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Diffstat (limited to 'src/H5Fcontig.c')
| -rw-r--r-- | src/H5Fcontig.c | 986 |
1 files changed, 0 insertions, 986 deletions
diff --git a/src/H5Fcontig.c b/src/H5Fcontig.c deleted file mode 100644 index 3e0c163..0000000 --- a/src/H5Fcontig.c +++ /dev/null @@ -1,986 +0,0 @@ -/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * - * Copyright by the Board of Trustees of the University of Illinois. * - * All rights reserved. * - * * - * This file is part of HDF5. The full HDF5 copyright notice, including * - * terms governing use, modification, and redistribution, is contained in * - * the files COPYING and Copyright.html. COPYING can be found at the root * - * of the source code distribution tree; Copyright.html can be found at the * - * root level of an installed copy of the electronic HDF5 document set and * - * is linked from the top-level documents page. It can also be found at * - * http://hdf.ncsa.uiuc.edu/HDF5/doc/Copyright.html. If you do not have * - * access to either file, you may request a copy from hdfhelp@ncsa.uiuc.edu. * - * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */ - -/* - * Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu> - * Thursday, September 28, 2000 - * - * Purpose: - * Contiguous dataset I/O functions. These routines are similar to - * the H5D_istore_* routines and really only an abstract way of dealing - * with the data sieve buffer from H5F_seq_read/write. - */ - -#define H5D_PACKAGE /*suppress error about including H5Dpkg */ - -/* Pablo information */ -/* (Put before include files to avoid problems with inline functions) */ -#define PABLO_MASK H5Dcontig_mask - -#include "H5private.h" /* Generic Functions */ -#include "H5Dpkg.h" /* Dataset functions */ -#include "H5Eprivate.h" /* Error handling */ -#include "H5Fprivate.h" /* Files */ -#include "H5FDprivate.h" /* File drivers */ -#include "H5FLprivate.h" /* Free Lists */ -#include "H5MFprivate.h" /* File memory management */ -#include "H5Oprivate.h" /* Object headers */ -#include "H5Pprivate.h" /* Property lists */ -#include "H5Sprivate.h" /* Dataspace functions */ -#include "H5Vprivate.h" /* Vector and array functions */ - -/* Private prototypes */ -static herr_t H5D_contig_write(H5F_t *f, hid_t dxpl_id, H5D_t *dset, - hsize_t offset, size_t size, const void *buf); - -/* Interface initialization */ -static int interface_initialize_g = 0; -#define INTERFACE_INIT NULL - -/* Declare a PQ free list to manage the sieve buffer information */ -H5FL_BLK_DEFINE(sieve_buf); - -/* Declare the free list to manage blocks of non-zero fill-value data */ -H5FL_BLK_DEFINE_STATIC(non_zero_fill); - -/* Declare the free list to manage blocks of zero fill-value data */ -H5FL_BLK_DEFINE_STATIC(zero_fill); - - -/*------------------------------------------------------------------------- - * Function: H5D_contig_create - * - * Purpose: Allocate file space for a contiguously stored dataset - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * April 19, 2003 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5D_contig_create(H5F_t *f, hid_t dxpl_id, H5D_t *dset) -{ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_contig_create, FAIL); - - /* check args */ - assert(f); - assert(dset); - - /* Allocate space for the contiguous data */ - if (HADDR_UNDEF==(dset->layout.u.contig.addr=H5MF_alloc(f, H5FD_MEM_DRAW, dxpl_id, dset->layout.u.contig.size))) - HGOTO_ERROR (H5E_IO, H5E_NOSPACE, FAIL, "unable to reserve file space"); - -done: - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_contig_create */ - - -/*------------------------------------------------------------------------- - * Function: H5D_contig_fill - * - * Purpose: Write fill values to a contiguously stored dataset. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * August 22, 2002 - * - * Modifications: - * Bill Wendling, February 20, 2003 - * Added support for getting the barrier COMM if you're using - * Flexible PHDF5. - * - *------------------------------------------------------------------------- - */ -herr_t -H5D_contig_fill(H5F_t *f, hid_t dxpl_id, H5D_t *dset) -{ - hssize_t snpoints; /* Number of points in space (for error checking) */ - size_t npoints; /* Number of points in space */ - size_t ptsperbuf; /* Maximum # of points which fit in the buffer */ - size_t elmt_size; /* Size of each element */ - size_t bufsize=64*1024; /* Size of buffer to write */ - size_t size; /* Current # of points to write */ - hsize_t offset; /* Offset of dataset */ - void *buf = NULL; /* Buffer for fill value writing */ -#ifdef H5_HAVE_PARALLEL - MPI_Comm mpi_comm=MPI_COMM_NULL; /* MPI communicator for file */ - int mpi_rank=(-1); /* This process's rank */ - int mpi_code; /* MPI return code */ - unsigned blocks_written=0; /* Flag to indicate that chunk was actually written */ - unsigned using_mpi=0; /* Flag to indicate that the file is being accessed with an MPI-capable file driver */ -#endif /* H5_HAVE_PARALLEL */ - int non_zero_fill_f=(-1); /* Indicate that a non-zero fill-value was used */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_contig_fill, FAIL); - - /* Check args */ - assert(f); - assert(TRUE==H5P_isa_class(dxpl_id,H5P_DATASET_XFER)); - assert(dset && H5D_CONTIGUOUS==dset->layout.type); - assert(H5F_addr_defined(dset->layout.u.contig.addr)); - assert(dset->layout.u.contig.size>0); - assert(dset->space); - -#ifdef H5_HAVE_PARALLEL - /* Retrieve MPI parameters */ - if(IS_H5FD_MPI(f)) { - /* Get the MPI communicator */ - if (MPI_COMM_NULL == (mpi_comm=H5F_mpi_get_comm(f))) - HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI communicator"); - - /* Get the MPI rank & size */ - if ((mpi_rank=H5F_mpi_get_rank(f))<0) - HGOTO_ERROR(H5E_INTERNAL, H5E_MPI, FAIL, "Can't retrieve MPI rank"); - - /* Set the MPI-capable file driver flag */ - using_mpi=1; - } /* end if */ -#endif /* H5_HAVE_PARALLEL */ - - /* Get size of elements */ - elmt_size=H5T_get_size(dset->type); - assert(elmt_size>0); - - /* Get the number of elements in the dataset's dataspace */ - snpoints = H5S_GET_SIMPLE_EXTENT_NPOINTS(dset->space); - assert(snpoints>=0); - H5_ASSIGN_OVERFLOW(npoints,snpoints,hssize_t,size_t); - - /* If fill value is not library default, use it to set the element size */ - if(dset->fill.buf) - elmt_size=dset->fill.size; - - /* - * Fill the entire current extent with the fill value. We can do - * this quite efficiently by making sure we copy the fill value - * in relatively large pieces. - */ - ptsperbuf = MAX(1, bufsize/elmt_size); - bufsize = ptsperbuf*elmt_size; - - /* Fill the buffer with the user's fill value */ - if(dset->fill.buf) { - /* Allocate temporary buffer */ - if ((buf=H5FL_BLK_MALLOC(non_zero_fill,bufsize))==NULL) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer"); - - H5V_array_fill(buf, dset->fill.buf, elmt_size, ptsperbuf); - - /* Indicate that a non-zero fill buffer was used */ - non_zero_fill_f=1; - } /* end if */ - else { /* Fill the buffer with the default fill value */ - htri_t buf_avail; - - /* Check if there is an already zeroed out buffer available */ - buf_avail=H5FL_BLK_AVAIL(zero_fill,bufsize); - assert(buf_avail!=FAIL); - - /* Allocate temporary buffer (zeroing it if no buffer is available) */ - if(!buf_avail) - buf=H5FL_BLK_CALLOC(zero_fill,bufsize); - else - buf=H5FL_BLK_MALLOC(zero_fill,bufsize); - if(buf==NULL) - HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for fill buffer"); - - /* Indicate that a zero fill buffer was used */ - non_zero_fill_f=0; - } /* end else */ - - /* Start at the beginning of the dataset */ - offset = 0; - - /* Loop through writing the fill value to the dataset */ - while (npoints>0) { - size = MIN(ptsperbuf, npoints) * elmt_size; - -#ifdef H5_HAVE_PARALLEL - /* Check if this file is accessed with an MPI-capable file driver */ - if(using_mpi) { - /* Write the chunks out from only one process */ - /* !! Use the internal "independent" DXPL!! -QAK */ - if(H5_PAR_META_WRITE==mpi_rank) { - if (H5D_contig_write(f, H5AC_ind_dxpl_id, dset, offset, size, buf)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); - } /* end