/* * Copyright (C) 2000-2001 NCSA * All rights reserved. * * Programmer: Quincey Koziol * Thursday, September 28, 2000 * * Purpose: Provides I/O facilities for sequences of bytes stored with various * layout policies. These routines are similar to the H5Farray.c routines, * these deal in terms of byte offsets and lengths, not coordinates and * hyperslab sizes. * */ #define H5F_PACKAGE /*suppress error about including H5Fpkg */ #include "H5private.h" #include "H5Dprivate.h" #include "H5Eprivate.h" #include "H5Fpkg.h" #include "H5FDprivate.h" /*file driver */ #include "H5Iprivate.h" #include "H5MFprivate.h" #include "H5MMprivate.h" /*memory management */ #include "H5Oprivate.h" #include "H5Pprivate.h" #include "H5Vprivate.h" /* MPIO & MPIPOSIX driver functions are needed for some special checks */ #include "H5FDmpio.h" #include "H5FDmpiposix.h" /* Interface initialization */ #define PABLO_MASK H5Fseq_mask #define INTERFACE_INIT NULL static int interface_initialize_g = 0; /*------------------------------------------------------------------------- * Function: H5F_seq_read * * Purpose: Reads a sequence of bytes from a file dataset into a buffer in * in memory. The data is read from file F and the array's size and * storage information is in LAYOUT. External files are described * according to the external file list, EFL. The sequence offset is * FILE_OFFSET in the file (offsets are * in terms of bytes) and the size of the hyperslab is SEQ_LEN. The * total size of the file array is implied in the LAYOUT argument. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Thursday, September 28, 2000 * * Modifications: * Re-written to use new vector I/O call - QAK, 7/7/01 * *------------------------------------------------------------------------- */ herr_t H5F_seq_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, H5P_genplist_t *dc_plist, const H5S_t *file_space, size_t elmt_size, size_t seq_len, hsize_t file_offset, void *buf/*out*/) { herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5F_seq_read, FAIL); /* Check args */ assert(f); assert(layout); assert(buf); if (H5F_seq_readv(f, dxpl_id, layout, dc_plist, file_space, elmt_size, 1, &seq_len, &file_offset, buf)<0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "vector read failed"); done: FUNC_LEAVE(ret_value); } /* H5F_seq_read() */ /*------------------------------------------------------------------------- * Function: H5F_seq_write * * Purpose: Writes a sequence of bytes to a file dataset from a buffer in * in memory. The data is written to file F and the array's size and * storage information is in LAYOUT. External files are described * according to the external file list, EFL. The sequence offset is * FILE_OFFSET in the file (offsets are * in terms of bytes) and the size of the hyperslab is SEQ_LEN. The * total size of the file array is implied in the LAYOUT argument. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Monday, October 9, 2000 * * Modifications: * Re-written to use new vector I/O routine - QAK, 7/7/01 * *------------------------------------------------------------------------- */ herr_t H5F_seq_write(H5F_t *f, hid_t dxpl_id, H5O_layout_t *layout, H5P_genplist_t *dc_plist, const H5S_t *file_space, size_t elmt_size, size_t seq_len, hsize_t file_offset, const void *buf) { herr_t ret_value=SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5F_seq_write, FAIL); /* Check args */ assert(f); assert(layout); assert(buf); if (H5F_seq_writev(f, dxpl_id, layout, dc_plist, file_space, elmt_size, 1, &seq_len, &file_offset, buf)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vector write failed"); done: FUNC_LEAVE(ret_value); } /* H5F_seq_write() */ /*------------------------------------------------------------------------- * Function: H5F_seq_readv * * Purpose: Reads in a vector of byte sequences from a file dataset into a * buffer in in memory. The data is read from file F and the array's size * and storage information is in LAYOUT. External files are described * according to the external file list, EFL. The vector of byte sequences * offsets is in the FILE_OFFSET array into the dataset (offsets are in * terms of bytes) and the size of each sequence is in the SEQ_LEN array. * The total size of the file array is implied in the LAYOUT argument. * Bytes read into BUF are sequentially stored in the buffer, each sequence * from the vector stored directly after the previous. The number of * sequences is NSEQ. * * Return: Non-negative on success/Negative on failure * * Programmer: Quincey Koziol * Wednesday, May 1, 2001 * * Modifications: * *------------------------------------------------------------------------- */ herr_t H5F_seq_readv(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, H5P_genplist_t *dc_plist, const H5S_t *file_space, size_t elmt_size, size_t nseq, size_t seq_len_arr[], hsize_t