[svn-r2652] Purpose:

    Maintainance & performance enhancements
Description:
    Re-arranged header files to protect private symbols better.

    Changed optimized regular hyperslab I/O to compute the offsets more
    efficiently from previous method of using matrix operations.

    Added sequential I/O operations at a more abstract level (at the same level
    as H5F_arr_read/write), to support the optimized hyperslab I/O.

Platforms tested:
    Solaris 2.6 (baldric) & FreeBSD 4.1.1 (hawkwind)

1 files changed, 494 insertions, 0 deletions

diff --git a/src/H5Dseq.c b/src/H5Dseq.c
new file mode 100644
index 0000000..9aa3a48
--- /dev/null
+++ b/src/H5Dseq.c
@@ -0,0 +1,494 @@
+/*
+ * Copyright (C) 2000 NCSA
+ *		      All rights reserved.
+ *
+ * Programmer: 	Quincey Koziol <koziol@ncsa.uiuc.edu>
+ *	       	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 driver functions are needed for some special checks */
+#include <H5FDmpio.h>
+
+/* Interface initialization */
+#define PABLO_MASK	H5Fseq_mask
+#define INTERFACE_INIT	NULL
+static intn 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 and MEM_OFFSET in memory (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:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5F_seq_read(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
+	     const struct H5O_pline_t *pline, const H5O_fill_t *fill,
+	     const struct H5O_efl_t *efl, const H5S_t *file_space, size_t elmt_size,
+         hsize_t seq_len, hssize_t mem_offset, hssize_t file_offset,
+         void *_buf/*out*/)
+{
+    uint8_t	*buf = (uint8_t*)_buf;		    /*cast for arithmetic	*/
+    hsize_t	dset_dims[H5O_LAYOUT_NDIMS];	/* dataspace dimensions */
+    hssize_t coords[H5O_LAYOUT_NDIMS];	    /* offset of hyperslab in dataspace */
+    hsize_t	hslab_size[H5O_LAYOUT_NDIMS];	/* hyperslab size in dataspace*/
+    intn ndims;
+    haddr_t	addr;				/*address in file	*/
+    intn	i;				    /*counters		*/
+#ifdef H5_HAVE_PARALLEL
+    H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
+#endif
+   
+    FUNC_ENTER(H5F_seq_read, FAIL);
+
+    /* Check args */
+    assert(f);
+    assert(layout);
+    assert(buf);
+
+#ifdef H5_HAVE_PARALLEL
+    {
+        /* Get the transfer mode */
+        H5F_xfer_t *dxpl;
+        H5FD_mpio_dxpl_t *dx;
+
+        if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
+                H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
+                H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
+            xfer_mode = dx->xfer_mode;
+        }
+    }
+
+    /* Collective MPIO access is unsupported for non-contiguous datasets */
+    if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
+        HRETURN_ERROR (H5E_DATASET, H5E_READERROR, FAIL,
+           "collective access on non-contiguous datasets not supported yet");
+    }
+#endif
+
+    switch (layout->type) {
+        case H5D_CONTIGUOUS:
+            /* Filters cannot be used for contiguous data. */
+            if (pline && pline->nfilters>0) {
+                HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
+                      "filters are not allowed for contiguous data");
+            }
+            
+            /*
+             * Initialize loop variables.  The loop is a multi-dimensional loop
+             * that counts from SIZE down to zero and IDX is the counter.  Each
+             * element of IDX is treated as a digit with IDX[0] being the least
+             * significant digit.
+             */
+            if (efl && efl->nused>0) {
+                addr = 0;
+            } else {
+                addr = layout->addr;
+            }
+            addr += file_offset;
+            buf += mem_offset;
+
+            /*
+             * Now begin to walk through the array, copying data from disk to
+             * memory.
+             */
+#ifdef H5_HAVE_PARALLEL
+            if (H5FD_MPIO_COLLECTIVE==xfer_mode) {
+                /*
+                 * Currently supports same number of collective access. Need to
+                 * be changed LATER to combine all reads into one collective MPIO
+                 * call.
+                 */
+                unsigned long max, min, temp;
+
+                temp = seq_len;
+                assert(temp==seq_len);	/* verify no overflow */
+                MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
