetscFunctionReturn(PETSC_SUCCESS);
129: }
131: static PetscErrorCode PetscViewerDestroy_Matlab(PetscViewer v)
132: {
133: PetscViewer_Matlab *vf = (PetscViewer_Matlab *)v->data;
135: PetscFunctionBegin;
136: if (vf->ep) matClose(vf->ep);
137: PetscCall(PetscFree(vf));
138: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileSetName_C", NULL));
139: PetscCall(PetscObjectComposeFunction((PetscObject)v, "PetscViewerFileSetMode_C", NULL));
140: PetscFunctionReturn(PETSC_SUCCESS);
141: }
143: /*MC
144: PETSCVIEWERMATLAB - A viewer that saves the variables into a MATLAB .mat file that may be read into MATLAB
145: with load('filename').
147: Level: intermediate
149: Notes:
150: Currently can only save PETSc vectors to .mat files, not matrices (use the `PETSCVIEWERBINARY` and
151: ${PETSC_DIR}/share/petsc/matlab/PetscBinaryRead.m to read matrices into MATLAB).
153: For parallel vectors obtained with `DMCreateGlobalVector()` or `DMGetGlobalVector()` the vectors are saved to
154: the .mat file in natural ordering. You can use DMView() to save the `DMDA` information to the .mat file
155: the fields in the MATLAB loaded da variable give the array dimensions so you can reshape the MATLAB
156: vector to the same multidimensional shape as it had in PETSc for plotting etc. For example,
158: In your PETSc C/C++ code (assuming a two dimensional `DMDA` with one degree of freedom per node)
159: .vb
160: PetscObjectSetName((PetscObject)x,"x");
161: VecView(x,PETSC_VIEWER_MATLAB_WORLD);
162: PetscObjectSetName((PetscObject)da,"da");
163: DMView(x,PETSC_VIEWER_MATLAB_WORLD);
164: .ve
165: Then from MATLAB
166: .vb
167: load('matlaboutput.mat') % matlaboutput.mat is the default filename
168: xnew = zeros(da.n,da.m);
169: xnew(:) = x; % reshape one dimensional vector back to two dimensions
170: .ve
172: If you wish to put the same variable into the .mat file several times you need to give it a new
173: name before each call to view.
175: Use `PetscViewerMatlabPutArray()` to just put an array of doubles into the .mat file
177: .seealso: `PETSC_VIEWER_MATLAB_()`, `PETSC_VIEWER_MATLAB_SELF`, `PETSC_VIEWER_MATLAB_WORLD`, `PetscViewerCreate()`,
178: `PetscViewerMatlabOpen()`, `VecView()`, `DMView()`, `PetscViewerMatlabPutArray()`, `PETSCVIEWERBINARY`, `PETSCVIEWERASCII`, `PETSCVIEWERDRAW`,
179: `PETSC_VIEWER_STDOUT_()`, `PetscViewerFileSetName()`, `PetscViewerFileSetMode()`, `PetscViewerFormat`, `PetscMatlabEngine`
180: M*/
181: PETSC_EXTERN PetscErrorCode PetscViewerCreate_Matlab(PetscViewer viewer)
182: {
183: PetscViewer_Matlab *e;
185: PetscFunctionBegin;
186: PetscCall(PetscNew(&e));
187: PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer), &e->rank));
188: e->btype = FILE_MODE_UNDEFINED;
189: viewer->data = (void *)e;
191: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileSetName_C", PetscViewerFileSetName_Matlab));
192: PetscCall(PetscObjectComposeFunction((PetscObject)viewer, "PetscViewerFileSetMode_C", PetscViewerFileSetMode_Matlab));
194: viewer->ops->destroy = PetscViewerDestroy_Matlab;
195: PetscFunctionReturn(PETSC_SUCCESS);
196: }
198: /*@C
199: PetscViewerMatlabOpen - Opens a MATLAB .mat file for output
201: Collective
203: Input Parameters:
204: + comm - MPI communicator
205: . name - name of file
206: - type - type of file
207: .vb
208: FILE_MODE_WRITE - create new file for MATLAB output
209: FILE_MODE_READ - open existing file for MATLAB input
210: FILE_MODE_WRITE - open existing file for MATLAB output
211: .ve
213: Output Parameter:
214: . binv - PetscViewer for MATLAB output to use with the specified file
216: Level: beginner
218: Notes:
219: This `PetscViewer` should be destroyed with `PetscViewerDestroy()`.
221: For writing files it only opens the file on processor 0 in the communicator.
223: This only saves `Vec`s it cannot be used to save `Mat`s. We recommend using the `PETSCVIEWERBINARY` to save objects to be loaded into MATLAB
224: instead of this routine.
