Merge branch 'develop' into feature/coding_standardsfeature/coding_standards

1 files changed, 147 insertions, 80 deletions

diff --git a/src/H5Fio.c b/src/H5Fio.c
index 34dd0d6..53fec97 100644
--- a/src/H5Fio.c
+++ b/src/H5Fio.c
@@ -6,7 +6,7 @@
  * This file is part of HDF5.  The full HDF5 copyright notice, including     *
  * terms governing use, modification, and redistribution, is contained in    *
  * the COPYING file, which can be found at the root of the source code       *
- * distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases.  *
+ * distribution tree, or in https://www.hdfgroup.org/licenses.               *
  * If you do not have access to either file, you may request a copy from     *
  * help@hdfgroup.org.                                                        *
  * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * */
@@ -15,7 +15,7 @@
  *
  * Created:             H5Fio.c
  *                      Jan 10 2008
- *                      Quincey Koziol <koziol@hdfgroup.org>
+ *                      Quincey Koziol
  *
  * Purpose:             File I/O routines.
  *
@@ -26,56 +26,46 @@
 /* Module Setup */
 /****************/
 
-#include "H5Fmodule.h"          /* This source code file is part of the H5F module */
-
+#include "H5Fmodule.h" /* This source code file is part of the H5F module */
 
 /***********/
 /* Headers */
 /***********/
-#include "H5private.h"		/* Generic Functions			*/
-#include "H5Eprivate.h"		/* Error handling		  	*/
-#include "H5Fpkg.h"             /* File access				*/
-#include "H5FDprivate.h"	/* File drivers				*/
-#include "H5Iprivate.h"		/* IDs			  		*/
-#include "H5PBprivate.h"	/* Page Buffer				*/
-
+#include "H5private.h"   /* Generic Functions			*/
+#include "H5Eprivate.h"  /* Error handling		  	*/
+#include "H5Fpkg.h"      /* File access				*/
+#include "H5FDprivate.h" /* File drivers				*/
+#include "H5Iprivate.h"  /* IDs			  		*/
+#include "H5PBprivate.h" /* Page Buffer				*/
 
 /****************/
 /* Local Macros */
 /****************/
 
-
 /******************/
 /* Local Typedefs */
 /******************/
 
-
 /********************/
 /* Package Typedefs */
 /********************/
 
-
 /********************/
 /* Local Prototypes */
 /********************/
 
-
 /*********************/
 /* Package Variables */
 /*********************/
 
-
 /*****************************/
 /* Library Private Variables */
 /*****************************/
 
-
 /*******************/
 /* Local Variables */
 /*******************/
 
-
-
 /*-------------------------------------------------------------------------
  * Function:	H5F_shared_block_read
  *
@@ -86,16 +76,15 @@
  * Return:	Non-negative on success/Negative on failure
  *
  * Programmer:	Robb Matzke
- *		matzke@llnl.gov
  *		Jul 10 1997
  *
  *-------------------------------------------------------------------------
  */
 herr_t
-H5F_shared_block_read(H5F_shared_t *f_sh, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/)
+H5F_shared_block_read(H5F_shared_t *f_sh, H5FD_mem_t type, haddr_t addr, size_t size, void *buf /*out*/)
 {
-    H5FD_mem_t  map_type;               /* Mapped memory type */
-    herr_t      ret_value = SUCCEED;    /* Return value */
+    H5FD_mem_t map_type;            /* Mapped memory type */
+    herr_t     ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_NOAPI(FAIL)
 
@@ -105,21 +94,20 @@ H5F_shared_block_read(H5F_shared_t *f_sh, H5FD_mem_t type, haddr_t addr, size_t
     HDassert(H5F_addr_defined(addr));
 
     /* Check for attempting I/O on 'temporary' file address */
-    if(H5F_addr_le(f_sh->tmp_addr, (addr + size)))
+    if (H5F_addr_le(f_sh->tmp_addr, (addr + size)))
         HGOTO_ERROR(H5E_IO, H5E_BADRANGE, FAIL, "attempting I/O in temporary file space")
 
