Updated to HDF5 1.10.0-alpha1

hdf5swmr/bin/h5cc

@@ -92,9 +92,9 @@ CLINKERBASE="gcc"
 # from the hdf5 build. The order of the flags is intended to give precedence
 # to the user's flags.
 H5BLD_CFLAGS=" "
-H5BLD_CPPFLAGS="-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE  "
+H5BLD_CPPFLAGS="-D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE  "
 H5BLD_LDFLAGS=" "
-H5BLD_LIBS=" -lpthread -lz -lrt -ldl -lm "
+H5BLD_LIBS="-lrt -lz -ldl -lm "
 
 CC="${HDF5_CC:-$CCBASE}"
 CLINKER="${HDF5_CLINKER:-$CLINKERBASE}"
@@ -347,7 +347,7 @@ if test "x$do_link" = "xyes"; then
     hpux*)                flag="-Wl,+b -Wl," ;;
     freebsd*|solaris*)    flag="-R" ;;
     rs6000*|aix*)         flag="-L" ;;
-    irix*|sgi)            flag="-rpath " ;;
+    sgi)                  flag="-rpath " ;;
     *)                    flag="" ;;
   esac
 

hdf5swmr/include/H5ACpublic.h

@@ -441,7 +441,7 @@ extern "C" {
  ****************************************************************************/
 
 #define H5AC__CURR_CACHE_CONFIG_VERSION 	1
-#define H5AC__MAX_TRACE_FILE_NAME_LEN           1024
+#define H5AC__MAX_TRACE_FILE_NAME_LEN		1024
 
 #define H5AC_METADATA_WRITE_STRATEGY__PROCESS_0_ONLY    0
 #define H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED       1
@@ -502,7 +502,7 @@ typedef struct H5AC_cache_config_t
 
 
     /* parallel configuration fields: */
-    int                      dirty_bytes_threshold;
+    size_t                   dirty_bytes_threshold;
     int                      metadata_write_strategy;
 
 } H5AC_cache_config_t;

hdf5swmr/include/H5DOpublic.h

@@ -22,22 +22,16 @@ extern "C" {
 
 /*-------------------------------------------------------------------------
  *
- * Direct chunk write function, Dataset append operation
+ * "Optimized dataset" routines.
  *
  *-------------------------------------------------------------------------
  */
 
-H5_HLDLL herr_t H5DOwrite_chunk(hid_t dset_id, 
-			hid_t dxpl_id, 
-			uint32_t filters, 
-			const hsize_t *offset, 
-         		size_t data_size, 
-			const void *buf);
-
-herr_t
-H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis, size_t extension,
-           hid_t memtype, const void *buf);
+H5_HLDLL herr_t H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, 
+    const hsize_t *offset, size_t data_size, const void *buf);
 
+H5_HLDLL herr_t H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis,
+    size_t extension, hid_t memtype, const void *buf);
 
 #ifdef __cplusplus
 }

hdf5swmr/include/H5Dpublic.h

@@ -54,16 +54,18 @@ typedef enum H5D_layout_t {
     H5D_COMPACT		= 0,	/*raw data is very small		     */
     H5D_CONTIGUOUS	= 1,	/*the default				     */
     H5D_CHUNKED		= 2,	/*slow and fancy			     */
-    H5D_NLAYOUTS	= 3	/*this one must be last!		     */
+    H5D_VIRTUAL         = 3,    /*actual data is stored in other datasets     */
+    H5D_NLAYOUTS	= 4	/*this one must be last!		     */
 } H5D_layout_t;
 
