#include /*I "petscviewerhdf5.h" I*/ static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer, const char[], PetscBool, PetscBool*, H5O_type_t*); static PetscErrorCode PetscViewerHDF5HasAttribute_Internal(PetscViewer, const char[], const char[], PetscBool*); static PetscErrorCode PetscViewerHDF5GetAbsolutePath_Internal(PetscViewer viewer, const char path[], char *abspath[]) { PetscBool relative = PETSC_FALSE; const char *group; char buf[PETSC_MAX_PATH_LEN] = ""; PetscFunctionBegin; PetscCall(PetscViewerHDF5GetGroup(viewer, &group)); PetscCall(PetscViewerHDF5PathIsRelative(path, PETSC_TRUE, &relative)); if (relative) { PetscCall(PetscStrcpy(buf, group)); PetscCall(PetscStrcat(buf, "/")); PetscCall(PetscStrcat(buf, path)); PetscCall(PetscStrallocpy(buf, abspath)); } else { PetscCall(PetscStrallocpy(path, abspath)); } PetscFunctionReturn(0); } static PetscErrorCode PetscViewerHDF5CheckNamedObject_Internal(PetscViewer viewer, PetscObject obj) { PetscBool has; PetscFunctionBegin; PetscCall(PetscViewerHDF5HasObject(viewer, obj, &has)); if (!has) { const char *group; PetscCall(PetscViewerHDF5GetGroup(viewer, &group)); SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Object (dataset) \"%s\" not stored in group %s", obj->name, group ? group : "/"); } PetscFunctionReturn(0); } static PetscErrorCode PetscViewerSetFromOptions_HDF5(PetscOptionItems *PetscOptionsObject,PetscViewer v) { PetscBool flg = PETSC_FALSE, set; PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)v->data; PetscFunctionBegin; PetscOptionsHeadBegin(PetscOptionsObject,"HDF5 PetscViewer Options"); PetscCall(PetscOptionsBool("-viewer_hdf5_base_dimension2","1d Vectors get 2 dimensions in HDF5","PetscViewerHDF5SetBaseDimension2",hdf5->basedimension2,&hdf5->basedimension2,NULL)); PetscCall(PetscOptionsBool("-viewer_hdf5_sp_output","Force data to be written in single precision","PetscViewerHDF5SetSPOutput",hdf5->spoutput,&hdf5->spoutput,NULL)); PetscCall(PetscOptionsBool("-viewer_hdf5_collective","Enable collective transfer mode","PetscViewerHDF5SetCollective",flg,&flg,&set)); if (set) PetscCall(PetscViewerHDF5SetCollective(v,flg)); flg = PETSC_FALSE; PetscCall(PetscOptionsBool("-viewer_hdf5_default_timestepping","Set default timestepping state","PetscViewerHDF5SetDefaultTimestepping",flg,&flg,&set)); if (set) PetscCall(PetscViewerHDF5SetDefaultTimestepping(v,flg)); PetscOptionsHeadEnd(); PetscFunctionReturn(0); } static PetscErrorCode PetscViewerView_HDF5(PetscViewer v,PetscViewer viewer) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)v->data; PetscBool flg; PetscFunctionBegin; if (hdf5->filename) { PetscCall(PetscViewerASCIIPrintf(viewer,"Filename: %s\n",hdf5->filename)); } PetscCall(PetscViewerASCIIPrintf(viewer,"Vectors with blocksize 1 saved as 2D datasets: %s\n",PetscBools[hdf5->basedimension2])); PetscCall(PetscViewerASCIIPrintf(viewer,"Enforce single precision storage: %s\n",PetscBools[hdf5->spoutput])); PetscCall(PetscViewerHDF5GetCollective(v,&flg)); PetscCall(PetscViewerASCIIPrintf(viewer,"MPI-IO transfer mode: %s\n",flg ? "collective" : "independent")); PetscCall(PetscViewerASCIIPrintf(viewer,"Default timestepping: %s\n",PetscBools[hdf5->defTimestepping])); PetscFunctionReturn(0); } static PetscErrorCode PetscViewerFileClose_HDF5(PetscViewer viewer) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)viewer->data; PetscFunctionBegin; PetscCall(PetscFree(hdf5->filename)); if (hdf5->file_id) PetscStackCallHDF5(H5Fclose,(hdf5->file_id)); PetscFunctionReturn(0); } static PetscErrorCode PetscViewerFlush_HDF5(PetscViewer viewer) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*)viewer->data; PetscFunctionBegin; if (hdf5->file_id) PetscStackCallHDF5(H5Fflush,(hdf5->file_id, H5F_SCOPE_LOCAL)); PetscFunctionReturn(0); } static PetscErrorCode PetscViewerDestroy_HDF5(PetscViewer viewer) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; PetscStackCallHDF5(H5Pclose,(hdf5->dxpl_id)); PetscCall(PetscViewerFileClose_HDF5(viewer)); while (hdf5->groups) { PetscViewerHDF5GroupList *tmp = hdf5->groups->next; PetscCall(PetscFree(hdf5->groups->name)); PetscCall(PetscFree(hdf5->groups)); hdf5->groups = tmp; } PetscCall(PetscFree(hdf5)); PetscCall(PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetName_C",NULL)); PetscCall(PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileGetName_C",NULL)); PetscCall(PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerFileSetMode_C",NULL)); PetscCall(PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerHDF5SetBaseDimension2_C",NULL)); PetscCall(PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerHDF5SetSPOutput_C",NULL)); PetscCall(PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerHDF5GetDefaultTimestepping_C",NULL)); PetscCall(PetscObjectComposeFunction((PetscObject)viewer,"PetscViewerHDF5SetDefaultTimestepping_C",NULL)); PetscFunctionReturn(0); } static PetscErrorCode PetscViewerFileSetMode_HDF5(PetscViewer viewer, PetscFileMode type) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; hdf5->btype = type; PetscFunctionReturn(0); } static PetscErrorCode PetscViewerFileGetMode_HDF5(PetscViewer viewer, PetscFileMode *type) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; *type = hdf5->btype; PetscFunctionReturn(0); } static PetscErrorCode PetscViewerHDF5SetBaseDimension2_HDF5(PetscViewer viewer, PetscBool flg) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; hdf5->basedimension2 = flg; PetscFunctionReturn(0); } /*@ PetscViewerHDF5SetBaseDimension2 - Vectors of 1 dimension (i.e. bs/dof is 1) will be saved in the HDF5 file with a dimension of 2. Logically Collective on PetscViewer Input Parameters: + viewer - the PetscViewer; if it is not hdf5 then this command is ignored - flg - if PETSC_TRUE the vector will always have at least a dimension of 2 even if that first dimension is of size 1 Options Database: . -viewer_hdf5_base_dimension2 - turns on (true) or off (false) using a dimension of 2 in the HDF5 file even if the bs/dof of the vector is 1 Notes: Setting this option allegedly makes code that reads the HDF5 in easier since they do not have a "special case" of a bs/dof of one when the dimension is lower. Others think the option is crazy. Level: intermediate .seealso: `PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()` @*/ PetscErrorCode PetscViewerHDF5SetBaseDimension2(PetscViewer viewer,PetscBool