[svn-r224] Initial implementation of the upper levels of PHDF5. The

MPIO lower interface layer (H5Fmpio.c) has been commited by Kim already.
All PHDF5 codes are "bracket'ed" by #ifdef HAVE_PARALLEL macro.

9 files changed, 207 insertions, 34 deletions

diff --git a/src/H5C.c b/src/H5C.c
index 4c4f4fe..7a20114 100644
--- a/src/H5C.c
+++ b/src/H5C.c
@@ -141,13 +141,14 @@ H5Ccreate(H5C_class_t type)
     /* Allocate a new template and initialize it with default values */
     switch (type) {
     case H5C_FILE_CREATE:
-        tmpl = H5MM_xmalloc(sizeof(H5F_create_t));
+	tmpl = H5MM_xmalloc(sizeof(H5F_create_t));
         memcpy(tmpl, &H5F_create_dflt, sizeof(H5F_create_t));
         break;
 
     case H5C_FILE_ACCESS:
-        HRETURN_ERROR(H5E_INTERNAL, H5E_UNSUPPORTED, FAIL,
-                      "not implemented yet");
+        tmpl = H5MM_xmalloc(sizeof(H5F_access_t));
+        memcpy(tmpl, &H5F_access_dflt, sizeof(H5F_access_t));
+        break;
 
     case H5C_DATASET_CREATE:
         tmpl = H5MM_xmalloc(sizeof(H5D_create_t));
@@ -233,6 +234,9 @@ H5Cclose(hid_t tid)
     if (NULL == (tmpl = H5A_remove(tid))) {
         HRETURN_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "unable to remove atom");
     }
+#ifdef LATER
+    /* this is for file access template too.  Need to free the COMM and INFO objects too. */
+#endif 
     H5MM_xfree(tmpl);
 
     FUNC_LEAVE(SUCCEED);
@@ -853,6 +857,69 @@ H5Cget_chunk(hid_t tid, int max_ndims, size_t dim[] /*out */ )
 
     FUNC_LEAVE(tmpl->chunk_ndims);
 }
+
+#ifdef HAVE_PARALLEL
+/*-------------------------------------------------------------------------
+ * Function:    H5Cset_mpi
+ *
+ * Purpose:     Sets the access mode for MPIO call and store the user supplied
+ *		communicator and info.
+ *
+ * Return:      Success:        SUCCEED
+ *
+ *              Failure:        FAIL
+ *
+ * Programmer:  Albert Cheng
+ *              Feb 3, 1998
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Cset_mpi (hid_t tid, MPI_Comm comm, MPI_Info info, uintn access_mode)
+{
+    int                     i;
+    H5F_access_t           *tmpl = NULL;
+    MPI_Comm		    lcomm;
+    int			    mrc;		/* MPI return code */
+
+    FUNC_ENTER(H5Cset_mpi, FAIL);
+
+    /* Check arguments */
+    if (H5C_FILE_ACCESS != H5Cget_class(tid) ||
+        NULL == (tmpl = H5A_object(tid))) {
+        HRETURN_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL,
+                      "not a file access template");
+    }
+    switch (access_mode){
+    case H5ACC_INDEPENDENT:
+	    /* fall through to next case */
+    case H5ACC_COLLECTIVE:
+	    tmpl->access_mode = access_mode;
+	    break;
+
+    default:
+            HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL,
+	                          "unknown access_mode");
+    }
+
+    /* store a duplicate copy of comm so that user may freely modify comm after this */
+    /* call.  */
+#ifdef LATER
+    /* need to verify comm and info contain sensible information */
+    /* need to duplicate info too but don't know a quick way to do it now. */
+#endif
+    if ((mrc = MPI_Comm_dup(comm, &lcomm) != MPI_SUCCESS))
+        HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL,
+                      "failure to duplicate communicator");
+    tmpl->comm = comm;
+    tmpl->info = info;
+
+    FUNC_LEAVE(SUCCEED);
+}
+
+#endif /*HAVE_PARALLEL*/
 