 /* Types of chunk index data structures */
 typedef enum H5D_chunk_index_t {
     H5D_CHUNK_IDX_BTREE	= 0,	/* v1 B-tree index (default)                 */
-    H5D_CHUNK_IDX_NONE = 1,     /* No Index (H5D_ALLOC_TIME_EARLY, non-filtered, fixed dims) */
-    H5D_CHUNK_IDX_FARRAY = 2,	/* Fixed array (for 0 unlimited dims)	     */
-    H5D_CHUNK_IDX_EARRAY = 3,	/* Extensible array (for 1 unlimited dim)    */
-    H5D_CHUNK_IDX_BT2 = 4,   	/* v2 B-tree index (for >1 unlimited dims)   */
+    H5D_CHUNK_IDX_SINGLE = 1,   /* Single Chunk index (cur dims[]=max dims[]=chunk dims[]; filtered & non-filtered) */
+    H5D_CHUNK_IDX_NONE = 2,     /* Implicit: No Index (H5D_ALLOC_TIME_EARLY, non-filtered, fixed dims) */
+    H5D_CHUNK_IDX_FARRAY = 3,	/* Fixed array (for 0 unlimited dims)	     */
+    H5D_CHUNK_IDX_EARRAY = 4,	/* Extensible array (for 1 unlimited dim)    */
+    H5D_CHUNK_IDX_BT2 = 5,   	/* v2 B-tree index (for >1 unlimited dims)   */
     H5D_CHUNK_IDX_NTYPES	/*this one must be last!		     */
 } H5D_chunk_index_t;
 
@@ -100,6 +102,13 @@ typedef enum H5D_fill_value_t {
     H5D_FILL_VALUE_USER_DEFINED =2
 } H5D_fill_value_t;
 
+/* Values for VDS bounds option */
+typedef enum H5D_vds_view_t {
+    H5D_VDS_ERROR               = -1,
+    H5D_VDS_FIRST_MISSING       = 0,
+    H5D_VDS_LAST_AVAILABLE      = 1
+} H5D_vds_view_t;
+
 /* Callback for H5Pset_append_flush() in a dataset access property list */
 typedef herr_t (*H5D_append_cb_t)(hid_t dataset_id, hsize_t *cur_dims, void *op_data);
 
@@ -159,6 +168,10 @@ H5_DLL herr_t H5Dgather(hid_t src_space_id, const void *src_buf, hid_t type_id,
     size_t dst_buf_size, void *dst_buf, H5D_gather_func_t op, void *op_data);
 H5_DLL herr_t H5Ddebug(hid_t dset_id);
 
+/* Internal API routines */
+H5_DLL herr_t H5Dformat_convert(hid_t dset_id);
+H5_DLL herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
+
 /* Symbols defined for compatibility with previous versions of the HDF5 API.
  *
  * Use of these symbols is deprecated.

hdf5swmr/include/H5Epubgen.h

@@ -20,6 +20,10 @@
 #ifndef _H5Epubgen_H
 #define _H5Epubgen_H
 
+#ifdef __cplusplus
+extern "C" {
+#endif
+
 /*********************/
 /* Major error codes */
 /*********************/
@@ -282,6 +286,8 @@ H5_DLLVAR hid_t H5E_NOIDS_g;         /* Out of IDs for group */
 #define H5E_CANTUNDEPEND     (H5OPEN H5E_CANTUNDEPEND_g)
 #define H5E_CANTNOTIFY       (H5OPEN H5E_CANTNOTIFY_g)
 #define H5E_LOGFAIL          (H5OPEN H5E_LOGFAIL_g)
+#define H5E_CANTCORK         (H5OPEN H5E_CANTCORK_g)
+#define H5E_CANTUNCORK       (H5OPEN H5E_CANTUNCORK_g)
 H5_DLLVAR hid_t H5E_CANTFLUSH_g;     /* Unable to flush data from cache */
 H5_DLLVAR hid_t H5E_CANTSERIALIZE_g; /* Unable to serialize data from cache */
 H5_DLLVAR hid_t H5E_CANTTAG_g;       /* Unable to tag metadata in the cache */
@@ -302,6 +308,8 @@ H5_DLLVAR hid_t H5E_CANTDEPEND_g;    /* Unable to create a flush dependency */
 H5_DLLVAR hid_t H5E_CANTUNDEPEND_g;  /* Unable to destroy a flush dependency */
 H5_DLLVAR hid_t H5E_CANTNOTIFY_g;    /* Unable to notify object about action */
 H5_DLLVAR hid_t H5E_LOGFAIL_g;       /* Failure in the cache logging framework */
+H5_DLLVAR hid_t H5E_CANTCORK_g;      /* Unable to cork an object */
+H5_DLLVAR hid_t H5E_CANTUNCORK_g;    /* Unable to uncork an object */
 
