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https://github.com/HDFGroup/hdf5.git
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057cbbf96c
Code optimization
Description:
Minor tweaks throughout the optimized regular hyperslab code to increase
speed. This set of improvements increase the benchmark time from taking
~5.46 seconds to ~4.50 seconds, or around a 20% further speedup.
Platforms tested:
Solaris 2.6 (baldric)
491 lines
18 KiB
C
491 lines
18 KiB
C
/*
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* Copyright (C) 2000 NCSA
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* All rights reserved.
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*
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* Programmer: Quincey Koziol <koziol@ncsa.uiuc.edu>
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* Thursday, September 28, 2000
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*
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* Purpose: Provides I/O facilities for sequences of bytes stored with various
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* layout policies. These routines are similar to the H5Farray.c routines,
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* these deal in terms of byte offsets and lengths, not coordinates and
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* hyperslab sizes.
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*
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*/
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#define H5F_PACKAGE /*suppress error about including H5Fpkg */
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#include <H5private.h>
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#include <H5Dprivate.h>
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#include <H5Eprivate.h>
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#include <H5Fpkg.h>
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#include <H5FDprivate.h> /*file driver */
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#include <H5Iprivate.h>
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#include <H5MFprivate.h>
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#include <H5MMprivate.h> /*memory management */
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#include <H5Oprivate.h>
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#include <H5Pprivate.h>
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#include <H5Vprivate.h>
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/* MPIO driver functions are needed for some special checks */
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#include <H5FDmpio.h>
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/* Interface initialization */
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#define PABLO_MASK H5Fseq_mask
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#define INTERFACE_INIT NULL
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static intn interface_initialize_g = 0;
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/*-------------------------------------------------------------------------
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* Function: H5F_seq_read
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*
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* Purpose: Reads a sequence of bytes from a file dataset into a buffer in
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* in memory. The data is read from file F and the array's size and
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* storage information is in LAYOUT. External files are described
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* according to the external file list, EFL. The sequence offset is
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* FILE_OFFSET in the file (offsets are
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* in terms of bytes) and the size of the hyperslab is SEQ_LEN. The
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* total size of the file array is implied in the LAYOUT argument.
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*
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* Return: Non-negative on success/Negative on failure
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*
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* Programmer: Quincey Koziol
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* Thursday, September 28, 2000
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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herr_t
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H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
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const struct H5O_pline_t *pline, const H5O_fill_t *fill,
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const struct H5O_efl_t *efl, const H5S_t *file_space, size_t elmt_size,
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hsize_t seq_len, hssize_t file_offset, void *_buf/*out*/)
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{
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uint8_t *buf = (uint8_t*)_buf; /*cast for arithmetic */
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hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */
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hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */
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hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/
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intn ndims;
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haddr_t addr; /*address in file */
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intn i; /*counters */
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#ifdef H5_HAVE_PARALLEL
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H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
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#endif
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FUNC_ENTER(H5F_seq_read, FAIL);
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/* Check args */
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assert(f);
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assert(layout);
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assert(buf);
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#ifdef H5_HAVE_PARALLEL
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{
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/* Get the transfer mode */
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H5D_xfer_t *dxpl;
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H5FD_mpio_dxpl_t *dx;
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if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
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H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
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H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
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xfer_mode = dx->xfer_mode;
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}
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}
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/* Collective MPIO access is unsupported for non-contiguous datasets */
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if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
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HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL,
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"collective access on non-contiguous datasets not supported yet");
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}
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#endif
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switch (layout->type) {
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case H5D_CONTIGUOUS:
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/* Filters cannot be used for contiguous data. */
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if (pline && pline->nfilters>0) {
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HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
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"filters are not allowed for contiguous data");
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}
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/*
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* Initialize loop variables. The loop is a multi-dimensional loop
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* that counts from SIZE down to zero and IDX is the counter. Each
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* element of IDX is treated as a digit with IDX[0] being the least
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* significant digit.
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*/
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if (efl && efl->nused>0) {
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addr = 0;
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} else {
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addr = layout->addr;
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}
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addr += file_offset;
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/*
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* Now begin to walk through the array, copying data from disk to
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* memory.
