[svn-r9354] Purpose:

    Bug fix & code cleanup

Description:
    More dataset cleanups to get to a point where we can fix the chunked I/O
bug.

    Also fix a couple of errors in the recent file object resurrection changes
which should hopefully address the recent daily test failres (H5T.c)

Platforms tested:
    FreeBSD 4.10 (sleipnir) w/parallel
    Solaris 2.7 (arabica)
    h5committest

1 files changed, 371 insertions, 0 deletions

diff --git a/src/H5Defl.c b/src/H5Defl.c
new file mode 100644
index 0000000..ab3e260
--- /dev/null
+++ b/src/H5Defl.c
@@ -0,0 +1,371 @@
+/* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ * 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 30, 2004
+ */
+
+#define H5D_PACKAGE		/*suppress error about including H5Dpkg	  */
+
+/* Pablo information */
+/* (Put before include files to avoid problems with inline functions) */
+#define PABLO_MASK	H5D_efl_mask
+
+#include "H5private.h"		/* Generic Functions			*/
+#include "H5Dpkg.h"		/* Datasets				*/
+#include "H5Eprivate.h"		/* Error handling		  	*/
+#include "H5Fprivate.h"		/* Files				*/
+
+/* PRIVATE PROTOTYPES */
+static herr_t H5D_efl_read (const H5O_efl_t *efl, haddr_t addr, size_t size,
+    uint8_t *buf);
+static herr_t H5D_efl_write(const H5O_efl_t *efl, haddr_t addr, size_t size,
+    const uint8_t *buf);
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D_efl_read
+ *
+ * Purpose:	Reads data from an external file list.  It is an error to
+ *		read past the logical end of file, but reading past the end
+ *		of any particular member of the external file list results in
+ *		zeros.
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, March  4, 1998
+ *
+ * Modifications:
+ *		Robb Matzke, 1999-07-28
+ *		The ADDR argument is passed by value.
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_efl_read (const H5O_efl_t *efl, haddr_t addr, size_t size, uint8_t *buf)
+{
+    int		fd=-1;
+    size_t	to_read;
+#ifndef NDEBUG
+    hsize_t     tempto_read;
+#endif /* NDEBUG */
+    hsize_t     skip=0;
+    haddr_t     cur;
+    ssize_t	n;
+    size_t      u;                      /* Local index variable */
+    herr_t      ret_value=SUCCEED;       /* Return value */
+    
+    FUNC_ENTER_NOAPI_NOINIT(H5D_efl_read);
+
+    /* Check args */
+    assert (efl && efl->nused>0);
+    assert (H5F_addr_defined (addr));
+    assert (size < SIZET_MAX);
+    assert (buf || 0==size);
+
+    /* Find the first efl member from which to read */
+    for (u=0, cur=0; u<efl->nused; u++) {
+	if (H5O_EFL_UNLIMITED==efl->slot[u].size || addr < cur+efl->slot[u].size) {
+	    skip = addr - cur;
+	    break;
+	}
+  	cur += efl->slot[u].size;
+    }
+    
+    /* Read the data */
+    while (size) {
+	if (u>=efl->nused)
+	    HGOTO_ERROR (H5E_EFL, H5E_OVERFLOW, FAIL, "read past logical end of file");
+	if (H5F_OVERFLOW_HSIZET2OFFT (efl->slot[u].offset+skip))
+	    HGOTO_ERROR (H5E_EFL, H5E_OVERFLOW, FAIL, "external file address overflowed");
+	if ((fd=HDopen (efl->slot[u].name, O_RDONLY, 0))<0)
+	    HGOTO_ERROR (H5E_EFL, H5E_CANTOPENFILE, FAIL, "unable to open external raw data file");
+	if (HDlseek (fd, (off_t)(efl->slot[u].offset+skip), SEEK_SET)<0)
+	    HGOTO_ERROR (H5E_EFL, H5E_SEEKERROR, FAIL, "unable to seek in external raw data file");
+#ifndef NDEBUG
+	tempto_read = MIN(efl->slot[u].size-skip,(hsize_t)size);
+        H5_CHECK_OVERFLOW(tempto_read,hsize_t,size_t);
+	to_read = (size_t)tempto_read;
+#else /* NDEBUG */
+	to_read = MIN((size_t)(efl->slot[u].size-skip), size);
+#endif /* NDEBUG */
+	if ((n=HDread (fd, buf, to_read))<0) {
+	    HGOTO_ERROR (H5E_EFL, H5E_READERROR, FAIL, "read error in external raw data file");
+	} else if ((size_t)n<to_read) {
+	    HDmemset (buf+n, 0, to_read-n);
+	}
+	HDclose (fd);
+	fd = -1;
+	size -= to_read;
+	buf += to_read;
+	skip = 0;
+	u++;
+    }
+    
+done:
+    if (fd>=0)
+        HDclose (fd);
+
+    FUNC_LEAVE_NOAPI(ret_value);
+}
+	
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D_efl_write
+ *
+ * Purpose:	Writes data to an external file list.  It is an error to
+ *		write past the logical end of file, but writing past the end
+ *		of any particular member of the external file list just
+ *		extends that file.
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Robb Matzke
+ *              Wednesday, March  4, 1998
+ *
+ * Modifications:
+ *		Robb Matzke, 1999-07-28
+ *		The ADDR argument is passed by value.
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D_efl_write (const H5O_efl_t *efl, haddr_t addr, size_t size, const uint8_t *buf)
+{
+    int		fd=-1;
+    size_t	to_write;
+#ifndef NDEBUG
+    hsize_t	tempto_write;
+#endif /* NDEBUG */
+    haddr_t     cur;
+    hsize_t     skip=0;
+    size_t	u;                      /* Local index variable */