+                      H5FD_mpio_communicator(f->shared->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)
+                    HRETURN_ERROR(H5E_DATASET, H5E_READERROR, FAIL,
+                      "collective access with unequal number of blocks not supported yet");
+            }
+#endif
+
+            /* Read directly from file if the dataset is in an external file */
+            /* 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
+             */
+            if (efl && efl->nused>0) {
+                if (H5O_efl_read(f, efl, addr, seq_len, buf)<0) {
+                    HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL,
+                          "external data read failed");
+                }
+            } else {
+                if (H5F_contig_read(f, addr, seq_len, dxpl_id, buf)<0) {
+                    HRETURN_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 && efl->nused>0) {
+                HRETURN_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)
+                HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions");
+            
+#ifdef QAK
+            /* The library shouldn't be reading partial elements currently */
+            assert(seq_len%elmt_size!=0);
+            assert(addr%elmt_size!=0);
+#endif /* QAK */
+
+#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);
+        printf("%s: file_offset=%d, mem_offset=%d\n",FUNC,(int)file_offset,(int)mem_offset);
+        count++;
+    }
+}
+#endif /* QAK */
+            /* Set location in dataset from the file_offset */
+            addr=file_offset;
+
+            /* Convert the bytes into elements */
+            seq_len/=elmt_size;
+            addr/=elmt_size;
+
+            /* Compute the hyperslab offset from the address given */
+            for(i=ndims-1; i>=0; i--) {
+                coords[i]=addr%dset_dims[i];
+                addr/=dset_dims[i];
+            } /* end for */
+            coords[ndims]=0;   /* No offset for element info */
+
+            /* 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(seq_len>dset_dims[i]) {
+                    if (0!=coords[i])
+                       HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
+                    hslab_size[i]=dset_dims[i];
+                } /* end if */
+                else 
+                    hslab_size[i]=seq_len;
+
+                /* Fold the length into the length in the next highest dimension */
+                seq_len/=dset_dims[i];
+
+                /* 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_read(f, dxpl_id, layout, pline, fill, coords,
+                         hslab_size, buf)<0) {
+                HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, "chunked read 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_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 and MEM_OFFSET in memory (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:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5F_seq_write(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
+	     const struct H5O_pline_t *pline, const H5O_fill_t *fill,
+	     const struct H5O_efl_t *efl, const H5S_t *file_space, size_t elmt_size,
+         hsize_t seq_len, hssize_t mem_offset, hssize_t file_offset,
+         const void *_buf)
+{
+    const uint8_t	*buf = (const uint8_t*)_buf;    /*cast for arithmetic */
+    hsize_t	dset_dims[H5O_LAYOUT_NDIMS];	/* dataspace dimensions */
+    hssize_t coords[H5O_LAYOUT_NDIMS];	    /* offset of hyperslab in dataspace */
+    hsize_t	hslab_size[H5O_LAYOUT_NDIMS];	/* hyperslab size in dataspace*/
+    intn ndims;
+    haddr_t	addr;				/*address in file	*/
+    intn	i;				    /*counters		*/
+#ifdef H5_HAVE_PARALLEL
+    H5FD_mpio_xfer_t xfer_mode=H5FD_MPIO_INDEPENDENT;
+#endif
+   
+    FUNC_ENTER(H5F_seq_write, FAIL);
+
+    /* Check args */
+    assert(f);
+    assert(layout);
+    assert(buf);
+
+#ifdef H5_HAVE_PARALLEL
+    {
+        /* Get the transfer mode */
+        H5F_xfer_t *dxpl;
+        H5FD_mpio_dxpl_t *dx;
+
+        if (H5P_DEFAULT!=dxpl_id && (dxpl=H5I_object(dxpl_id)) &&
+                H5FD_MPIO==dxpl->driver_id && (dx=dxpl->driver_info) &&
+                H5FD_MPIO_INDEPENDENT!=dx->xfer_mode) {
+            xfer_mode = dx->xfer_mode;
+        }
+    }
+
+    /* Collective MPIO access is unsupported for non-contiguous datasets */
+    if (H5D_CONTIGUOUS!=layout->type && H5FD_MPIO_COLLECTIVE==xfer_mode) {