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*/
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#ifdef H5_HAVE_PARALLEL
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if (H5FD_MPIO_COLLECTIVE==xfer_mode) {
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/*
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* Currently supports same number of collective access. Need to
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* be changed LATER to combine all reads into one collective MPIO
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* call.
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*/
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unsigned long max, min, temp;
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temp = seq_len;
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assert(temp==seq_len); /* verify no overflow */
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MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
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H5FD_mpio_communicator(f->shared->lf));
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MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
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H5FD_mpio_communicator(f->shared->lf));
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#ifdef AKC
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printf("seq_len=%lu, min=%lu, max=%lu\n", temp, min, max);
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#endif
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if (max != min)
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HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
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"collective access with unequal number of blocks not supported yet");
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}
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#endif
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/* Read directly from file if the dataset is in an external file */
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/* Note: We can't use data sieve buffers for datasets in external files
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* because the 'addr' of all external files is set to 0 (above) and
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* all datasets in external files would alias to the same set of
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* file offsets, totally mixing up the data sieve buffer information. -QAK
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*/
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if (efl && efl->nused>0) {
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if (H5O_efl_read(f, efl, addr, seq_len, buf)<0) {
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HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
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"external data read failed");
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}
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} else {
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if (H5F_contig_read(f, H5FD_MEM_DRAW, addr, seq_len, dxpl_id, buf)<0) {
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HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
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"block read failed");
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}
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} /* end else */
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break;
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case H5D_CHUNKED:
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/*
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* This method is unable to access external raw data files
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*/
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if (efl && efl->nused>0) {
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HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
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"chunking and external files are mutually exclusive");
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}
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/* Compute the file offset coordinates and hyperslab size */
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if((ndims=H5S_get_simple_extent_dims(file_space,dset_dims,NULL))<0)
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HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions");
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#ifdef QAK
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/* The library shouldn't be reading partial elements currently */
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assert(seq_len%elmt_size!=0);
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assert(addr%elmt_size!=0);
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#endif /* QAK */
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#ifdef QAK
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/* Print out the file offsets & hyperslab sizes */
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{
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static int count=0;
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if(count<10) {
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printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
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printf("%s: file_offset=%d\n",FUNC,(int)file_offset);
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count++;
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}
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}
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#endif /* QAK */
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/* Set location in dataset from the file_offset */
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addr=file_offset;
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/* Convert the bytes into elements */
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seq_len/=elmt_size;
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addr/=elmt_size;
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/* Compute the hyperslab offset from the address given */
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for(i=ndims-1; i>=0; i--) {
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coords[i]=addr%dset_dims[i];
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addr/=dset_dims[i];
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} /* end for */
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coords[ndims]=0; /* No offset for element info */
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/* Compute the hyperslab size from the length given */
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for(i=ndims-1; i>=0; i--) {
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/* Check if the hyperslab is wider than the width of the dimension */
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if(seq_len>dset_dims[i]) {
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if (0!=coords[i])
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HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
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hslab_size[i]=dset_dims[i];
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} /* end if */
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else
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hslab_size[i]=seq_len;
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/* Fold the length into the length in the next highest dimension */
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seq_len/=dset_dims[i];
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/* Make certain the hyperslab sizes don't go less than 1 */
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if(seq_len<1)
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seq_len=1;
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} /* end for */
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hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */
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#ifdef QAK
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/* Print out the file offsets & hyperslab sizes */
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{
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static int count=0;
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if(count<10) {
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printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
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for(i=0; i<=ndims; i++)
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printf("%s: dset_dims[%d]=%d\n",FUNC,i,(int)dset_dims[i]);
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for(i=0; i<=ndims; i++)
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printf("%s: coords[%d]=%d, hslab_size[%d]=%d\n",FUNC,i,(int)coords[i],(int)i,(int)hslab_size[i]);
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count++;
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}
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}
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#endif /* QAK */
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if (H5F_istore_read(f, dxpl_id, layout, pline, fill, coords,
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hslab_size, buf)<0) {
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HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read failed");
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}
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break;
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default:
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assert("not implemented yet" && 0);
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HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
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} /* end switch() */
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FUNC_LEAVE(SUCCEED);
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} /* H5F_seq_read() */
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/*-------------------------------------------------------------------------
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* Function: H5F_seq_write
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*
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* Purpose: Writes a sequence of bytes to a file dataset from a buffer in
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* in memory. The data is written to file F and the array's size and
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* storage information is in LAYOUT. External files are described
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* according to the external file list, EFL. The sequence offset is
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* FILE_OFFSET in the file (offsets are
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* in terms of bytes) and the size of the hyperslab is SEQ_LEN. The
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* total size of the file array is implied in the LAYOUT argument.