flg) { PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscTryMethod(viewer,"PetscViewerHDF5SetBaseDimension2_C",(PetscViewer,PetscBool),(viewer,flg)); PetscFunctionReturn(0); } /*@ PetscViewerHDF5GetBaseDimension2 - Vectors of 1 dimension (i.e. bs/dof is 1) will be saved in the HDF5 file with a dimension of 2. Logically Collective on PetscViewer Input Parameter: . viewer - the PetscViewer, must be of type HDF5 Output Parameter: . flg - if PETSC_TRUE the vector will always have at least a dimension of 2 even if that first dimension is of size 1 Notes: Setting this option allegedly makes code that reads the HDF5 in easier since they do not have a "special case" of a bs/dof of one when the dimension is lower. Others think the option is crazy. Level: intermediate .seealso: `PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()` @*/ PetscErrorCode PetscViewerHDF5GetBaseDimension2(PetscViewer viewer,PetscBool *flg) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); *flg = hdf5->basedimension2; PetscFunctionReturn(0); } static PetscErrorCode PetscViewerHDF5SetSPOutput_HDF5(PetscViewer viewer, PetscBool flg) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; hdf5->spoutput = flg; PetscFunctionReturn(0); } /*@ PetscViewerHDF5SetSPOutput - Data is written to disk in single precision even if PETSc is compiled with double precision PetscReal. Logically Collective on PetscViewer Input Parameters: + viewer - the PetscViewer; if it is not hdf5 then this command is ignored - flg - if PETSC_TRUE the data will be written to disk with single precision Options Database: . -viewer_hdf5_sp_output - turns on (true) or off (false) output in single precision Notes: Setting this option does not make any difference if PETSc is compiled with single precision in the first place. It does not affect reading datasets (HDF5 handle this internally). Level: intermediate .seealso: `PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()`, `PetscReal` @*/ PetscErrorCode PetscViewerHDF5SetSPOutput(PetscViewer viewer,PetscBool flg) { PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscTryMethod(viewer,"PetscViewerHDF5SetSPOutput_C",(PetscViewer,PetscBool),(viewer,flg)); PetscFunctionReturn(0); } /*@ PetscViewerHDF5GetSPOutput - Data is written to disk in single precision even if PETSc is compiled with double precision PetscReal. Logically Collective on PetscViewer Input Parameter: . viewer - the PetscViewer, must be of type HDF5 Output Parameter: . flg - if PETSC_TRUE the data will be written to disk with single precision Notes: Setting this option does not make any difference if PETSc is compiled with single precision in the first place. It does not affect reading datasets (HDF5 handle this internally). Level: intermediate .seealso: `PetscViewerFileSetMode()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerBinaryOpen()`, `PetscReal` @*/ PetscErrorCode PetscViewerHDF5GetSPOutput(PetscViewer viewer,PetscBool *flg) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); *flg = hdf5->spoutput; PetscFunctionReturn(0); } static PetscErrorCode PetscViewerHDF5SetCollective_HDF5(PetscViewer viewer, PetscBool flg) { PetscFunctionBegin; /* H5FD_MPIO_COLLECTIVE is wrong in hdf5 1.10.2, and is the same as H5FD_MPIO_INDEPENDENT in earlier versions - see e.g. https://gitlab.cosma.dur.ac.uk/swift/swiftsim/issues/431 */ #if H5_VERSION_GE(1,10,3) && defined(H5_HAVE_PARALLEL) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscStackCallHDF5(H5Pset_dxpl_mpio,(hdf5->dxpl_id, flg ? H5FD_MPIO_COLLECTIVE : H5FD_MPIO_INDEPENDENT)); } #else if (flg) PetscCall(PetscPrintf(PetscObjectComm((PetscObject)viewer), "Warning: PetscViewerHDF5SetCollective(viewer,PETSC_TRUE) is ignored for HDF5 versions prior to 1.10.3 or if built without MPI support\n")); #endif PetscFunctionReturn(0); } /*@ PetscViewerHDF5SetCollective - Use collective MPI-IO transfer mode for HDF5 reads and writes. Logically Collective; flg must contain common value Input Parameters: + viewer - the PetscViewer; if it is not hdf5 then this command is ignored - flg - PETSC_TRUE for collective mode; PETSC_FALSE for independent mode (default) Options Database: . -viewer_hdf5_collective - turns on (true) or off (false) collective transfers Notes: Collective mode gives the MPI-IO layer underneath HDF5 a chance to do some additional collective optimizations and hence can perform better. However, this works correctly only since HDF5 1.10.3 and if HDF5 is installed for MPI; hence, we ignore this setting for older versions. Developer notes: In the HDF5 layer, PETSC_TRUE / PETSC_FALSE means H5Pset_dxpl_mpio() is called with H5FD_MPIO_COLLECTIVE / H5FD_MPIO_INDEPENDENT, respectively. This in turn means use of MPI_File_{read,write}_all / MPI_File_{read,write} in the MPI-IO layer, respectively. See HDF5 documentation and MPI-IO documentation for details. Level: intermediate .seealso: `PetscViewerHDF5GetCollective()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerHDF5Open()` @*/ PetscErrorCode PetscViewerHDF5SetCollective(PetscViewer viewer,PetscBool flg) { PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscValidLogicalCollectiveBool(viewer,flg,2); PetscTryMethod(viewer,"PetscViewerHDF5SetCollective_C",(PetscViewer,PetscBool),(viewer,flg)); PetscFunctionReturn(0); } static PetscErrorCode PetscViewerHDF5GetCollective_HDF5(PetscViewer viewer, PetscBool *flg) { #if defined(H5_HAVE_PARALLEL) PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; H5FD_mpio_xfer_t mode; #endif PetscFunctionBegin; #if !defined(H5_HAVE_PARALLEL) *flg = PETSC_FALSE; #else PetscStackCallHDF5(H5Pget_dxpl_mpio,(hdf5->dxpl_id, &mode)); *flg = (mode == H5FD_MPIO_COLLECTIVE) ? PETSC_TRUE : PETSC_FALSE; #endif PetscFunctionReturn(0); } /*@ PetscViewerHDF5GetCollective - Return flag whether collective MPI-IO transfer mode is used for HDF5 reads and writes. Not Collective Input Parameters: . viewer - the HDF5 PetscViewer Output Parameters: . flg - the flag Level: intermediate Notes: This setting works correctly only since HDF5 1.10.3 and if HDF5 was installed for MPI. For older versions, PETSC_FALSE will be always returned. For more details, see PetscViewerHDF5SetCollective(). .seealso: `PetscViewerHDF5SetCollective()`, `PetscViewerCreate()`, `PetscViewerSetType()`, `PetscViewerHDF5Open()` @*/ PetscErrorCode PetscViewerHDF5GetCollective(PetscViewer viewer,PetscBool *flg) { PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscValidBoolPointer(flg,2); PetscUseMethod(viewer,"PetscViewerHDF5GetCollective_C",(PetscViewer,PetscBool*),(viewer,flg)); PetscFunctionReturn(0); } static PetscErrorCode PetscViewerFileSetName_HDF5(PetscViewer viewer, const char name[]) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; hid_t plist_id; PetscFunctionBegin; if (hdf5->file_id) PetscStackCallHDF5(H5Fclose,(hdf5->file_id)); if (hdf5->filename) PetscCall(PetscFree(hdf5->filename)); PetscCall(PetscStrallocpy(name, &hdf5->filename)); /* Set up file access property list with parallel I/O access */ PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_FILE_ACCESS)); #if defined(H5_HAVE_PARALLEL) PetscStackCallHDF5(H5Pset_fapl_mpio,(plist_id, PetscObjectComm((PetscObject)viewer), MPI_INFO_NULL)); #endif /* Create or open the file collectively */ switch (hdf5->btype) { case FILE_MODE_READ: if (PetscDefined(USE_DEBUG)) { PetscMPIInt rank; PetscBool flg; PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)viewer),&rank)); if (rank == 0) { PetscCall(PetscTestFile(hdf5->filename, 'r', &flg)); PetscCheck(flg,PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"File %s requested for reading does not exist",hdf5->filename); } PetscCallMPI(MPI_Barrier(PetscObjectComm((PetscObject)viewer))); } PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDONLY, plist_id)); break; case FILE_MODE_APPEND: case FILE_MODE_UPDATE: { PetscBool flg; PetscCall(PetscTestFile(hdf5->filename, 'r', &flg)); if (flg) PetscStackCallHDF5Return(hdf5->file_id,H5Fopen,(name, H5F_ACC_RDWR, plist_id)); else PetscStackCallHDF5Return(hdf5->file_id,H5Fcreate,(name, H5F_ACC_EXCL, H5P_DEFAULT, plist_id)); break; } case FILE_MODE_WRITE: PetscStackCallHDF5Return(hdf5->file_id,H5Fcreate,(name, H5F_ACC_TRUNC, H5P_DEFAULT, plist_id)); break; case FILE_MODE_UNDEFINED: SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_ORDER, "Must call PetscViewerFileSetMode() before PetscViewerFileSetName()"); default: SETERRQ(PetscObjectComm((PetscObject)viewer),PETSC_ERR_SUP, "Unsupported file mode %s",PetscFileModes[hdf5->btype]); } PetscCheck(hdf5->file_id >= 0,PETSC_COMM_SELF,PETSC_ERR_LIB, "H5Fcreate failed for %s", name); PetscStackCallHDF5(H5Pclose,(plist_id)); PetscFunctionReturn(0); } static PetscErrorCode PetscViewerFileGetName_HDF5(PetscViewer viewer,const char **name) { PetscViewer_HDF5 *vhdf5 = (PetscViewer_HDF5*)viewer->data; PetscFunctionBegin; *name = vhdf5->filename; PetscFunctionReturn(0); } static PetscErrorCode PetscViewerSetUp_HDF5(PetscViewer viewer) { /* PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; */ PetscFunctionBegin; PetscFunctionReturn(0); } static PetscErrorCode PetscViewerHDF5SetDefaultTimestepping_HDF5(PetscViewer viewer, PetscBool flg) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; hdf5->defTimestepping = flg; PetscFunctionReturn(0); } static PetscErrorCode PetscViewerHDF5GetDefaultTimestepping_HDF5(PetscViewer viewer, PetscBool *flg) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; *flg = hdf5->defTimestepping; PetscFunctionReturn(0); } /*@ PetscViewerHDF5SetDefaultTimestepping - Set the flag for default timestepping Logically Collective on PetscViewer Input Parameters: + viewer - the PetscViewer; if it is not hdf5 then this command is ignored - flg - if PETSC_TRUE we will assume that timestepping is on Options Database: . -viewer_hdf5_default_timestepping - turns on (true) or off (false) default timestepping Notes: If the timestepping attribute is not found for an object, then the default timestepping is used Level: intermediate .seealso: `PetscViewerHDF5GetDefaultTimestepping()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5GetTimestep()` @*/ PetscErrorCode PetscViewerHDF5SetDefaultTimestepping(PetscViewer viewer, PetscBool flg) { PetscFunctionBegin; PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1); PetscTryMethod(viewer, "PetscViewerHDF5SetDefaultTimestepping_C", (PetscViewer,PetscBool), (viewer,flg)); PetscFunctionReturn(0); } /*@ PetscViewerHDF5GetDefaultTimestepping - Get the flag for default timestepping Not collective Input Parameter: . viewer - the PetscViewer Output Parameter: . flg - if PETSC_TRUE we will assume that timestepping is on Notes: If the timestepping attribute is not found for an object, then the default timestepping is used Level: intermediate .seealso: `PetscViewerHDF5SetDefaultTimestepping()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5GetTimestep()` @*/ PetscErrorCode PetscViewerHDF5GetDefaultTimestepping(PetscViewer viewer, PetscBool *flg) { PetscFunctionBegin; PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 1); PetscUseMethod(viewer, "PetscViewerHDF5GetDefaultTimestepping_C", (PetscViewer,PetscBool*), (viewer,flg)); PetscFunctionReturn(0); } /*MC PETSCVIEWERHDF5 - A viewer that writes to an HDF5 file .seealso: `PetscViewerHDF5Open()`, `PetscViewerStringSPrintf()`, `PetscViewerSocketOpen()`, `PetscViewerDrawOpen()`, `PETSCVIEWERSOCKET`, `PetscViewerCreate()`, `PetscViewerASCIIOpen()`, `PetscViewerBinaryOpen()`, `PETSCVIEWERBINARY`, `PETSCVIEWERDRAW`, `PETSCVIEWERSTRING`, `PetscViewerMatlabOpen()`, `VecView()`, `DMView()`, `PetscViewerMatlabPutArray()`, `PETSCVIEWERASCII`, `PETSCVIEWERMATLAB`, `PetscViewerFileSetName()`, `PetscViewerFileSetMode()`, `PetscViewerFormat`, `PetscViewerType`, `PetscViewerSetType()` Level: beginner M*/ PETSC_EXTERN PetscErrorCode PetscViewerCreate_HDF5(PetscViewer v) { PetscViewer_HDF5 *hdf5; PetscFunctionBegin; #if !defined(H5_HAVE_PARALLEL) { PetscMPIInt size; PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)v), &size)); PetscCheck(size <= 1,PetscObjectComm((PetscObject)v), PETSC_ERR_SUP, "Cannot use parallel HDF5 viewer since the given HDF5 does not support parallel I/O (H5_HAVE_PARALLEL is unset)"); } #endif PetscCall(PetscNewLog(v,&hdf5)); v->data = (void*) hdf5; v->ops->destroy = PetscViewerDestroy_HDF5; v->ops->setfromoptions = PetscViewerSetFromOptions_HDF5; v->ops->setup = PetscViewerSetUp_HDF5; v->ops->view = PetscViewerView_HDF5; v->ops->flush = PetscViewerFlush_HDF5; hdf5->btype = FILE_MODE_UNDEFINED; hdf5->filename = NULL; hdf5->timestep = -1; hdf5->groups = NULL; PetscStackCallHDF5Return(hdf5->dxpl_id,H5Pcreate,(H5P_DATASET_XFER)); PetscCall(PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetName_C",PetscViewerFileSetName_HDF5)); PetscCall(PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetName_C",PetscViewerFileGetName_HDF5)); PetscCall(PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileSetMode_C",PetscViewerFileSetMode_HDF5)); PetscCall(PetscObjectComposeFunction((PetscObject)v,"PetscViewerFileGetMode_C",PetscViewerFileGetMode_HDF5)); PetscCall(PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetBaseDimension2_C",PetscViewerHDF5SetBaseDimension2_HDF5)); PetscCall(PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetSPOutput_C",PetscViewerHDF5SetSPOutput_HDF5)); PetscCall(PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetCollective_C",PetscViewerHDF5SetCollective_HDF5)); PetscCall(PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5GetCollective_C",PetscViewerHDF5GetCollective_HDF5)); PetscCall(PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5GetDefaultTimestepping_C",PetscViewerHDF5GetDefaultTimestepping_HDF5)); PetscCall(PetscObjectComposeFunction((PetscObject)v,"PetscViewerHDF5SetDefaultTimestepping_C",PetscViewerHDF5SetDefaultTimestepping_HDF5)); PetscFunctionReturn(0); } /*@C PetscViewerHDF5Open - Opens a file for HDF5 input/output. Collective Input Parameters: + comm - MPI communicator . name - name of file - type - type of file Output Parameter: . hdf5v - PetscViewer for HDF5 input/output to use with the specified file Options Database: + -viewer_hdf5_base_dimension2 - turns on (true) or off (false) using a dimension of 2 in the HDF5 file even if the bs/dof of the vector is 1 - -viewer_hdf5_sp_output - forces (if true) the viewer to write data in single precision independent on the precision of PetscReal Level: beginner Notes: Reading is always available, regardless of the mode. Available modes are + FILE_MODE_READ - open existing HDF5 file for read only access, fail if file does not exist [H5Fopen() with H5F_ACC_RDONLY] . FILE_MODE_WRITE - if file exists, fully overwrite it, else create new HDF5 file [H5FcreateH5Fcreate() with H5F_ACC_TRUNC] . FILE_MODE_APPEND - if file exists, keep existing contents [H5Fopen() with H5F_ACC_RDWR], else create new HDF5 file [H5FcreateH5Fcreate() with H5F_ACC_EXCL] - FILE_MODE_UPDATE - same as FILE_MODE_APPEND In case of FILE_MODE_APPEND / FILE_MODE_UPDATE, any stored object (dataset, attribute) can be selectively ovewritten if the same fully qualified name (/group/path/to/object) is specified. This PetscViewer should be destroyed with PetscViewerDestroy(). .seealso: `PetscViewerASCIIOpen()`, `PetscViewerPushFormat()`, `PetscViewerDestroy()`, `PetscViewerHDF5SetBaseDimension2()`, `PetscViewerHDF5SetSPOutput()`, `PetscViewerHDF5GetBaseDimension2()`, `VecView()`, `MatView()`, `VecLoad()`, `MatLoad()`, `PetscFileMode`, `PetscViewer`, `PetscViewerSetType()`, `PetscViewerFileSetMode()`, `PetscViewerFileSetName()` @*/ PetscErrorCode PetscViewerHDF5Open(MPI_Comm comm, const char name[], PetscFileMode type, PetscViewer *hdf5v) { PetscFunctionBegin; PetscCall(PetscViewerCreate(comm, hdf5v)); PetscCall(PetscViewerSetType(*hdf5v, PETSCVIEWERHDF5)); PetscCall(PetscViewerFileSetMode(*hdf5v, type)); PetscCall(PetscViewerFileSetName(*hdf5v, name)); PetscCall(PetscViewerSetFromOptions(*hdf5v)); PetscFunctionReturn(0); } /*@C PetscViewerHDF5GetFileId - Retrieve the file id, this file ID then can be used in direct HDF5 calls Not collective Input Parameter: . viewer - the PetscViewer Output Parameter: . file_id - The file id Level: intermediate .seealso: `PetscViewerHDF5Open()` @*/ PetscErrorCode PetscViewerHDF5GetFileId(PetscViewer viewer, hid_t *file_id) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); if (file_id) *file_id = hdf5->file_id; PetscFunctionReturn(0); } /*@C PetscViewerHDF5PushGroup - Set the current HDF5 group for output Not collective Input Parameters: + viewer - the PetscViewer - name - The group name Level: intermediate Notes: This is designed to mnemonically resemble the Unix cd command. + If name begins with '/', it is interpreted as an absolute path fully replacing current group, otherwise it is taken as relative to the current group. . NULL, empty string, or any sequence of all slashes (e.g. "///") is interpreted as the root group "/". - "." means the current group is pushed again. Example: Suppose the current group is "/a". + If name is NULL, empty string, or a sequence of all slashes (e.g. "///"), then the new group will be "/". . If name is ".", then the new group will be "/a". . If name is "b", then the new group will be "/a/b". - If name is "/b", then the new group will be "/b". Developer Notes: The root group "/" is internally stored as NULL. .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()`, `PetscViewerHDF5OpenGroup()` @*/ PetscErrorCode PetscViewerHDF5PushGroup(PetscViewer viewer, const char name[]) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscViewerHDF5GroupList *groupNode; size_t i,len; char buf[PETSC_MAX_PATH_LEN]; const char *gname; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); if (name) PetscValidCharPointer(name,2); PetscCall(PetscStrlen(name, &len)); gname = NULL; if (len) { if (len == 1 && name[0] == '.') { /* use current name */ gname = (hdf5->groups && hdf5->groups->name) ? hdf5->groups->name : NULL; } else if (name[0] == '/') { /* absolute */ for (i=1; igroups && hdf5->groups->name) ? hdf5->groups->name : ""; PetscCall(PetscSNPrintf(buf, sizeof(buf), "%s/%s", parent, name)); gname = buf; } } PetscCall(PetscNew(&groupNode)); PetscCall(PetscStrallocpy(gname, (char**) &groupNode->name)); groupNode->next = hdf5->groups; hdf5->groups = groupNode; PetscFunctionReturn(0); } /*@ PetscViewerHDF5PopGroup - Return the current HDF5 group for output to the previous value Not collective Input Parameter: . viewer - the PetscViewer Level: intermediate .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5GetGroup()`, `PetscViewerHDF5OpenGroup()` @*/ PetscErrorCode PetscViewerHDF5PopGroup(PetscViewer viewer) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscViewerHDF5GroupList *groupNode; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscCheck(hdf5->groups,PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "HDF5 group stack is empty, cannot pop"); groupNode = hdf5->groups; hdf5->groups = hdf5->groups->next; PetscCall(PetscFree(groupNode->name)); PetscCall(PetscFree(groupNode)); PetscFunctionReturn(0); } /*@C PetscViewerHDF5GetGroup - Get the current HDF5 group name (full path), set with PetscViewerHDF5PushGroup()/PetscViewerHDF5PopGroup(). If none has been assigned, returns NULL. Not collective Input Parameter: . viewer - the PetscViewer Output Parameter: . name - The group name Level: intermediate .