1 2 #if !defined(PETSCVIEWERHDF5_H) 3 #define PETSCVIEWERHDF5_H 4 5 #include <petscviewer.h> 6 7 #if defined(PETSC_HAVE_HDF5) 8 #include <hdf5.h> 9 #if !defined(H5_VERSION_GE) 10 /* H5_VERSION_GE was introduced in HDF5 1.8.7, we support >= 1.8.0 */ 11 /* So beware this will automatically 0 for HDF5 1.8.0 - 1.8.6 */ 12 #define H5_VERSION_GE(a,b,c) 0 13 #endif 14 15 PETSC_EXTERN PetscErrorCode PetscViewerHDF5GetFileId(PetscViewer,hid_t*); 16 PETSC_EXTERN PetscErrorCode PetscViewerHDF5OpenGroup(PetscViewer, hid_t *, hid_t *); 17 18 /* On 32 bit systems HDF5 is limited by size of integer, because hsize_t is defined as size_t */ 19 #define PETSC_HDF5_INT_MAX (~(hsize_t)0) 20 21 /* As per https://portal.hdfgroup.org/display/HDF5/Chunking+in+HDF5, max. chunk size is 4GB */ 22 #define PETSC_HDF5_MAX_CHUNKSIZE 2147483647 23 24 PETSC_STATIC_INLINE PetscErrorCode PetscViewerHDF5PathIsRelative(const char path[], PetscBool emptyIsRelative, PetscBool *has) 25 { 26 PetscErrorCode ierr; 27 size_t len; 28 29 PetscFunctionBegin; 30 *has = emptyIsRelative; 31 ierr = PetscStrlen(path,&len);CHKERRQ(ierr); 32 if (len) { 33 *has = (PetscBool) (path[0] != '/'); 34 } 35 PetscFunctionReturn(0); 36 } 37 38 PETSC_STATIC_INLINE PetscErrorCode PetscHDF5IntCast(PetscInt a,hsize_t *b) 39 { 40 PetscFunctionBegin; 41 if (a < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Cannot convert negative size"); 42 #if defined(PETSC_USE_64BIT_INDICES) && (H5_SIZEOF_HSIZE_T == 4) 43 if (a > PETSC_HDF5_INT_MAX) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_OUTOFRANGE,"Array too long for HDF5"); 44 #endif 45 *b = (hsize_t)(a); 46 PetscFunctionReturn(0); 47 } 48 PETSC_EXTERN PetscErrorCode PetscDataTypeToHDF5DataType(PetscDataType,hid_t*); 49 PETSC_EXTERN PetscErrorCode PetscHDF5DataTypeToPetscDataType(hid_t,PetscDataType*); 50 51 PETSC_EXTERN PetscErrorCode PetscViewerHDF5HasDataset(PetscViewer,const char[],PetscBool*); 52 PETSC_EXTERN PetscErrorCode PetscViewerHDF5HasObject(PetscViewer,PetscObject,PetscBool*); 53 PETSC_EXTERN PetscErrorCode PetscViewerHDF5ReadAttribute(PetscViewer,const char[],const char[],PetscDataType,const void*,void*); 54 PETSC_EXTERN PetscErrorCode PetscViewerHDF5WriteAttribute(PetscViewer,const char[],const char[],PetscDataType,const void*); 55 PETSC_EXTERN PetscErrorCode PetscViewerHDF5HasAttribute(PetscViewer,const char[],const char[],PetscBool*); 56 PETSC_EXTERN PetscErrorCode PetscViewerHDF5ReadObjectAttribute(PetscViewer,PetscObject,const char[],PetscDataType,void*,void*); 57 PETSC_EXTERN PetscErrorCode PetscViewerHDF5WriteObjectAttribute(PetscViewer,PetscObject,const char[],PetscDataType,const void*); 58 PETSC_EXTERN PetscErrorCode PetscViewerHDF5HasObjectAttribute(PetscViewer,PetscObject,const char[],PetscBool*); 59 60 PETSC_EXTERN PetscErrorCode PetscViewerHDF5Open(MPI_Comm,const char[],PetscFileMode,PetscViewer*); 61 PETSC_EXTERN PetscErrorCode PetscViewerHDF5PushGroup(PetscViewer,const char[]); 62 PETSC_EXTERN PetscErrorCode PetscViewerHDF5PopGroup(PetscViewer); 63 PETSC_EXTERN PetscErrorCode PetscViewerHDF5GetGroup(PetscViewer,const char*[]); 64 PETSC_EXTERN PetscErrorCode PetscViewerHDF5HasGroup(PetscViewer,const char[],PetscBool*); 65 66 PETSC_EXTERN PetscErrorCode PetscViewerHDF5PushTimestepping(PetscViewer); 67 PETSC_EXTERN PetscErrorCode PetscViewerHDF5PopTimestepping(PetscViewer); 68 PETSC_EXTERN PetscErrorCode PetscViewerHDF5IsTimestepping(PetscViewer,PetscBool*); 69 PETSC_EXTERN PetscErrorCode PetscViewerHDF5IncrementTimestep(PetscViewer); 70 PETSC_EXTERN PetscErrorCode PetscViewerHDF5SetTimestep(PetscViewer,PetscInt); 71 PETSC_EXTERN PetscErrorCode PetscViewerHDF5GetTimestep(PetscViewer,PetscInt*); 72 73 PETSC_EXTERN PetscErrorCode PetscViewerHDF5SetBaseDimension2(PetscViewer,PetscBool); 74 PETSC_EXTERN PetscErrorCode PetscViewerHDF5GetBaseDimension2(PetscViewer,PetscBool*); 75 76 PETSC_EXTERN PetscErrorCode PetscViewerHDF5SetSPOutput(PetscViewer,PetscBool); 77 PETSC_EXTERN PetscErrorCode PetscViewerHDF5GetSPOutput(PetscViewer,PetscBool*); 78 79 PETSC_EXTERN PetscErrorCode PetscViewerHDF5SetCollective(PetscViewer,PetscBool); 80 PETSC_EXTERN PetscErrorCode PetscViewerHDF5GetCollective(PetscViewer,PetscBool*); 81 #endif /* defined(PETSC_HAVE_HDF5) */ 82 #endif 83