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*
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* Return: Non-negative on success/Negative on failure
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*
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* Programmer: Quincey Koziol
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* Monday, October 9, 2000
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*
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* Modifications:
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*
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*-------------------------------------------------------------------------
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*/
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herr_t
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H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
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const struct H5O_pline_t *pline, const H5O_fill_t *fill,
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const struct H5O_efl_t *efl, const H5S_t *file_space, size_t elmt_size,
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hsize_t seq_len, hssize_t file_offset, const void *_buf)
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{
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const uint8_t *buf = (const uint8_t*)_buf; /*cast for arithmetic */
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hsize_t dset_dims[H5O_LAYOUT_NDIMS]; /* dataspace dimensions */
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hssize_t coords[H5O_LAYOUT_NDIMS]; /* offset of hyperslab in dataspace */
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hsize_t hslab_size[H5O_LAYOUT_NDIMS]; /* hyperslab size in dataspace*/
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intn ndims;
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haddr_t addr; /*address in file */
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intn i; /*counters */
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#ifdef H5_HAVE_PARALLEL
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H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
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#endif
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FUNC_ENTER(H5F_seq_write, FAIL);
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/* Check args */
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assert(f);
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assert(layout);
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assert(buf);
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#ifdef H5_HAVE_PARALLEL
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{
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/* Get the transfer mode */
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H5D_xfer_t *dxpl;
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H5FD_mpio_dxpl_t *dx;
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if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
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H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
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H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
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xfer_mode = dx->xfer_mode;
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}
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}
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/* Collective MPIO access is unsupported for non-contiguous datasets */
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if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
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HRETURN_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL,
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"collective access on non-contiguous datasets not supported yet");
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}
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#endif
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switch (layout->type) {
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case H5D_CONTIGUOUS:
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/* Filters cannot be used for contiguous data. */
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if (pline && pline->nfilters>0) {
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HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
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"filters are not allowed for contiguous data");
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}
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/*
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* Initialize loop variables. The loop is a multi-dimensional loop
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* that counts from SIZE down to zero and IDX is the counter. Each
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* element of IDX is treated as a digit with IDX[0] being the least
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* significant digit.
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*/
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if (efl && efl->nused>0) {
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addr = 0;
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} else {
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addr = layout->addr;
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}
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addr += file_offset;
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/*
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* Now begin to walk through the array, copying data from disk to
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* memory.
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*/
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#ifdef H5_HAVE_PARALLEL
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if (H5FD_MPIO_COLLECTIVE==xfer_mode) {
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/*
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* Currently supports same number of collective access. Need to
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* be changed LATER to combine all reads into one collective MPIO
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* call.