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5OpenGroup()` @*/ PetscErrorCode PetscViewerHDF5GetGroup(PetscViewer viewer, const char *name[]) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5 *) viewer->data; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscValidPointer(name,2); if (hdf5->groups) *name = hdf5->groups->name; else *name = NULL; PetscFunctionReturn(0); } /*@ PetscViewerHDF5OpenGroup - Open the HDF5 group with the name (full path) returned by PetscViewerHDF5GetGroup(), and return this group's ID and file ID. If PetscViewerHDF5GetGroup() yields NULL, then group ID is file ID. Not collective Input Parameter: . viewer - the PetscViewer Output Parameters: + fileId - The HDF5 file ID - groupId - The HDF5 group ID Notes: If the viewer is writable, the group is created if it doesn't exist yet. Level: intermediate .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()` @*/ PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer viewer, hid_t *fileId, hid_t *groupId) { hid_t file_id; H5O_type_t type; const char *groupName = NULL, *fileName = NULL; PetscBool writable, has; PetscFunctionBegin; PetscCall(PetscViewerWritable(viewer, &writable)); PetscCall(PetscViewerHDF5GetFileId(viewer, &file_id)); PetscCall(PetscViewerFileGetName(viewer, &fileName)); PetscCall(PetscViewerHDF5GetGroup(viewer, &groupName)); PetscCall(PetscViewerHDF5Traverse_Internal(viewer, groupName, writable, &has, &type)); if (!has) { PetscCheck(writable,PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Group %s does not exist and file %s is not open for writing", groupName, fileName); else SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_LIB, "HDF5 failed to create group %s although file %s is open for writing", groupName, fileName); } PetscCheck(type == H5O_TYPE_GROUP,PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Path %s in file %s resolves to something which is not a group", groupName, fileName); PetscStackCallHDF5Return(*groupId,H5Gopen2,(file_id, groupName ? groupName : "/", H5P_DEFAULT)); *fileId = file_id; PetscFunctionReturn(0); } /*@ PetscViewerHDF5PushTimestepping - Activate timestepping mode for subsequent HDF5 reading and writing. Not collective Input Parameter: . viewer - the PetscViewer Level: intermediate Notes: On first PetscViewerHDF5PushTimestepping(), the initial time step is set to 0. Next timesteps can then be set using PetscViewerHDF5IncrementTimestep() or PetscViewerHDF5SetTimestep(). Current timestep value determines which timestep is read from or written to any dataset on the next HDF5 I/O operation [e.g. VecView()]. Use PetscViewerHDF5PopTimestepping() to deactivate timestepping mode; calling it by the end of the program is NOT mandatory. Current timestep is remembered between PetscViewerHDF5PopTimestepping() and the next PetscViewerHDF5PushTimestepping(). If a dataset was stored with timestepping, it can be loaded only in the timestepping mode again. Loading a timestepped dataset with timestepping disabled, or vice-versa results in an error. Developer notes: Timestepped HDF5 dataset has an extra dimension and attribute "timestepping" set to true. .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5PopTimestepping()`, `PetscViewerHDF5IsTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()` @*/ PetscErrorCode PetscViewerHDF5PushTimestepping(PetscViewer viewer) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscCheck(!hdf5->timestepping,PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping is already pushed"); hdf5->timestepping = PETSC_TRUE; if (hdf5->timestep < 0) hdf5->timestep = 0; PetscFunctionReturn(0); } /*@ PetscViewerHDF5PopTimestepping - Deactivate timestepping mode for subsequent HDF5 reading and writing. Not collective Input Parameter: . viewer - the PetscViewer Level: intermediate Notes: See PetscViewerHDF5PushTimestepping() for details. .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5IsTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()` @*/ PetscErrorCode PetscViewerHDF5PopTimestepping(PetscViewer viewer) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscCheck(hdf5->timestepping,PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first"); hdf5->timestepping = PETSC_FALSE; PetscFunctionReturn(0); } /*@ PetscViewerHDF5IsTimestepping - Ask the viewer whether it is in timestepping mode currently. Not collective Input Parameter: . viewer - the PetscViewer Output Parameter: . flg - is timestepping active? Level: intermediate Notes: See PetscViewerHDF5PushTimestepping() for details. .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5PopTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()` @*/ PetscErrorCode PetscViewerHDF5IsTimestepping(PetscViewer viewer, PetscBool *flg) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); *flg = hdf5->timestepping; PetscFunctionReturn(0); } /*@ PetscViewerHDF5IncrementTimestep - Increments current timestep for the HDF5 output. Fields are stacked in time. Not collective Input Parameter: . viewer - the PetscViewer Level: intermediate Notes: This can be called only if the viewer is in timestepping mode. See PetscViewerHDF5PushTimestepping() for details. .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5SetTimestep()`, `PetscViewerHDF5GetTimestep()` @*/ PetscErrorCode PetscViewerHDF5IncrementTimestep(PetscViewer viewer) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscCheck(hdf5->timestepping,PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first"); ++hdf5->timestep; PetscFunctionReturn(0); } /*@ PetscViewerHDF5SetTimestep - Set the current timestep for the HDF5 output. Fields are stacked in time. Logically collective Input Parameters: + viewer - the PetscViewer - timestep - The timestep Level: intermediate Notes: This can be called only if the viewer is in timestepping mode. See PetscViewerHDF5PushTimestepping() for details. .