Actual source code: hdf5v.c

petsc-3.4.4 2014-03-13
  1: #include <petsc-private/viewerimpl.h>    /*I   "petscsys.h"   I*/
  2: #include <petscviewerhdf5.h>    /*I   "petscviewerhdf5.h"   I*/

  4: typedef struct GroupList {
  5:   const char       *name;
  6:   struct GroupList *next;
  7: } GroupList;

  9: typedef struct {
 10:   char          *filename;
 11:   PetscFileMode btype;
 12:   hid_t         file_id;
 13:   PetscInt      timestep;
 14:   GroupList     *groups;
 15: } PetscViewer_HDF5;

 19: static PetscErrorCode PetscViewerFileClose_HDF5(PetscViewer viewer)
 20: {
 21:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)viewer->data;
 22:   PetscErrorCode   ierr;

 25:   PetscFree(hdf5->filename);
 26:   if (hdf5->file_id) H5Fclose(hdf5->file_id);
 27:   return(0);
 28: }

 32: PetscErrorCode PetscViewerDestroy_HDF5(PetscViewer viewer)
 33: {
 34:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
 35:   PetscErrorCode   ierr;

 38:   PetscViewerFileClose_HDF5(viewer);
 39:   while (hdf5->groups) {
 40:     GroupList *tmp = hdf5->groups->next;

 42:     PetscFree(hdf5->groups->name);
 43:     PetscFree(hdf5->groups);
 44:     hdf5->groups = tmp;
 45:   }
 46:   PetscFree(hdf5);
 47:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetName_C",NULL);
 48:   PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetMode_C",NULL);
 49:   return(0);
 50: }

 54: PetscErrorCode  PetscViewerFileSetMode_HDF5(PetscViewer viewer, PetscFileMode type)
 55: {
 56:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

 60:   hdf5->btype = type;
 61:   return(0);
 62: }

 66: PetscErrorCode  PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[])
 67: {
 68:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
 69: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
 70:   MPI_Info          info = MPI_INFO_NULL;
 71: #endif
 72:   hid_t             plist_id;
 73:   herr_t            herr;
 74:   PetscErrorCode    ierr;

 77:   PetscStrallocpy(name, &hdf5->filename);
 78:   /* Set up file access property list with parallel I/O access */
 79:   plist_id = H5Pcreate(H5P_FILE_ACCESS);
 80: #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO)
 81:   herr = H5Pset_fapl_mpio(plist_id, PetscObjectComm((PetscObject)viewer), info);CHKERRQ(herr);
 82: #endif
 83:   /* Create or open the file collectively */
 84:   switch (hdf5->btype) {
 85:   case FILE_MODE_READ:
 86:     hdf5->file_id = H5Fopen(name, H5F_ACC_RDONLY, plist_id);
 87:     break;
 88:   case FILE_MODE_APPEND:
 89:     hdf5->file_id = H5Fopen(name, H5F_ACC_RDWR, plist_id);
 90:     break;
 91:   case FILE_MODE_WRITE:
 92:     hdf5->file_id = H5Fcreate(name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id);
 93:     break;
 94:   default:
 95:     SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()");
 96:   }
 97:   if (hdf5->file_id < 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_LIB, "H5Fcreate failed for %s", name);
 98:   H5Pclose(plist_id);
 99:   return(0);
100: }

104: PETSC_EXTERN PetscErrorCode PetscViewerCreate_HDF5(PetscViewer v)
105: {
106:   PetscViewer_HDF5 *hdf5;
107:   PetscErrorCode   ierr;

110:   PetscNewLog(v, PetscViewer_HDF5, &hdf5);

112:   v->data         = (void*) hdf5;
113:   v->ops->destroy = PetscViewerDestroy_HDF5;
114:   v->ops->flush   = 0;
115:   hdf5->btype     = (PetscFileMode) -1;
116:   hdf5->filename  = 0;
117:   hdf5->timestep  = -1;
118:   hdf5->groups    = NULL;

120:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetName_C",PetscViewerFileSetName_HDF5);
121:   PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetMode_C",PetscViewerFileSetMode_HDF5);
122:   return(0);
123: }

127: /*@C
128:    PetscViewerHDF5Open - Opens a file for HDF5 input/output.

130:    Collective on MPI_Comm

132:    Input Parameters:
133: +  comm - MPI communicator
134: .  name - name of file
135: -  type - type of file
136: $    FILE_MODE_WRITE - create new file for binary output
137: $    FILE_MODE_READ - open existing file for binary input
138: $    FILE_MODE_APPEND - open existing file for binary output

140:    Output Parameter:
141: .  hdf5v - PetscViewer for HDF5 input/output to use with the specified file

143:    Level: beginner

145:    Note:
146:    This PetscViewer should be destroyed with PetscViewerDestroy().