 /* Link related errors */
 #define H5E_TRAVERSE         (H5OPEN H5E_TRAVERSE_g)
@@ -330,12 +338,14 @@ H5_DLLVAR hid_t H5E_CANTRECV_g;      /* Can't receive data */
 #define H5E_CANTNEXT         (H5OPEN H5E_CANTNEXT_g)
 #define H5E_BADSELECT        (H5OPEN H5E_BADSELECT_g)
 #define H5E_CANTCOMPARE      (H5OPEN H5E_CANTCOMPARE_g)
+#define H5E_CANTAPPEND       (H5OPEN H5E_CANTAPPEND_g)
 H5_DLLVAR hid_t H5E_CANTCLIP_g;      /* Can't clip hyperslab region */
 H5_DLLVAR hid_t H5E_CANTCOUNT_g;     /* Can't count elements */
 H5_DLLVAR hid_t H5E_CANTSELECT_g;    /* Can't select hyperslab */
 H5_DLLVAR hid_t H5E_CANTNEXT_g;      /* Can't move to next iterator location */
 H5_DLLVAR hid_t H5E_BADSELECT_g;     /* Invalid selection */
 H5_DLLVAR hid_t H5E_CANTCOMPARE_g;   /* Can't compare objects */
+H5_DLLVAR hid_t H5E_CANTAPPEND_g;    /* Can't append object */
 
 /* Argument errors */
 #define H5E_UNINITIALIZED    (H5OPEN H5E_UNINITIALIZED_g)
@@ -379,4 +389,8 @@ H5_DLLVAR hid_t H5E_CANTREMOVE_g;    /* Unable to remove object */
 H5_DLLVAR hid_t H5E_CANTCONVERT_g;   /* Can't convert datatypes */
 H5_DLLVAR hid_t H5E_BADSIZE_g;       /* Bad size for object */
 
+#ifdef __cplusplus
+}
+#endif
+
 #endif /* H5Epubgen_H */

hdf5swmr/include/H5Epublic.h

@@ -26,7 +26,7 @@
 #include "H5Ipublic.h"
 
 /* Value for the default error stack */
-#define H5E_DEFAULT             0
+#define H5E_DEFAULT             (hid_t)0
 