 /*--------------------------------------------------------------------------
  NAME
diff --git a/src/H5Cpublic.h b/src/H5Cpublic.h
index aca09d2..b3b5348 100644
--- a/src/H5Cpublic.h
+++ b/src/H5Cpublic.h
@@ -61,6 +61,10 @@ herr_t H5Cset_layout (hid_t tid, H5D_layout_t layout);
 H5D_layout_t H5Cget_layout (hid_t tid);
 herr_t H5Cset_chunk (hid_t tid, int ndims, const size_t dim[]);
 int H5Cget_chunk (hid_t tid, int max_ndims, size_t dim[]/*out*/);
+#ifdef HAVE_PARALLEL
+herr_t H5Cset_mpi (hid_t tid, MPI_Comm comm, MPI_Info info, uintn access_mode);
+/* herr_t H5Cget_mpi (hid_t tid, int *ik); */  /* not defined yet */
+#endif
 
 #ifdef __cplusplus
 }
diff --git a/src/H5F.c b/src/H5F.c
index 1efc496..4b7d669 100644
--- a/src/H5F.c
+++ b/src/H5F.c
@@ -77,8 +77,8 @@ const H5F_create_t      H5F_create_dflt = {
         0,                      /* unused                               */
         0,                      /* unused                               */
     },
-    sizeof(size_t),             /* Default offset size */
-    sizeof(size_t),             /* Default length size */
+    4,             /* Default offset size */
+    4,             /* Default length size */
     HDF5_BOOTBLOCK_VERSION,     /* Current Boot-Block version # */
     HDF5_SMALLOBJECT_VERSION,   /* Current Small-Object heap version # */
     HDF5_FREESPACE_VERSION,     /* Current Free-Space info version # */
@@ -86,6 +86,18 @@ const H5F_create_t      H5F_create_dflt = {
     HDF5_SHAREDHEADER_VERSION,  /* Current Shared-Header format version # */
 };
 
+/*
+ * Define the default file access template.
+ */
+const H5F_access_t      H5F_access_dflt =
+{
+    H5ACC_DEFAULT,       	/* Default file access mode             */
+#ifdef HAVE_PARALLEL
+    MPI_COMM_NULL,              /* Default is not using MPIO            */
+    MPI_INFO_NULL,              /* Default no info                      */
+#endif
+};
+
 /* Interface initialization */
 static intn             interface_initialize_g = FALSE;
 #define INTERFACE_INIT H5F_init_interface
@@ -557,7 +569,7 @@ H5F_dest(H5F_t *f)
  */
 H5F_t                  *
 H5F_open(const H5F_low_class_t *type, const char *name, uintn flags,
-         const H5F_create_t *create_parms)
+         const H5F_create_t *create_parms, const H5F_access_t *access_parms)
 {
     H5F_t                  *f = NULL;   /*return value                  */
     H5F_t                  *ret_value = NULL;   /*a copy of `f'                 */
@@ -623,7 +635,7 @@ H5F_open(const H5F_low_class_t *type, const char *name, uintn flags,
                 fprintf(stderr, "HDF5-DIAG: opening a split file\n");
 #endif
                 fullname[s - name] = '\0';
-                f = H5F_open(H5F_LOW_SPLIT, fullname, flags, create_parms);
+                f = H5F_open(H5F_LOW_SPLIT, fullname, flags, create_parms, access_parms);
                 HRETURN(f);
             }
         }
@@ -984,6 +996,11 @@ H5Fcreate(const char *filename, uintn flags, hid_t create_temp,
     const H5F_create_t     *create_parms;       /* pointer to the parameters to
                                                    * use when creating the file
                                                  */
+    const H5F_access_t     *access_parms;       /* pointer to the file access
+    						 * parameters to use when creating
+						 * the file
+                                                 */
+    const H5F_low_class_t        *type;		/* File type */
     hid_t                   ret_value = FAIL;
 
