1 #include <petscis.h> /*I "petscis.h" I*/ 2 #include <petsc/private/isimpl.h> 3 #include <petscviewerhdf5.h> 4 5 #if defined(PETSC_HAVE_HDF5) 6 /* 7 This should handle properly the cases where PetscInt is 32 or 64 and hsize_t is 32 or 64. These means properly casting with 8 checks back and forth between the two types of variables. 9 */ 10 PetscErrorCode ISLoad_HDF5(IS is, PetscViewer viewer) 11 { 12 hid_t inttype; /* int type (H5T_NATIVE_INT or H5T_NATIVE_LLONG) */ 13 hid_t file_id, group, dset_id, filespace, memspace, plist_id; 14 int rdim, dim; 15 hsize_t dims[3], count[3], offset[3]; 16 PetscInt n, N, bs, bsInd, lenInd, low, timestep; 17 const PetscInt *ind; 18 const char *isname; 19 PetscErrorCode ierr; 20 21 PetscFunctionBegin; 22 if (!((PetscObject)is)->name) SETERRQ(PetscObjectComm((PetscObject)is), PETSC_ERR_SUP, "Since HDF5 format gives ASCII name for each object in file; must use ISLoad() after setting name of Vec with PetscObjectSetName()"); 23 ierr = PetscViewerHDF5OpenGroup(viewer, &file_id, &group);CHKERRQ(ierr); 24 ierr = PetscViewerHDF5GetTimestep(viewer, ×tep);CHKERRQ(ierr); 25 ierr = ISGetBlockSize(is, &bs);CHKERRQ(ierr); 26 /* Create the dataset with default properties and close filespace */ 27 ierr = PetscObjectGetName((PetscObject) is, &isname);CHKERRQ(ierr); 28 #if (H5_VERS_MAJOR * 10000 + H5_VERS_MINOR * 100 + H5_VERS_RELEASE >= 10800) 29 PetscStackCallHDF5Return(dset_id,H5Dopen2,(group, isname, H5P_DEFAULT)); 30 #else 31 PetscStackCallHDF5Return(dset_id,H5Dopen,(group, isname)); 32 #endif 33 /* Retrieve the dataspace for the dataset */ 34 PetscStackCallHDF5Return(filespace,H5Dget_space,(dset_id)); 35 dim = 0; 36 if (timestep >= 0) ++dim; 37 ++dim; 38 ++dim; 39 PetscStackCallHDF5Return(rdim,H5Sget_simple_extent_dims,(filespace, dims, NULL)); 40 bsInd = rdim-1; 41 lenInd = timestep >= 0 ? 1 : 0; 42 if (rdim != dim) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "Dimension of array in file %d not %d as expected",rdim,dim); 43 else if (bs != (PetscInt) dims[bsInd]) { 44 ierr = ISSetBlockSize(is, dims[bsInd]);CHKERRQ(ierr); 45 bs = dims[bsInd]; 46 } 47 48 /* Set Vec sizes,blocksize,and type if not already set */ 49 ierr = ISGetLocalSize(is, &n);CHKERRQ(ierr); 50 ierr = ISGetSize(is, &N);CHKERRQ(ierr); 51 if (n < 0 && N < 0) {ierr = PetscLayoutSetSize(is->map, dims[lenInd]*bs);CHKERRQ(ierr);} 52 ierr = PetscLayoutSetUp(is->map);CHKERRQ(ierr); 53 /* If sizes and type already set,check if the vector global size is correct */ 54 ierr = ISGetSize(is, &N);CHKERRQ(ierr); 55 if (N/bs != (PetscInt) dims[lenInd]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_FILE_UNEXPECTED, "IS in file different length (%d) then input vector (%d)", (PetscInt) dims[lenInd], N/bs); 56 57 /* Each process defines a dataset and reads it from the hyperslab in the file */ 58 ierr = ISGetLocalSize(is, &n);CHKERRQ(ierr); 59 dim = 0; 60 if (timestep >= 0) { 61 count[dim] = 1; 62 ++dim; 63 } 64 ierr = PetscHDF5IntCast(n/bs,count + dim);CHKERRQ(ierr); 