148:    Concepts: HDF5 files
149:    Concepts: PetscViewerHDF5^creating

151: .seealso: PetscViewerASCIIOpen(), PetscViewerSetFormat(), PetscViewerDestroy(),
152:           VecView(), MatView(), VecLoad(), MatLoad(),
153:           PetscFileMode, PetscViewer
154: @*/
155: PetscErrorCode  PetscViewerHDF5Open(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *hdf5v)
156: {

160:   PetscViewerCreate(comm, hdf5v);
161:   PetscViewerSetType(*hdf5v, PETSCVIEWERHDF5);
162:   PetscViewerFileSetMode(*hdf5v, type);
163:   PetscViewerFileSetName(*hdf5v, name);
164:   return(0);
165: }

169: /*@C
170:   PetscViewerHDF5GetFileId - Retrieve the file id, this file ID then can be used in direct HDF5 calls

172:   Not collective

174:   Input Parameter:
175: . viewer - the PetscViewer

177:   Output Parameter:
178: . file_id - The file id

180:   Level: intermediate

182: .seealso: PetscViewerHDF5Open()
183: @*/
184: PetscErrorCode  PetscViewerHDF5GetFileId(PetscViewer viewer, hid_t *file_id)
185: {
186:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

190:   if (file_id) *file_id = hdf5->file_id;
191:   return(0);
192: }

196: /*@C
197:   PetscViewerHDF5PushGroup - Set the current HDF5 group for output

199:   Not collective

201:   Input Parameters:
202: + viewer - the PetscViewer
203: - name - The group name

205:   Level: intermediate

207: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PopGroup(),PetscViewerHDF5GetGroup()
208: @*/
209: PetscErrorCode  PetscViewerHDF5PushGroup(PetscViewer viewer, const char *name)
210: {
211:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
212:   GroupList        *groupNode;
213:   PetscErrorCode   ierr;

218:   PetscMalloc(sizeof(GroupList), &groupNode);
219:   PetscStrallocpy(name, (char**) &groupNode->name);

221:   groupNode->next = hdf5->groups;
222:   hdf5->groups    = groupNode;
223:   return(0);
224: }

228: /*@
229:   PetscViewerHDF5PopGroup - Return the current HDF5 group for output to the previous value

231:   Not collective

233:   Input Parameter:
234: . viewer - the PetscViewer

236:   Level: intermediate

238: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5GetGroup()
239: @*/
240: PetscErrorCode  PetscViewerHDF5PopGroup(PetscViewer viewer)
241: {
242:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;
243:   GroupList        *groupNode;
244:   PetscErrorCode   ierr;

248:   if (!hdf5->groups) SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "HDF5 group stack is empty, cannot pop");
249:   groupNode    = hdf5->groups;
250:   hdf5->groups = hdf5->groups->next;
251:   PetscFree(groupNode->name);
252:   PetscFree(groupNode);
253:   return(0);
254: }

258: /*@C
259:   PetscViewerHDF5GetGroup - Get the current HDF5 group for output. If none has been assigned, returns NULL.

261:   Not collective

263:   Input Parameter:
264: . viewer - the PetscViewer

266:   Output Parameter:
267: . name - The group name

269:   Level: intermediate

271: .seealso: PetscViewerHDF5Open(),PetscViewerHDF5PushGroup(),PetscViewerHDF5PopGroup()
272: @*/
273: PetscErrorCode  PetscViewerHDF5GetGroup(PetscViewer viewer, const char **name)
274: {
275:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *) viewer->data;

280:   if (hdf5->groups) *name = hdf5->groups->name;
281:   else *name = NULL;
282:   return(0);
283: }

287: /*@
288:   PetscViewerHDF5IncrementTimestep - Increments the current timestep for the HDF5 output. Fields are stacked in time.

290:   Not collective

292:   Input Parameter:
293: . viewer - the PetscViewer

295:   Level: intermediate

297: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5SetTimestep(), PetscViewerHDF5GetTimestep()
298: @*/
299: PetscErrorCode PetscViewerHDF5IncrementTimestep(PetscViewer viewer)
300: {
301:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

305:   ++hdf5->timestep;
306:   return(0);
307: }

311: /*@
312:   PetscViewerHDF5SetTimestep - Set the current timestep for the HDF5 output. Fields are stacked in time. A timestep
313:   of -1 disables blocking with timesteps.

315:   Not collective

317:   Input Parameters:
318: + viewer - the PetscViewer
319: - timestep - The timestep number

321:   Level: intermediate

323: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5GetTimestep()
324: @*/
325: PetscErrorCode  PetscViewerHDF5SetTimestep(PetscViewer viewer, PetscInt timestep)
326: {
327:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

331:   hdf5->timestep = timestep;
332:   return(0);
333: }

337: /*@
338:   PetscViewerHDF5GetTimestep - Get the current timestep for the HDF5 output. Fields are stacked in time.

340:   Not collective

342:   Input Parameter:
343: . viewer - the PetscViewer

345:   Output Parameter:
346: . timestep - The timestep number

348:   Level: intermediate

350: .seealso: PetscViewerHDF5Open(), PetscViewerHDF5IncrementTimestep(), PetscViewerHDF5SetTimestep()
351: @*/
352: PetscErrorCode  PetscViewerHDF5GetTimestep(PetscViewer viewer, PetscInt *timestep)
353: {
354:   PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data;

359:   *timestep = hdf5->timestep;
360:   return(0);
361: }

363: #if defined(oldhdf4stuff)
366: PetscErrorCode  PetscViewerHDF5WriteSDS(PetscViewer viewer, float *xf, int d, int *dims,int bs)
367: {
368:   int              i;
369:   PetscViewer_HDF5 *vhdf5 = (PetscViewer_HDF5*)viewer->data;
370:   int32            sds_id,zero32[3],dims32[3];

373:   for (i = 0; i < d; i++) {
374:     zero32[i] = 0;
375:     dims32[i] = dims[i];
376:   }
377:   sds_id = SDcreate(vhdf5->sd_id, "Vec", DFNT_FLOAT32, d, dims32);
378:   if (sds_id < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_LIB,"SDcreate failed");
379:   SDwritedata(sds_id, zero32, 0, dims32, xf);
380:   SDendaccess(sds_id);
381:   return(0);
382: }

384: #endif