     /* Treat global heap as raw data */
     map_type = (type == H5FD_MEM_GHEAP) ? H5FD_MEM_DRAW : type;
 
     /* Pass through page buffer layer */
-    if(H5PB_read(f_sh, map_type, addr, size, buf) < 0)
+    if (H5PB_read(f_sh, map_type, addr, size, buf) < 0)
         HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "read through page buffer failed")
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5F_shared_block_read() */
 
-
 /*-------------------------------------------------------------------------
  * Function:	H5F_block_read
  *
@@ -130,16 +118,15 @@ done:
  * Return:	Non-negative on success/Negative on failure
  *
  * Programmer:	Robb Matzke
- *		matzke@llnl.gov
  *		Jul 10 1997
  *
  *-------------------------------------------------------------------------
  */
 herr_t
-H5F_block_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*out*/)
+H5F_block_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf /*out*/)
 {
-    H5FD_mem_t  map_type;               /* Mapped memory type */
-    herr_t      ret_value = SUCCEED;    /* Return value */
+    H5FD_mem_t map_type;            /* Mapped memory type */
+    herr_t     ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_NOAPI(FAIL)
 
@@ -150,21 +137,20 @@ H5F_block_read(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, void *buf/*
     HDassert(H5F_addr_defined(addr));
 
     /* Check for attempting I/O on 'temporary' file address */
-    if(H5F_addr_le(f->shared->tmp_addr, (addr + size)))
+    if (H5F_addr_le(f->shared->tmp_addr, (addr + size)))
         HGOTO_ERROR(H5E_IO, H5E_BADRANGE, FAIL, "attempting I/O in temporary file space")
 
     /* Treat global heap as raw data */
     map_type = (type == H5FD_MEM_GHEAP) ? H5FD_MEM_DRAW : type;
 
     /* Pass through page buffer layer */
-    if(H5PB_read(f->shared, map_type, addr, size, buf) < 0)
+    if (H5PB_read(f->shared, map_type, addr, size, buf) < 0)
         HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "read through page buffer failed")
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5F_block_read() */
 
-
 /*-------------------------------------------------------------------------
  * Function:	H5F_shared_block_write
  *
@@ -175,7 +161,6 @@ done:
  * Return:	Non-negative on success/Negative on failure
  *
  * Programmer:	Robb Matzke
- *		matzke@llnl.gov
  *		Jul 10 1997
  *
  *-------------------------------------------------------------------------
@@ -183,8 +168,8 @@ done:
 herr_t
 H5F_shared_block_write(H5F_shared_t *f_sh, H5FD_mem_t type, haddr_t addr, size_t size, const void *buf)
 {
-    H5FD_mem_t  map_type;               /* Mapped memory type */
-    herr_t      ret_value = SUCCEED;    /* Return value */
+    H5FD_mem_t map_type;            /* Mapped memory type */
+    herr_t     ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_NOAPI(FAIL)
 
@@ -195,21 +180,20 @@ H5F_shared_block_write(H5F_shared_t *f_sh, H5FD_mem_t type, haddr_t addr, size_t
     HDassert(H5F_addr_defined(addr));
 
     /* Check for attempting I/O on 'temporary' file address */
-    if(H5F_addr_le(f_sh->tmp_addr, (addr + size)))
+    if (H5F_addr_le(f_sh->tmp_addr, (addr + size)))
         HGOTO_ERROR(H5E_IO, H5E_BADRANGE, FAIL, "attempting I/O in temporary file space")
 
     /* Treat global heap as raw data */
     map_type = (type == H5FD_MEM_GHEAP) ? H5FD_MEM_DRAW : type;
 