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*/
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unsigned long max, min, temp;
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temp = seq_len;
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assert(temp==seq_len); /* verify no overflow */
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MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
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H5FD_mpio_communicator(f->shared->lf));
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MPI_Allreduce(&temp, &min, 1, MPI_UNSIGNED_LONG, MPI_MIN,
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H5FD_mpio_communicator(f->shared->lf));
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#ifdef AKC
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printf("seq_len=%lu, min=%lu, max=%lu\n", temp, min, max);
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#endif
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if (max != min)
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HRETURN_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
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"collective access with unequal number of blocks not supported yet");
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}
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#endif
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/* Write directly to file if the dataset is in an external file */
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/* Note: We can't use data sieve buffers for datasets in external files
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* because the 'addr' of all external files is set to 0 (above) and
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* all datasets in external files would alias to the same set of
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* file offsets, totally mixing up the data sieve buffer information. -QAK
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*/
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if (efl && efl->nused>0) {
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if (H5O_efl_write(f, efl, addr, seq_len, buf)<0) {
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HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
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"external data write failed");
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}
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} else {
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if (H5F_contig_write(f, H5FD_MEM_DRAW, addr, seq_len, dxpl_id, buf)<0) {
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HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
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"block write failed");
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}
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} /* end else */
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break;
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case H5D_CHUNKED:
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/*
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* This method is unable to access external raw data files
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*/
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if (efl && efl->nused>0) {
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HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL,
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"chunking and external files are mutually exclusive");
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}
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/* Compute the file offset coordinates and hyperslab size */
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if((ndims=H5S_get_simple_extent_dims(file_space,dset_dims,NULL))<0)
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HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions");
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#ifdef QAK
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/* Print out the file offsets & hyperslab sizes */
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{
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static int count=0;
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if(count<10) {
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printf("%s: elmt_size=%d, addr=%d, seq_len=%lu\n",FUNC,(int)elmt_size,(int)addr,(unsigned long)seq_len);
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printf("%s: file_offset=%d\n",FUNC,(int)file_offset);
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count++;
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}
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}
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#endif /* QAK */
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#ifdef QAK
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/* The library shouldn't be reading partial elements currently */
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assert((seq_len%elmt_size)!=0);
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assert((addr%elmt_size)!=0);
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#endif /* QAK */
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/* Set location in dataset from the file_offset */
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addr=file_offset;
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/* Convert the bytes into elements */
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seq_len/=elmt_size;
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addr/=elmt_size;
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/* Compute the hyperslab offset from the address given */
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for(i=ndims-1; i>=0; i--) {
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coords[i]=addr%dset_dims[i];
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addr/=dset_dims[i];
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} /* end for */
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coords[ndims]=0; /* No offset for element info */
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/* Compute the hyperslab size from the length given */
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for(i=ndims-1; i>=0; i--) {
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/* Check if the hyperslab is wider than the width of the dimension */
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if(seq_len>dset_dims[i]) {
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if (0!=coords[i])
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HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
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hslab_size[i]=dset_dims[i];
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} /* end if */
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else
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hslab_size[i]=seq_len;
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/* Fold the length into the length in the next highest dimension */
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seq_len/=dset_dims[i];
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||
/* Make certain the hyperslab sizes don't go less than 1 */
|
||
if(seq_len<1)
|
||
seq_len=1;
|
||
} /* end for */
|
||
hslab_size[ndims]=elmt_size; /* basic hyperslab size is the element */
|
||
|
||
#ifdef QAK
|
||
/* Print out the file offsets & hyperslab sizes */
|
||
{
|
||
static int count=0;
|
||
|
||
if(count<10) {
|
||
printf("%s: elmt_size=%d, addr=%d, seq_len=%d\n",FUNC,(int)elmt_size,(int)addr,(int)seq_len);
|
||
for(i=0; i<=ndims; i++)
|
||
printf("%s: dset_dims[%d]=%d\n",FUNC,i,(int)dset_dims[i]);
|
||
for(i=0; i<=ndims; i++)
|
||
printf("%s: coords[%d]=%d, hslab_size[%d]=%d\n",FUNC,i,(int)coords[i],(int)i,(int)hslab_size[i]);
|
||
count++;
|
||
}
|
||
}
|
||
#endif /* QAK */
|
||
|
||
if (H5F_istore_write(f, dxpl_id, layout, pline, fill, coords,
|
||
hslab_size, buf)<0) {
|
||
HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "chunked write failed");
|
||
}
|
||
break;
|
||
|
||
default:
|
||
assert("not implemented yet" && 0);
|
||
HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unsupported storage layout");
|
||
} /* end switch() */
|
||
|
||
FUNC_LEAVE(SUCCEED);
|
||
} /* H5F_seq_write() */
|
||
|