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5GetTimestep()` @*/ PetscErrorCode PetscViewerHDF5SetTimestep(PetscViewer viewer, PetscInt timestep) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscValidLogicalCollectiveInt(viewer, timestep, 2); PetscCheck(timestep >= 0,PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestep %" PetscInt_FMT " is negative", timestep); PetscCheck(hdf5->timestepping,PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first"); hdf5->timestep = timestep; PetscFunctionReturn(0); } /*@ PetscViewerHDF5GetTimestep - Get the current timestep for the HDF5 output. Fields are stacked in time. Not collective Input Parameter: . viewer - the PetscViewer Output Parameter: . timestep - The timestep Level: intermediate Notes: This can be called only if the viewer is in the timestepping mode. See PetscViewerHDF5PushTimestepping() for details. .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5PushTimestepping()`, `PetscViewerHDF5IncrementTimestep()`, `PetscViewerHDF5SetTimestep()` @*/ PetscErrorCode PetscViewerHDF5GetTimestep(PetscViewer viewer, PetscInt *timestep) { PetscViewer_HDF5 *hdf5 = (PetscViewer_HDF5*) viewer->data; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscValidIntPointer(timestep,2); PetscCheck(hdf5->timestepping,PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONGSTATE, "Timestepping has not been pushed yet. Call PetscViewerHDF5PushTimestepping() first"); *timestep = hdf5->timestep; PetscFunctionReturn(0); } /*@C PetscDataTypeToHDF5DataType - Converts the PETSc name of a datatype to its HDF5 name. Not collective Input Parameter: . ptype - the PETSc datatype name (for example PETSC_DOUBLE) Output Parameter: . mtype - the MPI datatype (for example MPI_DOUBLE, ...) Level: advanced .seealso: `PetscDataType`, `PetscHDF5DataTypeToPetscDataType()` @*/ PetscErrorCode PetscDataTypeToHDF5DataType(PetscDataType ptype, hid_t *htype) { PetscFunctionBegin; if (ptype == PETSC_INT) #if defined(PETSC_USE_64BIT_INDICES) *htype = H5T_NATIVE_LLONG; #else *htype = H5T_NATIVE_INT; #endif else if (ptype == PETSC_DOUBLE) *htype = H5T_NATIVE_DOUBLE; else if (ptype == PETSC_LONG) *htype = H5T_NATIVE_LONG; else if (ptype == PETSC_SHORT) *htype = H5T_NATIVE_SHORT; else if (ptype == PETSC_ENUM) *htype = H5T_NATIVE_INT; else if (ptype == PETSC_BOOL) *htype = H5T_NATIVE_INT; else if (ptype == PETSC_FLOAT) *htype = H5T_NATIVE_FLOAT; else if (ptype == PETSC_CHAR) *htype = H5T_NATIVE_CHAR; else if (ptype == PETSC_BIT_LOGICAL) *htype = H5T_NATIVE_UCHAR; else if (ptype == PETSC_STRING) *htype = H5Tcopy(H5T_C_S1); else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported PETSc datatype"); PetscFunctionReturn(0); } /*@C PetscHDF5DataTypeToPetscDataType - Finds the PETSc name of a datatype from its HDF5 name Not collective Input Parameter: . htype - the HDF5 datatype (for example H5T_NATIVE_DOUBLE, ...) Output Parameter: . ptype - the PETSc datatype name (for example PETSC_DOUBLE) Level: advanced .seealso: `PetscDataType`, `PetscHDF5DataTypeToPetscDataType()` @*/ PetscErrorCode PetscHDF5DataTypeToPetscDataType(hid_t htype, PetscDataType *ptype) { PetscFunctionBegin; #if defined(PETSC_USE_64BIT_INDICES) if (htype == H5T_NATIVE_INT) *ptype = PETSC_LONG; else if (htype == H5T_NATIVE_LLONG) *ptype = PETSC_INT; #else if (htype == H5T_NATIVE_INT) *ptype = PETSC_INT; #endif else if (htype == H5T_NATIVE_DOUBLE) *ptype = PETSC_DOUBLE; else if (htype == H5T_NATIVE_LONG) *ptype = PETSC_LONG; else if (htype == H5T_NATIVE_SHORT) *ptype = PETSC_SHORT; else if (htype == H5T_NATIVE_FLOAT) *ptype = PETSC_FLOAT; else if (htype == H5T_NATIVE_CHAR) *ptype = PETSC_CHAR; else if (htype == H5T_NATIVE_UCHAR) *ptype = PETSC_CHAR; else if (htype == H5T_C_S1) *ptype = PETSC_STRING; else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Unsupported HDF5 datatype"); PetscFunctionReturn(0); } /*@C PetscViewerHDF5WriteAttribute - Write an attribute Collective Input Parameters: + viewer - The HDF5 viewer . parent - The parent dataset/group name . name - The attribute name . datatype - The attribute type - value - The attribute value Level: advanced Notes: If parent starts with '/', it is taken as an absolute path overriding currently pushed group, else parent is relative to the current pushed group. NULL means the current pushed group. .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5WriteObjectAttribute()`, `PetscViewerHDF5ReadAttribute()`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()` @*/ PetscErrorCode PetscViewerHDF5WriteAttribute(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, const void *value) { char *parentAbsPath; hid_t h5, dataspace, obj, attribute, dtype; PetscBool has; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); if (parent) PetscValidCharPointer(parent, 2); PetscValidCharPointer(name, 3); PetscValidLogicalCollectiveEnum(viewer,datatype,4); PetscValidPointer(value, 5); PetscCall(PetscViewerHDF5GetAbsolutePath_Internal(viewer, parent, &parentAbsPath)); PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_TRUE, NULL, NULL)); PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, &has)); PetscCall(PetscDataTypeToHDF5DataType(datatype, &dtype)); if (datatype == PETSC_STRING) { size_t len; PetscCall(PetscStrlen((const char *) value, &len)); PetscStackCallHDF5(H5Tset_size,(dtype, len+1)); } PetscCall(PetscViewerHDF5GetFileId(viewer, &h5)); PetscStackCallHDF5Return(dataspace,H5Screate,(H5S_SCALAR)); PetscStackCallHDF5Return(obj,H5Oopen,(h5, parentAbsPath, H5P_DEFAULT)); if (has) { PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name)); } else { PetscStackCallHDF5Return(attribute,H5Acreate2,(obj, name, dtype, dataspace, H5P_DEFAULT, H5P_DEFAULT)); } PetscStackCallHDF5(H5Awrite,(attribute, dtype, value)); if (datatype == PETSC_STRING) PetscStackCallHDF5(H5Tclose,(dtype)); PetscStackCallHDF5(H5Aclose,(attribute)); PetscStackCallHDF5(H5Oclose,(obj)); PetscStackCallHDF5(H5Sclose,(dataspace)); PetscCall(PetscFree(parentAbsPath)); PetscFunctionReturn(0); } /*@C PetscViewerHDF5WriteObjectAttribute - Write an attribute to the dataset matching the given PetscObject by name Collective Input Parameters: + viewer - The HDF5 viewer . obj - The object whose name is used to lookup the parent dataset, relative to the current group. . name - The attribute name . datatype - The attribute type - value - The attribute value Notes: This fails if the path current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset). You might want to check first if it does using PetscViewerHDF5HasObject(). Level: advanced .