     /* Pass through page buffer layer */
-    if(H5PB_write(f_sh, map_type, addr, size, buf) < 0)
+    if (H5PB_write(f_sh, map_type, addr, size, buf) < 0)
         HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write through page buffer failed")
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5F_shared_block_write() */
 
-
 /*-------------------------------------------------------------------------
  * Function:	H5F_block_write
  *
@@ -220,7 +204,6 @@ done:
  * Return:	Non-negative on success/Negative on failure
  *
  * Programmer:	Robb Matzke
- *		matzke@llnl.gov
  *		Jul 10 1997
  *
  *-------------------------------------------------------------------------
@@ -228,8 +211,8 @@ done:
 herr_t
 H5F_block_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, const void *buf)
 {
-    H5FD_mem_t  map_type;               /* Mapped memory type */
-    herr_t      ret_value = SUCCEED;    /* Return value */
+    H5FD_mem_t map_type;            /* Mapped memory type */
+    herr_t     ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_NOAPI(FAIL)
 
@@ -241,21 +224,109 @@ H5F_block_write(H5F_t *f, H5FD_mem_t type, haddr_t addr, size_t size, const void
     HDassert(H5F_addr_defined(addr));
 
     /* Check for attempting I/O on 'temporary' file address */
-    if(H5F_addr_le(f->shared->tmp_addr, (addr + size)))
+    if (H5F_addr_le(f->shared->tmp_addr, (addr + size)))
         HGOTO_ERROR(H5E_IO, H5E_BADRANGE, FAIL, "attempting I/O in temporary file space")
 
     /* Treat global heap as raw data */
     map_type = (type == H5FD_MEM_GHEAP) ? H5FD_MEM_DRAW : type;
 
     /* Pass through page buffer layer */
-    if(H5PB_write(f->shared, map_type, addr, size, buf) < 0)
+    if (H5PB_write(f->shared, map_type, addr, size, buf) < 0)
         HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "write through page buffer failed")
-
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5F_block_write() */
 
-
+/*-------------------------------------------------------------------------
+ * Function:    H5F_shared_select_read
+ *
+ * Purpose:     Reads some data from a file/server/etc into a buffer.
+ *              The location of the data is defined by the mem_spaces and
+ *              file_spaces dataspace arrays, along with the offsets
+ *              array.  The addresses is relative to the base address for
+ *              the file.
+ *
+ * Return:      Non-negative on success/Negative on failure
+ *
+ * Programmer:  Neil Fortner
+ *              May 3 2021
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5F_shared_select_read(H5F_shared_t *f_sh, H5FD_mem_t type, uint32_t count, H5S_t **mem_spaces,
+                       H5S_t **file_spaces, haddr_t offsets[], size_t element_sizes[], void *bufs[] /* out */)
+{
+    H5FD_mem_t map_type;            /* Mapped memory type */
+    herr_t     ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_NOAPI(FAIL)
+
+    /* Sanity checks */
+    HDassert(f_sh);
+    HDassert((mem_spaces) || (count == 0));
+    HDassert((file_spaces) || (count == 0));
+    HDassert((offsets) || (count == 0));
+    HDassert((element_sizes) || (count == 0));
+    HDassert((bufs) || (count == 0));
+
+    /* Treat global heap as raw data */
+    map_type = (type == H5FD_MEM_GHEAP) ? H5FD_MEM_DRAW : type;
+
+    /* Pass down to file driver layer (bypass page buffer for now) */
+    if (H5FD_read_selection(f_sh->lf, map_type, count, mem_spaces, file_spaces, offsets, element_sizes,
+                            bufs) < 0)
+        HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "selection read through file driver failed")
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5F_shared_select_read() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5F_shared_select_write
+ *
+ * Purpose:     Writes some data from a buffer to a file/server/etc.
+ *              The location of the data is defined by the mem_spaces and
+ *              file_spaces dataspace arrays, along with the offsets
+ *              array.  The addresses is relative to the base address for
+ *              the file.
+ *
+ * Return:      Non-negative on success/Negative on failure
+ *
+ * Programmer:  Neil Fortner
+ *              May 4 2021
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5F_shared_select_write(H5F_shared_t *f_sh, H5FD_mem_t type, uint32_t count, H5S_t **mem_spaces,
+                        H5S_t **file_spaces, haddr_t offsets[], size_t element_sizes[], const void *bufs[])
+{
+    H5FD_mem_t map_type;            /* Mapped memory type */
+    herr_t     ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_NOAPI(FAIL)
+
+    /* Sanity checks */
+    HDassert(f_sh);
+    HDassert((mem_spaces) || (count == 0));
+    HDassert((file_spaces) || (count == 0));
+    HDassert((offsets) || (count == 0));
+    HDassert((element_sizes) || (count == 0));
+    HDassert((bufs) || (count == 0));
+
+    /* Treat global heap as raw data */
+    map_type = (type == H5FD_MEM_GHEAP) ? H5FD_MEM_DRAW : type;
+
+    /* Pass down to file driver layer (bypass page buffer for now) */
+    if (H5FD_write_selection(f_sh->lf, map_type, count, mem_spaces, file_spaces, offsets, element_sizes,
+                             bufs) < 0)
+        HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "selection write through file driver failed")
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5F_shared_select_write() */
+
 /*-------------------------------------------------------------------------
  * Function:    H5F_flush_tagged_metadata
  *
@@ -277,22 +348,21 @@ H5F_flush_tagged_metadata(H5F_t *f, haddr_t tag)
     FUNC_ENTER_NOAPI(FAIL)
 