file_offset_arr[], void *_buf/*out*/) { unsigned char *real_buf=(unsigned char *)_buf; /* Local pointer to buffer to fill */ unsigned char *buf; /* Local pointer to buffer to fill */ hsize_t file_offset; /* Offset in dataset */ hsize_t seq_len; /* Number of bytes to read */ hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */ hssize_t mem_offset[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in memory buffer */ hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */ hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/ hsize_t down_size[H5O_LAYOUT_NDIMS]; /* Cumulative yperslab sizes (in elements) */ hsize_t acc; /* Accumulator for hyperslab sizes (in elements) */ int ndims; hsize_t max_data; /*bytes in dataset */ haddr_t addr=0; /*address in file */ unsigned u; /*counters */ size_t v; /*counters */ int i,j; /*counters */ struct H5O_efl_t efl; /* External File List info */ #ifdef H5_HAVE_PARALLEL H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT; H5P_genplist_t *plist=NULL; /* Property list */ #endif /* H5_HAVE_PARALLEL */ herr_t ret_value = SUCCEED; /* Return value */ FUNC_ENTER_NOAPI(H5F_seq_readv, FAIL); /* Check args */ assert(f); assert(layout); assert(real_buf); /* Make certain we have the correct type of property list */ assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); #ifdef H5_HAVE_PARALLEL { H5FD_mpio_dxpl_t *dx; hid_t driver_id; /* VFL driver ID */ /* Get the transfer mode for MPIO transfers */ if(IS_H5FD_MPIO(f)) { /* Get the plist structure */ if(NULL == (plist = H5I_object(dxpl_id))) HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't find object for ID"); /* Get the driver ID */ if(H5P_get(plist, H5D_XFER_VFL_ID_NAME, &driver_id)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver ID"); /* Check if we are using the MPIO driver (for the DXPL) */ if(H5FD_MPIO==driver_id) { /* Get the driver information */ if(H5P_get(plist, H5D_XFER_VFL_INFO_NAME, &dx)<0) HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve VFL driver info"); /* Check if we are not using independent I/O */ if(H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) xfer_mode = dx->xfer_mode; } /* end if */ } /* end if */ } /* Collective MPIO access is unsupported for non-contiguous datasets */ if (H5D_CHUNKED==layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) HGOTO_ERROR (H5E_DATASET, H5E_READERROR, FAIL, "collective access on non-contiguous datasets not supported yet"); #endif /* H5_HAVE_PARALLEL */ /* Get necessary properties from property list */ if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get EFL value"); switch (layout->type) { case H5D_CONTIGUOUS: /* Read directly from file if the dataset is in an external file */ if (efl.nused>0) { /* Iterate through the sequence vectors */ for(v=0; vshared->lf)); MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN, H5FD_mpio_communicator(f->shared->lf)); #ifdef AKC printf("seq_len=%lu, min=%lu, max=%lu\n", temp, min, max); #endif if (max != min) HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "collective access with unequal number of blocks not supported yet"); } #endif /* H5_HAVE_PARALLEL */ /* Note: We can't use data sieve buffers for datasets in external files * because the 'addr' of all external files is set to 0 (above) and * all datasets in external files would alias to the same set of * file offsets, totally mixing up the data sieve buffer information. -QAK */ H5_CHECK_OVERFLOW(file_offset_arr[v],hsize_t,haddr_t); if (H5O_efl_read(f, &efl, (haddr_t)file_offset_arr[v], seq_len_arr[v], real_buf)<0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "external data read failed"); /* Increment offset in buffer */ real_buf += seq_len_arr[v]; } /* end for */ } else { /* Compute the size of the dataset in bytes */ for(u=1, max_data=layout->dim[0]; undims; u++) max_data *= layout->dim[u]; /* Pass along the vector of sequences to read */ if (H5F_contig_readv(f, max_data, H5FD_MEM_DRAW, layout->addr, nseq, seq_len_arr, file_offset_arr, dxpl_id, real_buf)<0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "block read failed"); } /* end else */ break; case H5D_CHUNKED: /* * This method is unable to access external raw data files */ if (efl.nused>0) HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "chunking and external files are mutually exclusive"); /* Compute the file offset coordinates and hyperslab size */ if((ndims=H5S_get_simple_extent_dims(file_space,dset_dims,NULL))<0) HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions"); /* Build the array of cumulative hyperslab sizes */ /* (And set the memory offset to zero) */ for(acc=1, i=(ndims-1); i>=0; i--) { mem_offset[i]=0; down_size[i]=acc; acc*=dset_dims[i]; } /* end for */ mem_offset[ndims]=0; /* Brute-force, stupid way to implement the vectors, but too complex to do other ways... */ for(v=0; v=0; i--) { coords[i]=addr%dset_dims[i]; addr/=dset_dims[i]; } /* end for */ coords[ndims]=0; /* No offset for element info */ /* * Peel off initial partial hyperslabs until we've got a hyperslab which starts * at coord[n]==0 for dimensions 1->(ndims-1) (i.e. starting at coordinate * zero for all dimensions except the slowest changing one */ for(i=ndims-1; i>0 && seq_len>=down_size[i]; i--) { hsize_t partial_size; /* Size of the partial hyperslab in bytes */ /* Check if we have a partial hyperslab in this lower dimension */ if(coords[i]>0) { /* Reset the partial hyperslab size */ partial_size=1; /* Build the partial hyperslab information */ for(j=0; ji) hslab_size[j]=dset_dims[j]; else hslab_size[j]=1; partial_size*=hslab_size[j]; } /* end for */ hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Read in the partial hyperslab */ if (H5F_istore_read(f, dxpl_id, layout, dc_plist, hslab_size, mem_offset, coords, hslab_size, buf)<0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); /* Increment the buffer offset */ buf=(unsigned char *)buf+(partial_size*elmt_size); /* Decrement the length of the sequence to read */ seq_len-=partial_size; /* Correct the coords array */ coords[i]=0; coords[i-1]++; /* Carry the coord array correction up the array, if the dimension is finished */ while(i>0 && coords[i-1]==(hssize_t)dset_dims[i-1]) { i--; coords[i]=0; if(i>0) { coords[i-1]++; assert(coords[i-1]<=(hssize_t)dset_dims[i-1]); } /* end if */ } /* end while */ } /* end if */ } /* end for */ /* Check if there is more than just a partial hyperslab to read */ if(seq_len>=down_size[0]) { hsize_t tmp_seq_len; /* Temp. size of the sequence in elements */ hsize_t full_size; /* Size of the full hyperslab in bytes */ /* Get the sequence length for computing the hyperslab sizes */ tmp_seq_len=seq_len; /* Reset the size of the hyperslab read in */ full_size=1; /* Compute the hyperslab size from the length given */ for(i=ndims-1; i>=0; i--) { /* Check if the hyperslab is wider than the width of the dimension */ if(tmp_seq_len>dset_dims[i]) { assert(0==coords[i]); hslab_size[i]=dset_dims[i]; } /* end if */ else hslab_size[i]=tmp_seq_len; /* compute the number of elements read in */ full_size*=hslab_size[i]; /* Fold the length into the length in the next highest dimension */ tmp_seq_len/=dset_dims[i]; /* Make certain the hyperslab sizes don't go less than 1 for dimensions less than 0*/ assert(tmp_seq_len>=1 || i==0); } /* end for */ hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Read the full hyperslab in */ if (H5F_istore_read(f, dxpl_id, layout, dc_plist, hslab_size, mem_offset, coords, hslab_size, buf)<0) HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed"); /* Increment the buffer offset */ buf=(unsigned char *)buf+(full_size*elmt_size); /* Decrement the sequence length left */ seq_len-=full_size; /* Increment coordinate of slowest changing dimension */ coords[0]+=hslab_size[0]; } /* end if */ /* * Peel off final partial hyperslabs until we've finished reading all the data */ if(seq_len>0) { hsize_t partial_size; /* Size of the partial hyperslab in bytes */ /* * Peel off remaining partial hyperslabs, from the next-slowest dimension * on down to the next-to-fastest changing dimension */ for(i=1; i<(ndims-1); i++) { /* Check if there are enough elements to read in a row in this dimension */ if(seq_len>=down_size[i]) { /* Reset the partial hyperslab size */ partial_size=1; /* Build the partial hyperslab information */ for(j=0; j0) { assert(seq_lenxfer_mode) xfer_mode = dx->xfer_mode; } /* end if */ } /* end if */ } /* Collective MPIO access is unsupported for non-contiguous datasets */ if (H5D_CHUNKED==layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "collective access on chunked datasets not supported yet"); #endif /* H5_HAVE_PARALLEL */ /* Get necessary properties from property list */ if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0) HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get EFL value"); switch (layout->type) { case H5D_CONTIGUOUS: /* Write directly to file if the dataset is in an external file */ if (efl.nused>0) { /* Iterate through the sequence vectors */ for(v=0; vshared->lf)); MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN, H5FD_mpio_communicator(f->shared->lf)); #ifdef AKC printf("seq_len=%lu, min=%lu, max=%lu\n", temp, min, max); #endif if (max != min) HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "collective access with unequal number of blocks not supported yet"); } #endif /* H5_HAVE_PARALLEL */ /* Note: We can't use data sieve buffers for datasets in external files * because the 'addr' of all external files is set to 0 (above) and * all datasets in external files would alias to the same set of * file offsets, totally mixing up the data sieve buffer information. -QAK */ H5_CHECK_OVERFLOW(file_offset_arr[v],hsize_t,haddr_t); if (H5O_efl_write(f, &efl, (haddr_t)file_offset_arr[v], seq_len_arr[v], real_buf)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "external data write failed"); /* Increment offset in buffer */ real_buf += seq_len_arr[v]; } /* end for */ } else { /* Compute the size of the dataset in bytes */ for(u=1, max_data=layout->dim[0]; undims; u++) max_data *= layout->dim[u]; /* Pass along the vector of sequences to write */ if (H5F_contig_writev(f, max_data, H5FD_MEM_DRAW, layout->addr, nseq, seq_len_arr, file_offset_arr, dxpl_id, real_buf)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); } /* end else */ break; case H5D_CHUNKED: /* * This method is unable to access external raw data files */ if (efl.nused>0) HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "chunking and external files are mutually exclusive"); /* Compute the file offset coordinates and hyperslab size */ if((ndims=H5S_get_simple_extent_dims(file_space,dset_dims,NULL))<0) HGOTO_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions"); /* Build the array of cumulative hyperslab sizes */ /* (And set the memory offset to zero) */ for(acc=1, i=(ndims-1); i>=0; i--) { mem_offset[i]=0; down_size[i]=acc; acc*=dset_dims[i]; } /* end for */ mem_offset[ndims]=0; /* Brute-force, stupid way to implement the vectors, but too complex to do other ways... */ for(v=0; v=0; i--) { coords[i]=addr%dset_dims[i]; addr/=dset_dims[i]; } /* end for */ coords[ndims]=0; /* No offset for element info */ /* * Peel off initial partial hyperslabs until we've got a hyperslab which starts * at coord[n]==0 for dimensions 1->(ndims-1) (i.e. starting at coordinate * zero for all dimensions except the slowest changing one */ for(i=ndims-1; i>0 && seq_len>=down_size[i]; i--) { hsize_t partial_size; /* Size of the partial hyperslab in bytes */ /* Check if we have a partial hyperslab in this lower dimension */ if(coords[i]>0) { /* Reset the partial hyperslab size */ partial_size=1; /* Build the partial hyperslab information */ for(j=0; ji) hslab_size[j]=dset_dims[j]; else hslab_size[j]=1; partial_size*=hslab_size[j]; } /* end for */ hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Write out the partial hyperslab */ if (H5F_istore_write(f, dxpl_id, layout, dc_plist, hslab_size, mem_offset,coords, hslab_size, buf)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); /* Increment the buffer offset */ buf=(const unsigned char *)buf+(partial_size*elmt_size); /* Decrement the length of the sequence to read */ seq_len-=partial_size; /* Correct the coords array */ coords[i]=0; coords[i-1]++; /* Carry the coord array correction up the array, if the dimension is finished */ while(i>0 && coords[i-1]==(hssize_t)dset_dims[i-1]) { i--; coords[i]=0; if(i>0) { coords[i-1]++; assert(coords[i-1]<=(hssize_t)dset_dims[i-1]); } /* end if */ } /* end while */ } /* end if */ } /* end for */ /* Check if there is more than just a partial hyperslab to read */ if(seq_len>=down_size[0]) { hsize_t tmp_seq_len; /* Temp. size of the sequence in elements */ hsize_t full_size; /* Size of the full hyperslab in bytes */ /* Get the sequence length for computing the hyperslab sizes */ tmp_seq_len=seq_len; /* Reset the size of the hyperslab read in */ full_size=1; /* Compute the hyperslab size from the length given */ for(i=ndims-1; i>=0; i--) { /* Check if the hyperslab is wider than the width of the dimension */ if(tmp_seq_len>dset_dims[i]) { assert(0==coords[i]); hslab_size[i]=dset_dims[i]; } /* end if */ else hslab_size[i]=tmp_seq_len; /* compute the number of elements read in */ full_size*=hslab_size[i]; /* Fold the length into the length in the next highest dimension */ tmp_seq_len/=dset_dims[i]; /* Make certain the hyperslab sizes don't go less than 1 for dimensions less than 0*/ assert(tmp_seq_len>=1 || i==0); } /* end for */ hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */ /* Write the full hyperslab in */ if (H5F_istore_write(f, dxpl_id, layout, dc_plist, hslab_size, mem_offset, coords, hslab_size, buf)<0) HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed"); /* Increment the buffer offset */ buf=(const unsigned char *)buf+(full_size*elmt_size); /* Decrement the sequence length left */ seq_len-=full_size; /* Increment coordinate of slowest changing dimension */ coords[0]+=hslab_size[0]; } /* end if */ /* * Peel off final partial hyperslabs until we've finished reading all the data */ if(seq_len>0) { hsize_t partial_size; /* Size of the partial hyperslab in bytes */ /* * Peel off remaining partial hyperslabs, from the next-slowest dimension * on down to the next-to-fastest changing dimension */ for(i=1; i<(ndims-1); i++) { /* Check if there are enough elements to read in a row in this dimension */ if(seq_len>=down_size[i]) { /* Reset the partial hyperslab size */ partial_size=1; /* Build the partial hyperslab information */ for(j=0; j0) { assert(seq_len