226: PETSc must be configured with the option `--with-matlab` for this functionality
228: .seealso: `PETSCVIEWERMATLAB`, `PetscViewerASCIIOpen()`, `PetscViewerPushFormat()`, `PetscViewerDestroy()`, `PETSCVIEWERBINARY`, `PetscViewerBinaryOpen()`
229: `VecView()`, `MatView()`, `VecLoad()`, `MatLoad()`
230: @*/
231: PetscErrorCode PetscViewerMatlabOpen(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *binv)
232: {
233: PetscFunctionBegin;
234: PetscCall(PetscViewerCreate(comm, binv));
235: PetscCall(PetscViewerSetType(*binv, PETSCVIEWERMATLAB));
236: PetscCall(PetscViewerFileSetMode(*binv, type));
237: PetscCall(PetscViewerFileSetName(*binv, name));
238: PetscFunctionReturn(PETSC_SUCCESS);
239: }
241: static PetscMPIInt Petsc_Viewer_Matlab_keyval = MPI_KEYVAL_INVALID;
243: /*@C
244: PETSC_VIEWER_MATLAB_ - Creates a `PETSCVIEWERMATLAB` `PetscViewer` shared by all processors
245: in a communicator.
247: Collective
249: Input Parameter:
250: . comm - the MPI communicator to share the MATLAB `PetscViewer`
252: Options Database Key:
253: . -viewer_matlab_filename <name> - name of the MATLAB file
255: Environmental variable:
256: . `PETSC_VIEWER_MATLAB_FILENAME` - name of the MATLAB file
258: Level: intermediate
260: Notes:
261: This object is destroyed in `PetscFinalize()`, `PetscViewerDestroy()` should never be called on it
263: Unlike almost all other PETSc routines, `PETSC_VIEWER_MATLAB_()` does not return
264: an error code. The MATLAB `PetscViewer` is usually used in the form `XXXView(XXX object, PETSC_VIEWER_MATLAB_(comm))`
266: Use `PETSC_VIEWER_SOCKET_()` or `PetscViewerSocketOpen()` to communicator with an interactive MATLAB session.
268: .seealso: `PETSC_VIEWER_MATLAB_WORLD`, `PETSC_VIEWER_MATLAB_SELF`, `PetscViewerMatlabOpen()`, `PetscViewerCreate()`,
269: `PetscViewerDestroy()`
270: @*/
271: PetscViewer PETSC_VIEWER_MATLAB_(MPI_Comm comm)
272: {
273: PetscErrorCode ierr;
274: PetscBool flg;
275: PetscViewer viewer;
276: char fname[PETSC_MAX_PATH_LEN];
277: MPI_Comm ncomm;
279: PetscFunctionBegin;
280: ierr = PetscCommDuplicate(comm, &ncomm, NULL);
281: if (ierr) {
282: PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_MATLAB_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
283: PetscFunctionReturn(NULL);
284: }
285: if (Petsc_Viewer_Matlab_keyval == MPI_KEYVAL_INVALID) {
286: ierr = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN, MPI_COMM_NULL_DELETE_FN, &Petsc_Viewer_Matlab_keyval, 0);
287: if (ierr) {
288: PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_MATLAB_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
289: PetscFunctionReturn(NULL);
290: }
291: }
292: ierr = MPI_Comm_get_attr(ncomm, Petsc_Viewer_Matlab_keyval, (void **)&viewer, (int *)&flg);
293: if (ierr) {
294: PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_MATLAB_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
295: PetscFunctionReturn(NULL);
296: }
297: if (!flg) { /* PetscViewer not yet created */
298: ierr = PetscOptionsGetenv(ncomm, "PETSC_VIEWER_MATLAB_FILENAME", fname, PETSC_MAX_PATH_LEN, &flg);
299: if (ierr) {
300: PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_MATLAB_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
301: PetscFunctionReturn(NULL);
302: }
303: if (!flg) {
304: ierr = PetscStrncpy(fname, "matlaboutput.mat", sizeof(fname));
305: if (ierr) {
306: PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_MATLAB_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
307: PetscFunctionReturn(NULL);
308: }
309: }
310: ierr = PetscViewerMatlabOpen(ncomm, fname, FILE_MODE_WRITE, &viewer);
311: ((PetscObject)viewer)->persistent = PETSC_TRUE;
312: if (ierr) {
313: PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_MATLAB_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
314: PetscFunctionReturn(NULL);
315: }
316: ierr = PetscObjectRegisterDestroy((PetscObject)viewer);
317: if (ierr) {
318: PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_MATLAB_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
319: PetscFunctionReturn(NULL);
320: }
321: ierr = MPI_Comm_set_attr(ncomm, Petsc_Viewer_Matlab_keyval, (void *)viewer);
322: if (ierr) {
323: PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_MATLAB_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_INITIAL, " ");
324: PetscFunctionReturn(NULL);
325: }
326: }
327: ierr = PetscCommDestroy(&ncomm);
328: if (ierr) {
329: PetscError(PETSC_COMM_SELF, __LINE__, "PETSC_VIEWER_MATLAB_", __FILE__, PETSC_ERR_PLIB, PETSC_ERROR_REPEAT, " ");
330: PetscFunctionReturn(NULL);
331: }
332: PetscFunctionReturn(viewer);
333: }