65 ++dim; 66 if (bs >= 1) { 67 count[dim] = bs; 68 ++dim; 69 } 70 PetscStackCallHDF5Return(memspace,H5Screate_simple,(dim, count, NULL)); 71 72 /* Select hyperslab in the file */ 73 ierr = PetscLayoutGetRange(is->map, &low, NULL);CHKERRQ(ierr); 74 dim = 0; 75 if (timestep >= 0) { 76 offset[dim] = timestep; 77 ++dim; 78 } 79 ierr = PetscHDF5IntCast(low/bs,offset + dim);CHKERRQ(ierr); 80 ++dim; 81 if (bs >= 1) { 82 offset[dim] = 0; 83 ++dim; 84 } 85 PetscStackCallHDF5(H5Sselect_hyperslab,(filespace, H5S_SELECT_SET, offset, NULL, count, NULL)); 86 87 /* Create property list for collective dataset read */ 88 PetscStackCallHDF5Return(plist_id,H5Pcreate,(H5P_DATASET_XFER)); 89 #if defined(PETSC_HAVE_H5PSET_FAPL_MPIO) 90 PetscStackCallHDF5(H5Pset_dxpl_mpio,(plist_id, H5FD_MPIO_COLLECTIVE)); 91 #endif 92 /* To write dataset independently use H5Pset_dxpl_mpio(plist_id, H5FD_MPIO_INDEPENDENT) */ 93 94 #if defined(PETSC_USE_64BIT_INDICES) 95 inttype = H5T_NATIVE_LLONG; 96 #else 97 inttype = H5T_NATIVE_INT; 98 #endif 99 ierr = PetscMalloc1(n,&ind);CHKERRQ(ierr); 100 PetscStackCallHDF5(H5Dread,(dset_id, inttype, memspace, filespace, plist_id, (void *) ind)); 101 ierr = ISGeneralSetIndices(is, n, ind, PETSC_OWN_POINTER);CHKERRQ(ierr); 102 103 /* Close/release resources */ 104 if (group != file_id) PetscStackCallHDF5(H5Gclose,(group)); 105 PetscStackCallHDF5(H5Pclose,(plist_id)); 106 PetscStackCallHDF5(H5Sclose,(filespace)); 107 PetscStackCallHDF5(H5Sclose,(memspace)); 108 PetscStackCallHDF5(H5Dclose,(dset_id)); 109 PetscFunctionReturn(0); 110 } 111 #endif 112 113 PetscErrorCode ISLoad_Binary(IS is, PetscViewer viewer) 114 { 115 PetscErrorCode ierr; 116 PetscBool isgeneral,skipHeader,useMPIIO; 117 int fd; 118 PetscInt tr[2],N,ln,*idx; 119 MPI_Request request; 120 MPI_Status status; 121 MPI_Comm comm; 122 PetscMPIInt rank,size,tag; 123 124 PetscFunctionBegin; 125 ierr = PetscObjectGetComm((PetscObject)is,&comm);CHKERRQ(ierr); 126 ierr = PetscObjectTypeCompare((PetscObject)is,ISGENERAL,&isgeneral);CHKERRQ(ierr); 127 if (!isgeneral) SETERRQ(comm,PETSC_ERR_ARG_INCOMP,"IS must be of type ISGENERAL to load into it"); 128 ierr = PetscViewerBinaryGetSkipHeader(viewer,&skipHeader);CHKERRQ(ierr); 129 if (skipHeader) SETERRQ(comm,PETSC_ERR_USER, "Currently no support for binary files without headers"); 130 /* force binary viewer to load .info file if it has not yet done so */ 131 ierr = PetscViewerSetUp(viewer);CHKERRQ(ierr); 132 133 ierr = PetscViewerBinaryRead(viewer,tr,2,NULL,PETSC_INT);CHKERRQ(ierr); 134 if (tr[0] != IS_FILE_CLASSID) SETERRQ(comm,PETSC_ERR_ARG_WRONG,"Not an IS next in file"); 135 136 /* Has IS already had its layout defined */ 137 /* ierr = ISGetLayout(is,&map);CHKERRQ(ierr); */ 138 ierr = PetscLayoutGetSize(is->map,&N);CHKERRQ(ierr); 139 if (N > -1 && N != tr[1]) SETERRQ2(comm,PETSC_ERR_ARG_SIZ,"Size of IS in file %D does not match size of IS provided",tr[1],N); 140 if (N == -1) { 141 N = tr[1]; 142 ierr = PetscLayoutSetSize(is->map,N);CHKERRQ(ierr); 