 /* Different kinds of error information */
 typedef enum H5E_type_t {

hdf5swmr/include/H5FDpublic.h

@@ -156,13 +156,13 @@ typedef enum H5F_mem_t	H5FD_mem_t;
 /* Define VFL driver features that can be enabled on a per-driver basis */
 /* These are returned with the 'query' function pointer in H5FD_class_t */
     /*
-     * Defining the H5FD_FEAT_AGGREGATE_METADATA for a VFL driver means that
+     * Defining H5FD_FEAT_AGGREGATE_METADATA for a VFL driver means that
      * the library will attempt to allocate a larger block for metadata and
      * then sub-allocate each metadata request from that larger block.
      */
 #define H5FD_FEAT_AGGREGATE_METADATA    0x00000001
     /*
-     * Defining the H5FD_FEAT_ACCUMULATE_METADATA for a VFL driver means that
+     * Defining H5FD_FEAT_ACCUMULATE_METADATA for a VFL driver means that
      * the library will attempt to cache metadata as it is written to the file
      * and build up a larger block of metadata to eventually pass to the VFL
      * 'write' routine.
@@ -177,64 +177,68 @@ typedef enum H5F_mem_t	H5FD_mem_t;
 #define H5FD_FEAT_ACCUMULATE_METADATA_READ      0x00000004
 #define H5FD_FEAT_ACCUMULATE_METADATA   (H5FD_FEAT_ACCUMULATE_METADATA_WRITE|H5FD_FEAT_ACCUMULATE_METADATA_READ)
     /*
-     * Defining the H5FD_FEAT_DATA_SIEVE for a VFL driver means that
+     * Defining H5FD_FEAT_DATA_SIEVE for a VFL driver means that
      * the library will attempt to cache raw data as it is read from/written to
      * a file in a "data seive" buffer.  See Rajeev Thakur's papers:
      *  http://www.mcs.anl.gov/~thakur/papers/romio-coll.ps.gz
      *  http://www.mcs.anl.gov/~thakur/papers/mpio-high-perf.ps.gz
      */
 #define H5FD_FEAT_DATA_SIEVE            0x00000008
     /*
-     * Defining the H5FD_FEAT_AGGREGATE_SMALLDATA for a VFL driver means that
+     * Defining H5FD_FEAT_AGGREGATE_SMALLDATA for a VFL driver means that
      * the library will attempt to allocate a larger block for "small" raw data
      * and then sub-allocate "small" raw data requests from that larger block.
      */
 #define H5FD_FEAT_AGGREGATE_SMALLDATA   0x00000010
     /*
-     * Defining the H5FD_FEAT_IGNORE_DRVRINFO for a VFL driver means that
+     * Defining H5FD_FEAT_IGNORE_DRVRINFO for a VFL driver means that
      * the library will ignore the driver info that is encoded in the file
      * for the VFL driver.  (This will cause the driver info to be eliminated
      * from the file when it is flushed/closed, if the file is opened R/W).
      */
 #define H5FD_FEAT_IGNORE_DRVRINFO       0x00000020
     /*
-     * Defining the H5FD_FEAT_DIRTY_SBLK_LOAD for a VFL driver means that
-     * the library will mark the superblock dirty when the file is opened
+     * Defining the H5FD_FEAT_DIRTY_DRVRINFO_LOAD for a VFL driver means that
+     * the library will mark the driver info dirty when the file is opened
      * R/W.  This will cause the driver info to be re-encoded when the file
      * is flushed/closed.
      */
-#define H5FD_FEAT_DIRTY_SBLK_LOAD       0x00000040
+#define H5FD_FEAT_DIRTY_DRVRINFO_LOAD   0x00000040
     /*
-     * Defining the H5FD_FEAT_POSIX_COMPAT_HANDLE for a VFL driver means that
+     * Defining H5FD_FEAT_POSIX_COMPAT_HANDLE for a VFL driver means that
      * the handle for the VFD (returned with the 'get_handle' callback) is
      * of type 'int' and is compatible with POSIX I/O calls.
      */
 #define H5FD_FEAT_POSIX_COMPAT_HANDLE   0x00000080    
     /*
-     * Defining the H5FD_FEAT_HAS_MPI for a VFL driver means that
+     * Defining H5FD_FEAT_HAS_MPI for a VFL driver means that
      * the driver makes use of MPI communication and code may retrieve
      * communicator/rank information from it
      */
 #define H5FD_FEAT_HAS_MPI               0x00000100
     /*
-     * Defining the H5FD_FEAT_ALLOCATE_EARLY for a VFL driver means that
-     * the library will use the H5D_ALLOC_TIME_EARLY on dataset create
+     * Defining the H5FD_FEAT_ALLOCATE_EARLY for a VFL driver will force
+     * the library to use the H5D_ALLOC_TIME_EARLY on dataset create
      * instead of the default H5D_ALLOC_TIME_LATE
      */
 #define H5FD_FEAT_ALLOCATE_EARLY        0x00000200
     /* 
-     * Defining the H5FD_FEAT_ALLOW_FILE_IMAGE for a VFL driver means that
+     * Defining H5FD_FEAT_ALLOW_FILE_IMAGE for a VFL driver means that
      * the driver is able to use a file image in the fapl as the initial
      * contents of a file.
      */
 #define H5FD_FEAT_ALLOW_FILE_IMAGE      0x00000400
     /*
-     * Defining the H5FD_FEAT_CAN_USE_FILE_IMAGE_CALLBACKS for a VFL driver
+     * Defining H5FD_FEAT_CAN_USE_FILE_IMAGE_CALLBACKS for a VFL driver
      * means that the driver is able to use callbacks to make a copy of the
      * image to store in memory.
      */
 #define H5FD_FEAT_CAN_USE_FILE_IMAGE_CALLBACKS 0x00000800
-
+    /*
+     * Defining H5FD_FEAT_SUPPORTS_SWMR_IO for a VFL driver means that the
+     * driver supports the single-writer/multiple-readers I/O pattern.
+     */
+#define H5FD_FEAT_SUPPORTS_SWMR_IO      0x00001000
 