if */ - - /* Indicate that blocks are being written */ - blocks_written=1; - } /* end if */ - else { -#endif /* H5_HAVE_PARALLEL */ - H5_CHECK_OVERFLOW(size,size_t,hsize_t); - if (H5D_contig_write(f, dxpl_id, dset, offset, size, buf)<0) - HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to write fill value to dataset"); -#ifdef H5_HAVE_PARALLEL - } /* end else */ -#endif /* H5_HAVE_PARALLEL */ - - npoints -= MIN(ptsperbuf, npoints); - offset += size; - } /* end while */ - -#ifdef H5_HAVE_PARALLEL - /* Only need to block at the barrier if we actually wrote fill values */ - /* And if we are using an MPI-capable file driver */ - if(using_mpi && blocks_written) { - /* Wait at barrier to avoid race conditions where some processes are - * still writing out fill values and other processes race ahead to data - * in, getting bogus data. - */ - if (MPI_SUCCESS != (mpi_code=MPI_Barrier(mpi_comm))) - HMPI_GOTO_ERROR(FAIL, "MPI_Barrier failed", mpi_code); - } /* end if */ -#endif /* H5_HAVE_PARALLEL */ - -done: - /* Free the buffer for fill values */ - if (buf) { - assert(non_zero_fill_f>=0); - if(non_zero_fill_f) - H5FL_BLK_FREE(non_zero_fill,buf); - else - H5FL_BLK_FREE(zero_fill,buf); - } /* end if */ - - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_contig_fill() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_contig_delete - * - * Purpose: Delete the file space for a contiguously stored dataset - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * March 20, 2003 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -herr_t -H5D_contig_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout) -{ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_contig_delete, FAIL); - - /* check args */ - assert(f); - assert(layout); - - /* Free the file space for the chunk */ - if (H5MF_xfree(f, H5FD_MEM_DRAW, dxpl_id, layout->u.contig.addr, layout->u.contig.size)<0) - HGOTO_ERROR(H5E_OHDR, H5E_CANTFREE, FAIL, "unable to free object header"); - -done: - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_contig_delete */ - - -/*------------------------------------------------------------------------- - * Function: H5D_contig_get_addr - * - * Purpose: Get the offset of the contiguous data on disk - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * June 2, 2004 - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -haddr_t -H5D_contig_get_addr(const H5D_t *dset) -{ - haddr_t ret_value; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_contig_get_addr, HADDR_UNDEF); - - /* check args */ - assert(dset); - assert(dset->layout.type==H5D_CONTIGUOUS); - - /* Get the address */ - ret_value=dset->layout.u.contig.addr; - -done: - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_contig_get_addr */ - - -/*------------------------------------------------------------------------- - * Function: H5D_contig_write - * - * Purpose: Writes some data from a dataset into a buffer. - * The data is contiguous. The address is relative to the base - * address for the file. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Thursday, September 28, 2000 - * - * Modifications: - * Re-written in terms of the new writevv call, QAK, 5/7/03 - * - *------------------------------------------------------------------------- - */ -static herr_t -H5D_contig_write(H5F_t *f, hid_t dxpl_id, H5D_t *dset, - hsize_t offset, size_t size, const void *buf) -{ - hsize_t dset_off=offset; /* Offset in dataset */ - size_t dset_len=size; /* Length in dataset */ - size_t dset_curr_seq=0; /* "Current sequence" in dataset */ - hsize_t mem_off=0; /* Offset in memory */ - size_t mem_len=size; /* Length in memory */ - size_t mem_curr_seq=0; /* "Current sequence" in memory */ - herr_t ret_value=SUCCEED; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_contig_write, FAIL); - - assert (f); - assert (dset); - assert (buf); - - if (H5D_contig_writevv(f, dxpl_id, dset, dset->layout.u.contig.addr, dset->layout.u.contig.size, - 1, &dset_curr_seq, &dset_len, &dset_off, 1, &mem_curr_seq, &mem_len, &mem_off, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vector write failed"); - -done: - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_contig_write() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_contig_readvv - * - * Purpose: Reads some data vectors from a dataset into a buffer. - * The data is contiguous. The address is the start of the dataset, - * relative to the base address for the file and the offsets and - * sequence lengths are in bytes. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Friday, May 3, 2001 - * - * Notes: - * Offsets in the sequences must be monotonically increasing - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -ssize_t -H5D_contig_readvv(H5F_t *f, hid_t dxpl_id, H5D_t *dset, - haddr_t dset_addr, hsize_t dset_size, - size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[], - size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[], - void *_buf) -{ - unsigned char *buf=(unsigned char *)_buf; /* Pointer to buffer to fill */ - haddr_t abs_eoa; /* Absolute end of file address */ - haddr_t rel_eoa; /* Relative end of file address */ - haddr_t addr; /* Actual address to read */ - hsize_t max_data; /* Actual maximum size of data to cache */ - size_t size; /* Size of sequence in bytes */ - size_t u; /* Counting variable */ - size_t v; /* Counting variable */ - ssize_t ret_value=0; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_contig_readvv, FAIL); - - /* Check args */ - assert(f); - assert(dset); - assert(buf); - - /* Check if data sieving is enabled */ - if(H5F_HAS_FEATURE(f,H5FD_FEAT_DATA_SIEVE)) { - haddr_t sieve_start, sieve_end; /* Start & end locations of sieve buffer */ - haddr_t contig_end; /* End locations of block to write */ - size_t sieve_size; /* size of sieve buffer */ - - /* Set offsets in sequence lists */ - u=*dset_curr_seq; - v=*mem_curr_seq; - - /* No data sieve buffer yet, go allocate one */ - if(dset->cache.contig.sieve_buf==NULL) { - /* Choose smallest buffer to write */ - if(mem_len_arr[v]<dset_len_arr[u]) - size=mem_len_arr[v]; - else - size=dset_len_arr[u]; - - /* Compute offset on disk */ - addr=dset_addr+dset_offset_arr[u]; - - /* Compute offset in memory */ - buf = (unsigned char *)_buf + mem_offset_arr[v]; - - /* Set up the buffer parameters */ - max_data=dset_size-dset_offset_arr[u]; - - /* Check if we can actually hold the I/O request in the sieve buffer */ - if(size>dset->cache.contig.sieve_buf_size) { - if (H5F_block_read(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "block read failed"); - } /* end if */ - else { - /* Allocate room for the data sieve buffer */ - if (NULL==(dset->cache.contig.sieve_buf=H5FL_BLK_MALLOC(sieve_buf,dset->cache.contig.sieve_buf_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); - - /* Determine the new sieve buffer size & location */ - dset->cache.contig.sieve_loc=addr; - - /* Make certain we don't read off the end of the file */ - if (HADDR_UNDEF==(abs_eoa=H5F_get_eoa(f))) - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, FAIL, "unable to determine file size"); - - /* Adjust absolute EOA address to relative EOA address */ - rel_eoa=abs_eoa-H5F_get_base_addr(f); - - /* Compute the size of the sieve buffer */ - H5_ASSIGN_OVERFLOW(dset->cache.contig.sieve_size,MIN3(rel_eoa-dset->cache.contig.sieve_loc,max_data,dset->cache.contig.sieve_buf_size),hsize_t,size_t); - - /* Read the new sieve buffer */ - if (H5F_block_read(f, H5FD_MEM_DRAW, dset->cache.contig.sieve_loc, dset->cache.contig.sieve_size, dxpl_id, dset->cache.contig.sieve_buf)<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "block read failed"); - - /* Grab the data out of the buffer (must be first piece of data in buffer ) */ - HDmemcpy(buf,dset->cache.contig.sieve_buf,size); - - /* Reset sieve buffer dirty flag */ - dset->cache.contig.sieve_dirty=0; - } /* end else */ - - /* Update memory information */ - mem_len_arr[v]-=size; - mem_offset_arr[v]+=size; - if(mem_len_arr[v]==0) - v++; - - /* Update file information */ - dset_len_arr[u]-=size; - dset_offset_arr[u]+=size; - if(dset_len_arr[u]==0) - u++; - - /* Increment number of bytes copied */ - ret_value+=size; - } /* end if */ - - /* Stash local copies of these value */ - sieve_start=dset->cache.contig.sieve_loc; - sieve_size=dset->cache.contig.sieve_size; - sieve_end=sieve_start+sieve_size; - - /* Works through sequences as fast as possible */ - for(; u<dset_max_nseq && v<mem_max_nseq; ) { - /* Choose smallest buffer to write */ - if(mem_len_arr[v]<dset_len_arr[u]) - size=mem_len_arr[v]; - else - size=dset_len_arr[u]; - - /* Compute offset on disk */ - addr=dset_addr+dset_offset_arr[u]; - - /* Compute offset in memory */ - buf = (unsigned char *)_buf + mem_offset_arr[v]; - - /* Compute end of sequence to retrieve */ - contig_end=addr+size-1; - - /* If entire read is within the sieve buffer, read it from the buffer */ - if(addr>=sieve_start && contig_end<sieve_end) { - unsigned char *base_sieve_buf=dset->cache.contig.sieve_buf+(addr-sieve_start); - - /* Grab the data out of the buffer */ - HDmemcpy(buf,base_sieve_buf,size); - } /* end if */ - /* Entire request is not within this data sieve buffer */ - else { - /* Check if we can actually hold the I/O request in the sieve buffer */ - if(size>dset->cache.contig.sieve_buf_size) { - /* Check for any overlap with the current sieve buffer */ - if((sieve_start>=addr && sieve_start<(contig_end+1)) - || ((sieve_end-1)>=addr && (sieve_end-1)<(contig_end+1))) { - /* Flush the sieve buffer, if it's dirty */ - if(dset->cache.contig.sieve_dirty) { - /* Write to file */ - if (H5F_block_write(f, H5FD_MEM_DRAW, sieve_start, sieve_size, dxpl_id, dset->cache.contig.sieve_buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); - - /* Reset sieve buffer dirty flag */ - dset->cache.contig.sieve_dirty=0; - } /* end if */ - } /* end if */ - - /* Read directly into the user's buffer */ - if (H5F_block_read(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "block read failed"); - } /* end if */ - /* Element size fits within the buffer size */ - else { - /* Flush the sieve buffer if it's dirty */ - if(dset->cache.contig.sieve_dirty) { - /* Write to file */ - if (H5F_block_write(f, H5FD_MEM_DRAW, sieve_start, sieve_size, dxpl_id, dset->cache.contig.sieve_buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); - - /* Reset sieve buffer dirty flag */ - dset->cache.contig.sieve_dirty=0; - } /* end if */ - - /* Determine the new sieve buffer size & location */ - dset->cache.contig.sieve_loc=addr; - - /* Make certain we don't read off the end of the file */ - if (HADDR_UNDEF==(abs_eoa=H5F_get_eoa(f))) - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, FAIL, "unable to determine file size"); - - /* Adjust absolute EOA address to relative EOA address */ - rel_eoa=abs_eoa-H5F_get_base_addr(f); - - /* Only need this when resizing sieve buffer */ - max_data=dset_size-dset_offset_arr[u]; - - /* Compute the size of the sieve buffer */ - /* Don't read off the end of the file, don't read past the end of the data element and don't read more than the buffer size */ - H5_ASSIGN_OVERFLOW(dset->cache.contig.sieve_size,MIN3(rel_eoa-dset->cache.contig.sieve_loc,max_data,dset->cache.contig.sieve_buf_size),hsize_t,size_t); - - /* Update local copies of sieve information */ - sieve_start=dset->cache.contig.sieve_loc; - sieve_size=dset->cache.contig.sieve_size; - sieve_end=sieve_start+sieve_size; - - /* Read the new sieve buffer */ - if (H5F_block_read(f, H5FD_MEM_DRAW, dset->cache.contig.sieve_loc, dset->cache.contig.sieve_size, dxpl_id, dset->cache.contig.sieve_buf)<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "block read failed"); - - /* Grab the data out of the buffer (must be first piece of data in buffer ) */ - HDmemcpy(buf,dset->cache.contig.sieve_buf,size); - - /* Reset sieve buffer dirty flag */ - dset->cache.contig.sieve_dirty=0; - } /* end else */ - } /* end else */ - - /* Update memory information */ - mem_len_arr[v]-=size; - mem_offset_arr[v]+=size; - if(mem_len_arr[v]==0) - v++; - - /* Update file information */ - dset_len_arr[u]-=size; - dset_offset_arr[u]+=size; - if(dset_len_arr[u]==0) - u++; - - /* Increment number of bytes copied */ - ret_value+=size; - } /* end for */ - } /* end if */ - else { - /* Work through all the sequences */ - for(u=*dset_curr_seq, v=*mem_curr_seq; u<dset_max_nseq && v<mem_max_nseq; ) { - /* Choose smallest buffer to write */ - if(mem_len_arr[v]<dset_len_arr[u]) - size=mem_len_arr[v]; - else - size=dset_len_arr[u]; - - /* Compute offset on disk */ - addr=dset_addr+dset_offset_arr[u]; - - /* Compute offset in memory */ - buf = (unsigned char *)_buf + mem_offset_arr[v]; - - /* Write data */ - if (H5F_block_read(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); - - /* Update memory information */ - mem_len_arr[v]-=size; - mem_offset_arr[v]+=size; - if(mem_len_arr[v]==0) - v++; - - /* Update file information */ - dset_len_arr[u]-=size; - dset_offset_arr[u]+=size; - if(dset_len_arr[u]==0) - u++; - - /* Increment number of bytes copied */ - ret_value+=size; - } /* end for */ - } /* end else */ - - /* Update current sequence vectors */ - *dset_curr_seq=u; - *mem_curr_seq=v; - -done: - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_contig_readvv() */ - - -/*------------------------------------------------------------------------- - * Function: H5D_contig_writevv - * - * Purpose: Writes some data vectors into a dataset from vectors into a - * buffer. The address is the start of the dataset, - * relative to the base address for the file and the offsets and - * sequence lengths are in bytes. - * - * Return: Non-negative on success/Negative on failure - * - * Programmer: Quincey Koziol - * Friday, May 2, 2003 - * - * Notes: - * Offsets in the sequences must be monotonically increasing - * - * Modifications: - * - *------------------------------------------------------------------------- - */ -ssize_t -H5D_contig_writevv(H5F_t *f, hid_t dxpl_id, H5D_t *dset, - haddr_t dset_addr, hsize_t dset_size, - size_t dset_max_nseq, size_t *dset_curr_seq, size_t dset_len_arr[], hsize_t dset_offset_arr[], - size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[], - const void *_buf) -{ - const unsigned char *buf=_buf; /* Pointer to buffer to fill */ - haddr_t abs_eoa; /* Absolute end of file address */ - haddr_t rel_eoa; /* Relative end of file address */ - haddr_t addr; /* Actual address to read */ - hsize_t max_data; /* Actual maximum size of data to cache */ - size_t size; /* Size of sequence in bytes */ - size_t u; /* Counting variable */ - size_t v; /* Counting variable */ - ssize_t ret_value=0; /* Return value */ - - FUNC_ENTER_NOAPI(H5D_contig_writevv, FAIL); - - /* Check args */ - assert(f); - assert(dset); - assert(buf); - - /* Check if data sieving is enabled */ - if(H5F_HAS_FEATURE(f,H5FD_FEAT_DATA_SIEVE)) { - haddr_t sieve_start, sieve_end; /* Start & end locations of sieve buffer */ - haddr_t contig_end; /* End locations of block to write */ - size_t sieve_size; /* size of sieve buffer */ - - /* Set offsets in sequence lists */ - u=*dset_curr_seq; - v=*mem_curr_seq; - - /* No data sieve buffer yet, go allocate one */ - if(dset->cache.contig.sieve_buf==NULL) { - /* Choose smallest buffer to write */ - if(mem_len_arr[v]<dset_len_arr[u]) - size=mem_len_arr[v]; - else - size=dset_len_arr[u]; - - /* Compute offset on disk */ - addr=dset_addr+dset_offset_arr[u]; - - /* Compute offset in memory */ - buf = (const unsigned char *)_buf + mem_offset_arr[v]; - - /* Set up the buffer parameters */ - max_data=dset_size-dset_offset_arr[u]; - - /* Check if we can actually hold the I/O request in the sieve buffer */ - if(size>dset->cache.contig.sieve_buf_size) { - if (H5F_block_write(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); - } /* end if */ - else { - /* Allocate room for the data sieve buffer */ - if (NULL==(dset->cache.contig.sieve_buf=H5FL_BLK_MALLOC(sieve_buf,dset->cache.contig.sieve_buf_size))) - HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed"); - - /* Determine the new sieve buffer size & location */ - dset->cache.contig.sieve_loc=addr; - - /* Make certain we don't