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5WriteAttribute()`, `PetscViewerHDF5ReadObjectAttribute()`, `PetscViewerHDF5HasObjectAttribute()`, `PetscViewerHDF5HasObject()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()` @*/ PetscErrorCode PetscViewerHDF5WriteObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, const void *value) { PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscValidHeader(obj,2); PetscValidCharPointer(name,3); PetscValidPointer(value,5); PetscCall(PetscViewerHDF5CheckNamedObject_Internal(viewer, obj)); PetscCall(PetscViewerHDF5WriteAttribute(viewer, obj->name, name, datatype, value)); PetscFunctionReturn(0); } /*@C PetscViewerHDF5ReadAttribute - Read an attribute Collective Input Parameters: + viewer - The HDF5 viewer . parent - The parent dataset/group name . name - The attribute name . datatype - The attribute type - defaultValue - The pointer to the default value Output Parameter: . value - The pointer to the read HDF5 attribute value Notes: If defaultValue is NULL and the attribute is not found, an error occurs. If defaultValue is not NULL and the attribute is not found, defaultValue is copied to value. The pointers defaultValue and value can be the same; for instance $ flg = PETSC_FALSE; $ PetscCall(PetscViewerHDF5ReadAttribute(viewer,name,"attr",PETSC_BOOL,&flg,&flg)); is valid, but make sure the default value is initialized. If the datatype is PETSC_STRING, the output string is newly allocated so one must PetscFree() it when no longer needed. If parent starts with '/', it is taken as an absolute path overriding currently pushed group, else parent is relative to the current pushed group. NULL means the current pushed group. Level: advanced .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5ReadObjectAttribute()`, `PetscViewerHDF5WriteAttribute()`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5HasObject()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()` @*/ PetscErrorCode PetscViewerHDF5ReadAttribute(PetscViewer viewer, const char parent[], const char name[], PetscDataType datatype, const void *defaultValue, void *value) { char *parentAbsPath; hid_t h5, obj, attribute, dtype; PetscBool has; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); if (parent) PetscValidCharPointer(parent, 2); PetscValidCharPointer(name, 3); if (defaultValue) PetscValidPointer(defaultValue, 5); PetscValidPointer(value, 6); PetscCall(PetscDataTypeToHDF5DataType(datatype, &dtype)); PetscCall(PetscViewerHDF5GetAbsolutePath_Internal(viewer, parent, &parentAbsPath)); PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_FALSE, &has, NULL)); if (has) PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, &has)); if (!has) { if (defaultValue) { if (defaultValue != value) { if (datatype == PETSC_STRING) { PetscCall(PetscStrallocpy(*(char**)defaultValue, (char**)value)); } else { size_t len; PetscStackCallHDF5ReturnNoCheck(len,H5Tget_size,(dtype)); PetscCall(PetscMemcpy(value, defaultValue, len)); } } PetscCall(PetscFree(parentAbsPath)); PetscFunctionReturn(0); } else SETERRQ(PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Attribute %s/%s does not exist and default value not provided", parentAbsPath, name); } PetscCall(PetscViewerHDF5GetFileId(viewer, &h5)); PetscStackCallHDF5Return(obj,H5Oopen,(h5, parentAbsPath, H5P_DEFAULT)); PetscStackCallHDF5Return(attribute,H5Aopen_name,(obj, name)); if (datatype == PETSC_STRING) { size_t len; hid_t atype; PetscStackCallHDF5Return(atype,H5Aget_type,(attribute)); PetscStackCallHDF5ReturnNoCheck(len,H5Tget_size,(atype)); PetscCall(PetscMalloc((len+1) * sizeof(char), value)); PetscStackCallHDF5(H5Tset_size,(dtype, len+1)); PetscStackCallHDF5(H5Aread,(attribute, dtype, *(char**)value)); } else { PetscStackCallHDF5(H5Aread,(attribute, dtype, value)); } PetscStackCallHDF5(H5Aclose,(attribute)); /* H5Oclose can be used to close groups, datasets, or committed datatypes */ PetscStackCallHDF5(H5Oclose,(obj)); PetscCall(PetscFree(parentAbsPath)); PetscFunctionReturn(0); } /*@C PetscViewerHDF5ReadObjectAttribute - Read an attribute from the dataset matching the given PetscObject by name Collective Input Parameters: + viewer - The HDF5 viewer . obj - The object whose name is used to lookup the parent dataset, relative to the current group. . name - The attribute name - datatype - The attribute type Output Parameter: . value - The attribute value Notes: This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset). You might want to check first if it does using PetscViewerHDF5HasObject(). Level: advanced .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5ReadAttribute()` `PetscViewerHDF5WriteObjectAttribute()`, `PetscViewerHDF5HasObjectAttribute()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()` @*/ PetscErrorCode PetscViewerHDF5ReadObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscDataType datatype, void *defaultValue, void *value) { PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscValidHeader(obj,2); PetscValidCharPointer(name,3); PetscValidPointer(value, 6); PetscCall(PetscViewerHDF5CheckNamedObject_Internal(viewer, obj)); PetscCall(PetscViewerHDF5ReadAttribute(viewer, obj->name, name, datatype, defaultValue, value)); PetscFunctionReturn(0); } static inline PetscErrorCode PetscViewerHDF5Traverse_Inner_Internal(hid_t h5, const char name[], PetscBool createGroup, PetscBool *exists_) { htri_t exists; hid_t group; PetscFunctionBegin; PetscStackCallHDF5Return(exists,H5Lexists,(h5, name, H5P_DEFAULT)); if (exists) PetscStackCallHDF5Return(exists,H5Oexists_by_name,(h5, name, H5P_DEFAULT)); if (!exists && createGroup) { PetscStackCallHDF5Return(group,H5Gcreate2,(h5, name, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT)); PetscStackCallHDF5(H5Gclose,(group)); exists = PETSC_TRUE; } *exists_ = (PetscBool) exists; PetscFunctionReturn(0); } static PetscErrorCode PetscViewerHDF5Traverse_Internal(PetscViewer viewer, const char name[], PetscBool createGroup, PetscBool *has, H5O_type_t *otype) { const char rootGroupName[] = "/"; hid_t h5; PetscBool exists=PETSC_FALSE; PetscInt i; int n; char **hierarchy; char buf[PETSC_MAX_PATH_LEN]=""; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); if (name) PetscValidCharPointer(name, 2); else name = rootGroupName; if (has) { PetscValidBoolPointer(has, 4); *has = PETSC_FALSE; } if (otype) { PetscValidIntPointer(otype, 5); *otype = H5O_TYPE_UNKNOWN; } PetscCall(PetscViewerHDF5GetFileId(viewer, &h5)); /* Unfortunately, H5Oexists_by_name() fails if any object in hierarchy is missing. Hence, each of them needs to be tested separately: 1) whether it's a valid link 2) whether this link resolves to an object See H5Oexists_by_name() documentation. */ PetscCall(PetscStrToArray(name,'/',&n,&hierarchy)); if (!n) { /* Assume group "/" always exists in accordance with HDF5 >= 1.10.0. See H5Lexists() documentation. */ if (has) *has = PETSC_TRUE; if (otype) *otype = H5O_TYPE_GROUP; PetscCall(PetscStrToArrayDestroy(n,hierarchy)); PetscFunctionReturn(0); } for (i=0; iname, &len)); PetscCheck(len,PetscObjectComm((PetscObject)viewer), PETSC_ERR_ARG_WRONG, "Object must be named"); PetscCall(PetscViewerHDF5HasDataset(viewer, obj->name, has)); PetscFunctionReturn(0); } /*@C PetscViewerHDF5HasAttribute - Check whether an attribute exists Collective Input Parameters: + viewer - The HDF5 viewer . parent - The parent dataset/group name - name - The attribute name Output Parameter: . has - Flag for attribute existence Level: advanced Notes: If parent starts with '/', it is taken as an absolute path overriding currently pushed group, else parent is relative to the current pushed group. NULL means the current pushed group. .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5HasObjectAttribute()`, `PetscViewerHDF5WriteAttribute()`, `PetscViewerHDF5ReadAttribute()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()` @*/ PetscErrorCode PetscViewerHDF5HasAttribute(PetscViewer viewer, const char parent[], const char name[], PetscBool *has) { char *parentAbsPath; PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); if (parent) PetscValidCharPointer(parent,2); PetscValidCharPointer(name,3); PetscValidBoolPointer(has,4); PetscCall(PetscViewerHDF5GetAbsolutePath_Internal(viewer, parent, &parentAbsPath)); PetscCall(PetscViewerHDF5Traverse_Internal(viewer, parentAbsPath, PETSC_FALSE, has, NULL)); if (*has) PetscCall(PetscViewerHDF5HasAttribute_Internal(viewer, parentAbsPath, name, has)); PetscCall(PetscFree(parentAbsPath)); PetscFunctionReturn(0); } /*@C PetscViewerHDF5HasObjectAttribute - Check whether an attribute is attached to the dataset matching the given PetscObject by name Collective Input Parameters: + viewer - The HDF5 viewer . obj - The object whose name is used to lookup the parent dataset, relative to the current group. - name - The attribute name Output Parameter: . has - Flag for attribute existence Notes: This fails if current_group/object_name doesn't resolve to a dataset (the path doesn't exist or is not a dataset). You might want to check first if it does using PetscViewerHDF5HasObject(). Level: advanced .seealso: `PetscViewerHDF5Open()`, `PetscViewerHDF5HasAttribute()`, `PetscViewerHDF5WriteObjectAttribute()`, `PetscViewerHDF5ReadObjectAttribute()`, `PetscViewerHDF5HasObject()`, `PetscViewerHDF5PushGroup()`, `PetscViewerHDF5PopGroup()`, `PetscViewerHDF5GetGroup()` @*/ PetscErrorCode PetscViewerHDF5HasObjectAttribute(PetscViewer viewer, PetscObject obj, const char name[], PetscBool *has) { PetscFunctionBegin; PetscValidHeaderSpecific(viewer,PETSC_VIEWER_CLASSID,1); PetscValidHeader(obj,2); PetscValidCharPointer(name,3); PetscValidBoolPointer(has,4); PetscCall(PetscViewerHDF5CheckNamedObject_Internal(viewer, obj)); PetscCall(PetscViewerHDF5HasAttribute(viewer, obj->name, name, has)); PetscFunctionReturn(0); } static PetscErrorCode PetscViewerHDF5HasAttribute_Internal(PetscViewer viewer, const char parent[], const char name[], PetscBool *has) { hid_t h5; htri_t hhas; PetscFunctionBegin; PetscCall(PetscViewerHDF5GetFileId(viewer, &h5)); PetscStackCallHDF5Return(hhas,H5Aexists_by_name,(h5, parent, name, H5P_DEFAULT)); *has = hhas ? PETSC_TRUE : PETSC_FALSE; PetscFunctionReturn(0); } /* The variable Petsc_Viewer_HDF5_keyval is used to indicate an MPI attribute that is attached to a communicator, in this case the attribute is a PetscViewer. */ PetscMPIInt Petsc_Viewer_HDF5_keyval = MPI_KEYVAL_INVALID; /*@C PETSC_VIEWER_HDF5_ - Creates an HDF5 PetscViewer shared by all processors in a communicator. Collective Input Parameter: . comm - the MPI communicator to share the HDF5 PetscViewer Level: intermediate Options Database Keys: . -viewer_hdf5_filename - name of the HDF5 file Environmental variables: . PETSC_VIEWER_HDF5_FILENAME - name of the HDF5 file Notes: Unlike almost all other PETSc routines, PETSC_VIEWER_HDF5_ does not return an error code. The HDF5 PetscViewer is usually used in the form $ XXXView(XXX object, PETSC_VIEWER_HDF5_(comm)); .seealso: `PetscViewerHDF5Open()`, `PetscViewerCreate()`, `PetscViewerDestroy()` @*/ PetscViewer PETSC_VIEWER_HDF5_(MPI_Comm comm) { PetscErrorCode ierr; PetscBool flg; PetscViewer viewer; char fname[PETSC_MAX_PATH_LEN]; MPI_Comm ncomm; PetscFunctionBegin; ierr = PetscCommDuplicate(comm,&ncomm,NULL);if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);} if (Petsc_Viewer_HDF5_keyval == MPI_KEYVAL_INVALID) { ierr = MPI_Comm_create_keyval(MPI_COMM_NULL_COPY_FN,MPI_COMM_NULL_DELETE_FN,&Petsc_Viewer_HDF5_keyval,NULL); if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);} } ierr = MPI_Comm_get_attr(ncomm,Petsc_Viewer_HDF5_keyval,(void**)&viewer,(int*)&flg); if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);} if (!flg) { /* PetscViewer not yet created */ ierr = PetscOptionsGetenv(ncomm,"PETSC_VIEWER_HDF5_FILENAME",fname,PETSC_MAX_PATH_LEN,&flg); if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_REPEAT," ");PetscFunctionReturn(NULL);} if (!flg) { ierr = PetscStrcpy(fname,"output.h5"); if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_REPEAT," ");PetscFunctionReturn(NULL);} } ierr = PetscViewerHDF5Open(ncomm,fname,FILE_MODE_WRITE,&viewer); if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_REPEAT," ");PetscFunctionReturn(NULL);} ierr = PetscObjectRegisterDestroy((PetscObject)viewer); if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_REPEAT," ");PetscFunctionReturn(NULL);} ierr = MPI_Comm_set_attr(ncomm,Petsc_Viewer_HDF5_keyval,(void*)viewer); if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_INITIAL," ");PetscFunctionReturn(NULL);} } ierr = PetscCommDestroy(&ncomm); if (ierr) {PetscError(PETSC_COMM_SELF,__LINE__,"PETSC_VIEWER_HDF5_",__FILE__,PETSC_ERR_PLIB,PETSC_ERROR_REPEAT," ");PetscFunctionReturn(NULL);} PetscFunctionReturn(viewer); }