 /* Forward declaration */
 typedef struct H5FD_t H5FD_t;
@@ -267,7 +271,7 @@ typedef struct H5FD_class_t {
                     haddr_t addr, hsize_t size);
     haddr_t (*get_eoa)(const H5FD_t *file, H5FD_mem_t type);
     herr_t  (*set_eoa)(H5FD_t *file, H5FD_mem_t type, haddr_t addr);
-    haddr_t (*get_eof)(const H5FD_t *file);
+    haddr_t (*get_eof)(const H5FD_t *file, H5FD_mem_t type);
     herr_t  (*get_handle)(H5FD_t *file, hid_t fapl, void**file_handle);
     herr_t  (*read)(H5FD_t *file, H5FD_mem_t type, hid_t dxpl,
                     haddr_t addr, size_t size, void *buffer);
@@ -298,6 +302,8 @@ struct H5FD_t {
     unsigned long       feature_flags;  /* VFL Driver feature Flags */
     haddr_t             maxaddr;        /* For this file, overrides class */
     haddr_t             base_addr;      /* Base address for HDF5 data w/in file */
+    hbool_t     	swmr_read;	/* Whether the file is open for SWMR read access */
+					/* Information from file open flags, for SWMR access */
 
     /* Space allocation management fields */
     hsize_t             threshold;      /* Threshold for alignment  */
@@ -348,14 +354,16 @@ H5_DLL herr_t H5FDfree(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id,
                        haddr_t addr, hsize_t size);
 H5_DLL haddr_t H5FDget_eoa(H5FD_t *file, H5FD_mem_t type);
 H5_DLL herr_t H5FDset_eoa(H5FD_t *file, H5FD_mem_t type, haddr_t eoa);
-H5_DLL haddr_t H5FDget_eof(H5FD_t *file);
+H5_DLL haddr_t H5FDget_eof(H5FD_t *file, H5FD_mem_t type);
 H5_DLL herr_t H5FDget_vfd_handle(H5FD_t *file, hid_t fapl, void**file_handle);
 H5_DLL herr_t H5FDread(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id,
                        haddr_t addr, size_t size, void *buf/*out*/);
 H5_DLL herr_t H5FDwrite(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id,
                         haddr_t addr, size_t size, const void *buf);
 H5_DLL herr_t H5FDflush(H5FD_t *file, hid_t dxpl_id, unsigned closing);
 H5_DLL herr_t H5FDtruncate(H5FD_t *file, hid_t dxpl_id, hbool_t closing);
+H5_DLL herr_t H5FDlock(H5FD_t *file, hbool_t rw);
+H5_DLL herr_t H5FDunlock(H5FD_t *file);
 
 #ifdef __cplusplus
 }