read off the end of the file */ - if (HADDR_UNDEF==(abs_eoa=H5F_get_eoa(f))) - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, FAIL, "unable to determine file size"); - - /* Adjust absolute EOA address to relative EOA address */ - rel_eoa=abs_eoa-H5F_get_base_addr(f); - - /* Compute the size of the sieve buffer */ - H5_ASSIGN_OVERFLOW(dset->cache.contig.sieve_size,MIN3(rel_eoa-dset->cache.contig.sieve_loc,max_data,dset->cache.contig.sieve_buf_size),hsize_t,size_t); - - /* Check if there is any point in reading the data from the file */ - if(dset->cache.contig.sieve_size>size) { - /* Read the new sieve buffer */ - if (H5F_block_read(f, H5FD_MEM_DRAW, dset->cache.contig.sieve_loc, dset->cache.contig.sieve_size, dxpl_id, dset->cache.contig.sieve_buf)<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "block read failed"); - } /* end if */ - - /* Grab the data out of the buffer (must be first piece of data in buffer ) */ - HDmemcpy(dset->cache.contig.sieve_buf,buf,size); - - /* Set sieve buffer dirty flag */ - dset->cache.contig.sieve_dirty=1; - } /* end else */ - - /* Update memory information */ - mem_len_arr[v]-=size; - mem_offset_arr[v]+=size; - if(mem_len_arr[v]==0) - v++; - - /* Update file information */ - dset_len_arr[u]-=size; - dset_offset_arr[u]+=size; - if(dset_len_arr[u]==0) - u++; - - /* Increment number of bytes copied */ - ret_value+=size; - } /* end if */ - - /* Stash local copies of these value */ - sieve_start=dset->cache.contig.sieve_loc; - sieve_size=dset->cache.contig.sieve_size; - sieve_end=sieve_start+sieve_size; - - /* Works through sequences as fast as possible */ - for(; u<dset_max_nseq && v<mem_max_nseq; ) { - /* Choose smallest buffer to write */ - if(mem_len_arr[v]<dset_len_arr[u]) - size=mem_len_arr[v]; - else - size=dset_len_arr[u]; - - /* Compute offset on disk */ - addr=dset_addr+dset_offset_arr[u]; - - /* Compute offset in memory */ - buf = (const unsigned char *)_buf + mem_offset_arr[v]; - - /* Compute end of sequence to retrieve */ - contig_end=addr+size-1; - - /* If entire write is within the sieve buffer, write it to the buffer */ - if(addr>=sieve_start && contig_end<sieve_end) { - unsigned char *base_sieve_buf=dset->cache.contig.sieve_buf+(addr-sieve_start); - - /* Put the data into the sieve buffer */ - HDmemcpy(base_sieve_buf,buf,size); - - /* Set sieve buffer dirty flag */ - dset->cache.contig.sieve_dirty=1; - - } /* end if */ - /* Entire request is not within this data sieve buffer */ - else { - /* Check if we can actually hold the I/O request in the sieve buffer */ - if(size>dset->cache.contig.sieve_buf_size) { - /* Check for any overlap with the current sieve buffer */ - if((sieve_start>=addr && sieve_start<(contig_end+1)) - || ((sieve_end-1)>=addr && (sieve_end-1)<(contig_end+1))) { - /* Flush the sieve buffer, if it's dirty */ - if(dset->cache.contig.sieve_dirty) { - /* Write to file */ - if (H5F_block_write(f, H5FD_MEM_DRAW, sieve_start, sieve_size, dxpl_id, dset->cache.contig.sieve_buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); - - /* Reset sieve buffer dirty flag */ - dset->cache.contig.sieve_dirty=0; - } /* end if */ - - /* Force the sieve buffer to be re-read the next time */ - dset->cache.contig.sieve_loc=HADDR_UNDEF; - dset->cache.contig.sieve_size=0; - } /* end if */ - - /* Write directly from the user's buffer */ - if (H5F_block_write(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); - } /* end if */ - /* Element size fits within the buffer size */ - else { - /* Check if it is possible to (exactly) prepend or append to existing (dirty) sieve buffer */ - if(((addr+size)==sieve_start || addr==sieve_end) && - (size+sieve_size)<=dset->cache.contig.sieve_buf_size && - dset->cache.contig.sieve_dirty) { - /* Prepend to existing sieve buffer */ - if((addr+size)==sieve_start) { - /* Move existing sieve information to correct location */ - HDmemmove(dset->cache.contig.sieve_buf+size,dset->cache.contig.sieve_buf,sieve_size); - - /* Copy in new information (must be first in sieve buffer) */ - HDmemcpy(dset->cache.contig.sieve_buf,buf,size); - - /* Adjust sieve location */ - dset->cache.contig.sieve_loc=addr; - - } /* end if */ - /* Append to existing sieve buffer */ - else { - /* Copy in new information */ - HDmemcpy(dset->cache.contig.sieve_buf+sieve_size,buf,size); - } /* end else */ - - /* Adjust sieve size */ - dset->cache.contig.sieve_size += size; - - /* Update local copies of sieve information */ - sieve_start=dset->cache.contig.sieve_loc; - sieve_size=dset->cache.contig.sieve_size; - sieve_end=sieve_start+sieve_size; - - } /* end if */ - /* Can't add the new data onto the existing sieve buffer */ - else { - /* Flush the sieve buffer if it's dirty */ - if(dset->cache.contig.sieve_dirty) { - /* Write to file */ - if (H5F_block_write(f, H5FD_MEM_DRAW, sieve_start, sieve_size, dxpl_id, dset->cache.contig.sieve_buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); - - /* Reset sieve buffer dirty flag */ - dset->cache.contig.sieve_dirty=0; - } /* end if */ - - /* Determine the new sieve buffer size & location */ - dset->cache.contig.sieve_loc=addr; - - /* Make certain we don't read off the end of the file */ - if (HADDR_UNDEF==(abs_eoa=H5F_get_eoa(f))) - HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, FAIL, "unable to determine file size"); - - /* Adjust absolute EOA address to relative EOA address */ - rel_eoa=abs_eoa-H5F_get_base_addr(f); - - /* Only need this when resizing sieve buffer */ - max_data=dset_size-dset_offset_arr[u]; - - /* Compute the size of the sieve buffer */ - /* Don't read off the end of the file, don't read past the end of the data element and don't read more than the buffer size */ - H5_ASSIGN_OVERFLOW(dset->cache.contig.sieve_size,MIN3(rel_eoa-dset->cache.contig.sieve_loc,max_data,dset->cache.contig.sieve_buf_size),hsize_t,size_t); - - /* Update local copies of sieve information */ - sieve_start=dset->cache.contig.sieve_loc; - sieve_size=dset->cache.contig.sieve_size; - sieve_end=sieve_start+sieve_size; - - /* Check if there is any point in reading the data from the file */ - if(dset->cache.contig.sieve_size>size) { - /* Read the new sieve buffer */ - if (H5F_block_read(f, H5FD_MEM_DRAW, dset->cache.contig.sieve_loc, dset->cache.contig.sieve_size, dxpl_id, dset->cache.contig.sieve_buf)<0) - HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "block read failed"); - } /* end if */ - - /* Grab the data out of the buffer (must be first piece of data in buffer ) */ - HDmemcpy(dset->cache.contig.sieve_buf,buf,size); - - /* Set sieve buffer dirty flag */ - dset->cache.contig.sieve_dirty=1; - - } /* end else */ - } /* end else */ - } /* end else */ - - /* Update memory information */ - mem_len_arr[v]-=size; - mem_offset_arr[v]+=size; - if(mem_len_arr[v]==0) - v++; - - /* Update file information */ - dset_len_arr[u]-=size; - dset_offset_arr[u]+=size; - if(dset_len_arr[u]==0) - u++; - - /* Increment number of bytes copied */ - ret_value+=size; - } /* end for */ - } /* end if */ - else { - /* Work through all the sequences */ - for(u=*dset_curr_seq, v=*mem_curr_seq; u<dset_max_nseq && v<mem_max_nseq; ) { - /* Choose smallest buffer to write */ - if(mem_len_arr[v]<dset_len_arr[u]) - size=mem_len_arr[v]; - else - size=dset_len_arr[u]; - - /* Compute offset on disk */ - addr=dset_addr+dset_offset_arr[u]; - - /* Compute offset in memory */ - buf = (const unsigned char *)_buf + mem_offset_arr[v]; - - /* Write data */ - if (H5F_block_write(f, H5FD_MEM_DRAW, addr, size, dxpl_id, buf)<0) - HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "block write failed"); - - /* Update memory information */ - mem_len_arr[v]-=size; - mem_offset_arr[v]+=size; - if(mem_len_arr[v]==0) - v++; - - /* Update file information */ - dset_len_arr[u]-=size; - dset_offset_arr[u]+=size; - if(dset_len_arr[u]==0) - u++; - - /* Increment number of bytes copied */ - ret_value+=size; - } /* end for */ - } /* end else */ - - /* Update current sequence vectors */ - *dset_curr_seq=u; - *mem_curr_seq=v; - -done: - FUNC_LEAVE_NOAPI(ret_value); -} /* end H5D_contig_writevv() */ - |