     /* Use tag to search for and flush associated metadata */
-    if(H5AC_flush_tagged_metadata(f, tag) < 0)
+    if (H5AC_flush_tagged_metadata(f, tag) < 0)
         HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to flush tagged metadata")
 
     /* Flush and reset the accumulator */
-    if(H5F__accum_reset(f->shared, TRUE) < 0)
+    if (H5F__accum_reset(f->shared, TRUE) < 0)
         HGOTO_ERROR(H5E_IO, H5E_CANTRESET, FAIL, "can't reset accumulator")
 
     /* Flush file buffers to disk. */
-    if(H5FD_flush(f->shared->lf, FALSE) < 0)
+    if (H5FD_flush(f->shared->lf, FALSE) < 0)
         HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "low level flush failed")
 
 done:
     FUNC_LEAVE_NOAPI(ret_value);
 } /* end H5F_flush_tagged_metadata */
 
-
 /*-------------------------------------------------------------------------
  * Function:    H5F_evict_tagged_metadata
  *
@@ -313,14 +383,13 @@ H5F_evict_tagged_metadata(H5F_t *f, haddr_t tag)
     FUNC_ENTER_NOAPI(FAIL)
 
     /* Evict the object's metadata */
-    if(H5AC_evict_tagged_metadata(f, tag, TRUE) < 0)
+    if (H5AC_evict_tagged_metadata(f, tag, TRUE) < 0)
         HGOTO_ERROR(H5E_CACHE, H5E_CANTEXPUNGE, FAIL, "unable to evict tagged metadata")
 
 done:
     FUNC_LEAVE_NOAPI(ret_value);
 } /* end H5F_evict_tagged_metadata */
 
-
 /*-------------------------------------------------------------------------
  * Function:    H5F__evict_cache_entries
  *
@@ -344,37 +413,36 @@ H5F__evict_cache_entries(H5F_t *f)
     HDassert(f->shared);
 
     /* Evict all except pinned entries in the cache */
-    if(H5AC_evict(f) < 0)
+    if (H5AC_evict(f) < 0)
         HGOTO_ERROR(H5E_CACHE, H5E_CANTEXPUNGE, FAIL, "unable to evict all except pinned entries")
 