143 ierr = PetscLayoutSetUp(is->map);CHKERRQ(ierr); 144 } 145 ierr = PetscLayoutGetLocalSize(is->map,&ln);CHKERRQ(ierr); 146 ierr = PetscMalloc1(ln,&idx);CHKERRQ(ierr); 147 148 ierr = PetscViewerBinaryGetUseMPIIO(viewer,&useMPIIO);CHKERRQ(ierr); 149 #if defined(PETSC_HAVE_MPIIO) 150 if (useMPIIO) { 151 MPI_File mfdes; 152 MPI_Offset off; 153 PetscMPIInt lsize; 154 PetscInt rstart; 155 156 ierr = PetscMPIIntCast(ln,&lsize);CHKERRQ(ierr); 157 ierr = PetscViewerBinaryGetMPIIODescriptor(viewer,&mfdes);CHKERRQ(ierr); 158 ierr = PetscViewerBinaryGetMPIIOOffset(viewer,&off);CHKERRQ(ierr); 159 ierr = PetscLayoutGetRange(is->map,&rstart,NULL);CHKERRQ(ierr); 160 off += rstart*(MPI_Offset)sizeof(PetscInt); 161 ierr = MPI_File_set_view(mfdes,off,MPIU_INT,MPIU_INT,(char*)"native",MPI_INFO_NULL);CHKERRQ(ierr); 162 ierr = MPIU_File_read_all(mfdes,idx,lsize,MPIU_INT,MPI_STATUS_IGNORE);CHKERRQ(ierr); 163 ierr = PetscViewerBinaryAddMPIIOOffset(viewer,N*(MPI_Offset)sizeof(PetscInt));CHKERRQ(ierr); 164 ierr = ISGeneralSetIndices(is,ln,idx,PETSC_OWN_POINTER);CHKERRQ(ierr); 165 PetscFunctionReturn(0); 166 } 167 #endif 168 169 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 170 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 171 ierr = PetscObjectGetNewTag((PetscObject)viewer,&tag);CHKERRQ(ierr); 172 ierr = PetscViewerBinaryGetDescriptor(viewer,&fd);CHKERRQ(ierr); 173 174 if (!rank) { 175 ierr = PetscBinaryRead(fd,idx,ln,PETSC_INT);CHKERRQ(ierr); 176 177 if (size > 1) { 178 PetscInt *range,n,i,*idxwork; 179 180 /* read in other chuncks and send to other processors */ 181 /* determine maximum chunck owned by other */ 182 range = is->map->range; 183 n = 1; 184 for (i=1; i<size; i++) n = PetscMax(n,range[i+1] - range[i]); 185 186 ierr = PetscMalloc1(n,&idxwork);CHKERRQ(ierr); 187 for (i=1; i<size; i++) { 188 n = range[i+1] - range[i]; 189 ierr = PetscBinaryRead(fd,idxwork,n,PETSC_INT);CHKERRQ(ierr); 190 ierr = MPI_Isend(idxwork,n,MPIU_INT,i,tag,comm,&request);CHKERRQ(ierr); 191 ierr = MPI_Wait(&request,&status);CHKERRQ(ierr); 192 } 193 ierr = PetscFree(idxwork);CHKERRQ(ierr); 194 } 195 } else { 196 ierr = MPI_Recv(idx,ln,MPIU_INT,0,tag,comm,&status);CHKERRQ(ierr); 197 } 198 ierr = ISGeneralSetIndices(is,ln,idx,PETSC_OWN_POINTER);CHKERRQ(ierr); 199 PetscFunctionReturn(0); 200 } 201 202 PetscErrorCode ISLoad_Default(IS is, PetscViewer viewer) 203 { 204 PetscBool isbinary; 205 #if defined(PETSC_HAVE_HDF5) 206 PetscBool ishdf5; 207 #endif 208 PetscErrorCode ierr; 209 210 PetscFunctionBegin; 211 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERBINARY,&isbinary);CHKERRQ(ierr); 212 #if defined(PETSC_HAVE_HDF5) 213 ierr = PetscObjectTypeCompare((PetscObject)viewer,PETSCVIEWERHDF5,&ishdf5);CHKERRQ(ierr); 214 #endif 215 if (isbinary) { 216 ierr = ISLoad_Binary(is, viewer);CHKERRQ(ierr); 217 #if defined(PETSC_HAVE_HDF5) 218 } else if (ishdf5) { 219 ierr = ISLoad_HDF5(is, viewer);CHKERRQ(ierr); 220 #endif 221 } 222 PetscFunctionReturn(0); 223 } 224