+    herr_t      ret_value=SUCCEED;       /* Return value */
+    
+    FUNC_ENTER_NOAPI_NOINIT(H5D_efl_write);
+
+    /* Check args */
+    assert (efl && efl->nused>0);
+    assert (H5F_addr_defined (addr));
+    assert (size < SIZET_MAX);
+    assert (buf || 0==size);
+
+    /* Find the first efl member in which to write */
+    for (u=0, cur=0; u<efl->nused; u++) {
+	if (H5O_EFL_UNLIMITED==efl->slot[u].size || addr < cur+efl->slot[u].size) {
+	    skip = addr - cur;
+	    break;
+	}
+	cur += efl->slot[u].size;
+    }
+    
+    /* Write the data */
+    while (size) {
+	if (u>=efl->nused)
+	    HGOTO_ERROR (H5E_EFL, H5E_OVERFLOW, FAIL, "write past logical end of file");
+	if (H5F_OVERFLOW_HSIZET2OFFT (efl->slot[u].offset+skip))
+	    HGOTO_ERROR (H5E_EFL, H5E_OVERFLOW, FAIL, "external file address overflowed");
+	if ((fd=HDopen (efl->slot[u].name, O_CREAT|O_RDWR, 0666))<0) {
+	    if (HDaccess (efl->slot[u].name, F_OK)<0) {
+		HGOTO_ERROR (H5E_EFL, H5E_CANTOPENFILE, FAIL, "external raw data file does not exist");
+	    } else {
+		HGOTO_ERROR (H5E_EFL, H5E_CANTOPENFILE, FAIL, "unable to open external raw data file");
+	    }
+	}
+	if (HDlseek (fd, (off_t)(efl->slot[u].offset+skip), SEEK_SET)<0)
+	    HGOTO_ERROR (H5E_EFL, H5E_SEEKERROR, FAIL, "unable to seek in external raw data file");
+#ifndef NDEBUG
+	tempto_write = MIN(efl->slot[u].size-skip,(hsize_t)size);
+        H5_CHECK_OVERFLOW(tempto_write,hsize_t,size_t);
+        to_write = (size_t)tempto_write;
+#else /* NDEBUG */
+	to_write = MIN((size_t)(efl->slot[u].size-skip), size);
+#endif /* NDEBUG */
+	if ((size_t)HDwrite (fd, buf, to_write)!=to_write)
+	    HGOTO_ERROR (H5E_EFL, H5E_READERROR, FAIL, "write error in external raw data file");
+	HDclose (fd);
+	fd = -1;
+	size -= to_write;
+	buf += to_write;
+	skip = 0;
+	u++;
+    }
+    
+done:
+    if (fd>=0)
+        HDclose (fd);
+
+    FUNC_LEAVE_NOAPI(ret_value);
+}
+	
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D_efl_readvv
+ *
+ * Purpose:	Reads data from an external file list.  It is an error to
+ *		read past the logical end of file, but reading past the end
+ *		of any particular member of the external file list results in
+ *		zeros.
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Quincey Koziol
+ *              Wednesday, May  7, 2003
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+ssize_t
+H5D_efl_readvv(H5D_io_info_t *io_info,
+    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)
+{
+    const H5O_efl_t *efl=&(io_info->store->efl); /* Pointer to efl info */
+    unsigned char *buf;         /* Pointer to buffer to write */
+    haddr_t addr;               /* Actual address to read */
+    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_efl_readvv, FAIL);
+
+    /* Check args */
+    assert (efl && efl->nused>0);
+    assert (_buf);
+
+    /* 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_offset_arr[u];
+
+        /* Compute offset in memory */
+        buf = (unsigned char *)_buf + mem_offset_arr[v];
+
+        /* Read data */
+        if (H5D_efl_read(efl, addr, size, 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 */
+
+    /* Update current sequence vectors */
+    *dset_curr_seq=u;
+    *mem_curr_seq=v;
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value);
+} /* end H5D_efl_readvv() */
+	
+
+/*-------------------------------------------------------------------------
+ * Function:	H5D_efl_writevv
+ *
+ * Purpose:	Writes data to an external file list.  It is an error to
+ *		write past the logical end of file, but writing past the end
+ *		of any particular member of the external file list just
+ *		extends that file.
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Quincey Koziol
+ *              Friday, May  2, 2003
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+ssize_t
+H5D_efl_writevv(H5D_io_info_t *io_info,
+    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 H5O_efl_t *efl=&(io_info->store->efl); /* Pointer to efl info */
+    const unsigned char *buf;   /* Pointer to buffer to write */
+    haddr_t addr;               /* Actual address to read */
+    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_efl_writevv, FAIL);
+
+    /* Check args */
+    assert (efl && efl->nused>0);
+    assert (_buf);
+
+    /* 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_offset_arr[u];
+
+        /* Compute offset in memory */
+        buf = (const unsigned char *)_buf + mem_offset_arr[v];
+
+        /* Write data */
+        if (H5D_efl_write(efl, addr, size, 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 */
+
+    /* Update current sequence vectors */
+    *dset_curr_seq=u;
+    *mem_curr_seq=v;
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value);
+} /* end H5D_efl_writevv() */
+