 #ifndef NDEBUG
-{
-    unsigned status = 0;
-    uint32_t cur_num_entries;
-
-    /* Retrieve status of the superblock */
-    if(H5AC_get_entry_status(f, (haddr_t)0, &status) < 0)
-        HGOTO_ERROR(H5E_HEAP, H5E_CANTGET, FAIL, "unable to get entry status")
-
-    /* Verify status of the superblock entry in the cache */
-    if(!(status & H5AC_ES__IN_CACHE) || !(status & H5AC_ES__IS_PINNED))
-        HGOTO_ERROR(H5E_HEAP, H5E_CANTGET, FAIL, "unable to get entry status")
-
-    /* Get the number of cache entries */
-    if(H5AC_get_cache_size(f->shared->cache, NULL, NULL, NULL, &cur_num_entries) < 0)
-        HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "H5AC_get_cache_size() failed.")
-
-    /* Should be the only one left in the cache (the superblock) */
-    if(cur_num_entries != 1)
-        HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "number of cache entries is not correct")
-}
+    {
+        unsigned status = 0;
+        uint32_t cur_num_entries;
+
+        /* Retrieve status of the superblock */
+        if (H5AC_get_entry_status(f, (haddr_t)0, &status) < 0)
+            HGOTO_ERROR(H5E_HEAP, H5E_CANTGET, FAIL, "unable to get entry status")
+
+        /* Verify status of the superblock entry in the cache */
+        if (!(status & H5AC_ES__IN_CACHE) || !(status & H5AC_ES__IS_PINNED))
+            HGOTO_ERROR(H5E_HEAP, H5E_CANTGET, FAIL, "unable to get entry status")
+
+        /* Get the number of cache entries */
+        if (H5AC_get_cache_size(f->shared->cache, NULL, NULL, NULL, &cur_num_entries) < 0)
+            HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "H5AC_get_cache_size() failed.")
+
+        /* Should be the only one left in the cache (the superblock) */
+        if (cur_num_entries != 1)
+            HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "number of cache entries is not correct")
+    }
 #endif /* NDEBUG */
 
 done:
     FUNC_LEAVE_NOAPI(ret_value);
 } /* end H5F__evict_cache_entries() */
 
-
 /*-------------------------------------------------------------------------
  * Function:    H5F_get_checksums
  *
@@ -391,7 +459,7 @@ done:
  *-------------------------------------------------------------------------
  */
 herr_t
-H5F_get_checksums(const uint8_t *buf, size_t buf_size, uint32_t *s_chksum/*out*/, uint32_t *c_chksum/*out*/)
+H5F_get_checksums(const uint8_t *buf, size_t buf_size, uint32_t *s_chksum /*out*/, uint32_t *c_chksum /*out*/)
 {
     FUNC_ENTER_NOAPI_NOINIT_NOERR
 
@@ -400,8 +468,8 @@ H5F_get_checksums(const uint8_t *buf, size_t buf_size, uint32_t *s_chksum/*out*/
     HDassert(buf_size);
 
     /* Return the stored checksum */
-    if(s_chksum) {
-        const uint8_t *chk_p;      	/* Pointer into raw data buffer */
+    if (s_chksum) {
+        const uint8_t *chk_p; /* Pointer into raw data buffer */
 
         /* Offset to the checksum in the buffer */
         chk_p = buf + buf_size - H5_SIZEOF_CHKSUM;
@@ -411,9 +479,8 @@ H5F_get_checksums(const uint8_t *buf, size_t buf_size, uint32_t *s_chksum/*out*/
     } /* end if */
 
     /* Return the computed checksum for the buffer */
-    if(c_chksum)
-	*c_chksum = H5_checksum_metadata(buf, buf_size - H5_SIZEOF_CHKSUM, 0);
+    if (c_chksum)
+        *c_chksum = H5_checksum_metadata(buf, buf_size - H5_SIZEOF_CHKSUM, 0);
 
     FUNC_LEAVE_NOAPI(SUCCEED)
 } /* end H5F_get_chksums() */
-