+        HRETURN_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL,
+           "collective access on non-contiguous datasets not supported yet");
+    }
+#endif
+
+    switch (layout->type) {
+        case H5D_CONTIGUOUS:
+            /* Filters cannot be used for contiguous data. */
+            if (pline && pline->nfilters>0) {
+                HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
+                      "filters are not allowed for contiguous data");
+            }
+            
+            /*
+             * Initialize loop variables.  The loop is a multi-dimensional loop
+             * that counts from SIZE down to zero and IDX is the counter.  Each
+             * element of IDX is treated as a digit with IDX[0] being the least
+             * significant digit.
+             */
+            if (efl && efl->nused>0) {
+                addr = 0;
+            } else {
+                addr = layout->addr;
+            }
+            addr += file_offset;
+            buf += mem_offset;
+
+            /*
+             * Now begin to walk through the array, copying data from disk to
+             * memory.
+             */
+#ifdef H5_HAVE_PARALLEL
+            if (H5FD_MPIO_COLLECTIVE==xfer_mode) {
+                /*
+                 * Currently supports same number of collective access. Need to
+                 * be changed LATER to combine all reads into one collective MPIO
+                 * call.
+                 */
+                unsigned long max, min, temp;
+
+                temp = seq_len;
+                assert(temp==seq_len);	/* verify no overflow */
+                MPI_Allreduce(&temp, &max, 1, MPI_UNSIGNED_LONG, MPI_MAX,
+                      H5FD_mpio_communicator(f->shared->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)
+                    HRETURN_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL,
+                      "collective access with unequal number of blocks not supported yet");
+            }
+#endif
+
+            /* Write directly to file if the dataset is in an external file */
+            /* 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
+             */
+            if (efl && efl->nused>0) {
+                if (H5O_efl_write(f, efl, addr, seq_len, buf)<0) {
+                    HRETURN_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
+                          "external data write failed");
+                }
+            } else {
+                if (H5F_contig_write(f, H5FD_MEM_DRAW, addr, seq_len, dxpl_id, buf)<0) {
+                    HRETURN_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 && efl->nused>0) {
+                HRETURN_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)
+                HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to retrieve dataspace dimensions");
+            
+#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=%lu\n",FUNC,(int)elmt_size,(int)addr,(unsigned long)seq_len);
+        printf("%s: file_offset=%d, mem_offset=%d\n",FUNC,(int)file_offset,(int)mem_offset);
+        count++;
+    }
+}
+#endif /* QAK */
+#ifdef QAK
+            /* The library shouldn't be reading partial elements currently */
+            assert((seq_len%elmt_size)!=0);
+            assert((addr%elmt_size)!=0);
+#endif /* QAK */
+
+            /* Set location in dataset from the file_offset */
+            addr=file_offset;
+
+            /* Convert the bytes into elements */
+            seq_len/=elmt_size;
+            addr/=elmt_size;
+
+            /* Compute the hyperslab offset from the address given */
+            for(i=ndims-1; i>=0; i--) {
+                coords[i]=addr%dset_dims[i];
+                addr/=dset_dims[i];
+            } /* end for */
+            coords[ndims]=0;   /* No offset for element info */
+
+            /* 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(seq_len>dset_dims[i]) {
+                    if (0!=coords[i])
+                       HRETURN_ERROR(H5E_IO, H5E_UNSUPPORTED, FAIL, "unable to copy into a proper hyperslab");
+                    hslab_size[i]=dset_dims[i];
+                } /* end if */
+                else 
+                    hslab_size[i]=seq_len;
+
+                /* Fold the length into the length in the next highest dimension */
+                seq_len/=dset_dims[i];
+
+                /* 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() */
+