     FUNC_ENTER(H5Fcreate, FAIL);
@@ -1001,19 +1018,35 @@ H5Fcreate(const char *filename, uintn flags, hid_t create_temp,
     } else if (NULL == (create_parms = H5A_object(create_temp))) {
         HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't unatomize template");
     }
-#ifdef LATER
     if (access_temp <= 0) {
         access_parms = &H5F_access_dflt;
     } else if (NULL == (access_parms = H5A_object(access_temp))) {
-        HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL);       /*can't unatomize template */
+        HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't unatomize template");
     }
+    /* figure out what kind of file I/O to use. */
+    /* Currently, MPIO is the only alternative than default I/O */
+    switch (access_parms->access_mode){
+    case H5ACC_DEFAULT:
+	type = H5F_LOW_DFLT;
+	break;
+#ifdef HAVE_PARALLEL
+    case H5ACC_INDEPENDENT:
+	type = H5F_LOW_MPIO;
+	break;
+    case H5ACC_COLLECTIVE:
+	/* not implemented yet */
+	/* type = H5F_LOW_MPIO; */
+	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Invalid file access mode");
 #endif
-
+    default:
+	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Invalid file access mode");
+    }
+	
     /*
      * Create a new file or truncate an existing file.
      */
-    if (NULL == (new_file = H5F_open(H5F_LOW_DFLT, filename, flags,
-                                     create_parms))) {
+    if (NULL == (new_file = H5F_open(type, filename, flags,
+                                     create_parms, access_parms))) {
         HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, FAIL, "can't create file");
     }
     /* Get an atom for the file */
@@ -1076,6 +1109,11 @@ hid_t
 H5Fopen(const char *filename, uintn flags, hid_t access_temp)
 {
     H5F_t                  *new_file = NULL;    /* file struct for new file */
+    const H5F_access_t     *access_parms;       /* pointer to the file access
+    						 * parameters to use when creating
+						 * the file
+                                                 */
+    const H5F_low_class_t        *type;		/* File type */
     hid_t                   ret_value = FAIL;
 
     FUNC_ENTER(H5Fopen, FAIL);
@@ -1085,15 +1123,32 @@ H5Fopen(const char *filename, uintn flags, hid_t access_temp)
         HGOTO_ERROR(H5E_ARGS, H5E_BADRANGE, FAIL, "invalid file name");
     flags = flags & H5ACC_WRITE ? H5F_ACC_WRITE : 0;
 
-#ifdef LATER
-    if (access_temp <= 0)
-        access_temp = H5CPget_default_atom(H5_TEMPLATE);
-    if (NULL == (f_access_parms = H5A_object(access_temp)))
-        HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL);       /*can't unatomize template */
+    if (access_temp <= 0) {
+        access_parms = &H5F_access_dflt;
+    } else if (NULL == (access_parms = H5A_object(access_temp))) {
+        HGOTO_ERROR(H5E_ATOM, H5E_BADATOM, FAIL, "can't unatomize template");
+    }
+    /* figure out what kind of file I/O to use. */
+    /* Currently, MPIO is the only alternative than default I/O */
+    switch (access_parms->access_mode){
+    case H5ACC_DEFAULT:
+	type = H5F_LOW_DFLT;
+	break;
+#ifdef HAVE_PARALLEL
+    case H5ACC_INDEPENDENT:
+	type = H5F_LOW_MPIO;
+	break;
+    case H5ACC_COLLECTIVE:
+	/* not implemented yet */
+	/* type = H5F_LOW_MPIO; */
+	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Invalid file access mode");
 #endif
+    default:
+	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Invalid file access mode");
+    }
 
     /* Open the file */
-    if (NULL == (new_file = H5F_open(H5F_LOW_DFLT, filename, flags, NULL))) {
+    if (NULL == (new_file = H5F_open(type, filename, flags, NULL, access_parms))) {
         HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, FAIL, "cant open file");
     }
     /* Get an atom for the file */
diff --git a/src/H5Fmpio.c b/src/H5Fmpio.c
index 6db6bc8..b9f2238 100644
--- a/src/H5Fmpio.c
+++ b/src/H5Fmpio.c
@@ -127,7 +127,7 @@ ino_t mpio_inode_num = 0;      /* fake "inode" number */
  *-------------------------------------------------------------------------
  */
 static hbool_t
-H5F_mpio_access(char *name, int mode, H5F_search_t *key /*out */ )
+H5F_mpio_access(const char *name, int mode, H5F_search_t *key /*out */ )
 {
     hbool_t		   ret_val = FALSE;
     MPI_File		   fh;
@@ -150,24 +150,25 @@ H5F_mpio_access(char *name, int mode, H5F_search_t *key /*out */ )
 		   break;
 	case W_OK: mpi_mode = MPI_MODE_WRONLY;
 		   break;
-	default:   HRETURN_ERROR(H5E_IO, H5E_ARGS, FAIL,
+	default:   HRETURN_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL,
                           "invalid mode parameter");
     }
 
-    mpierr = MPI_File_open( MPI_COMM_SELF, name, mpi_mode, MPI_INFO_NULL, &fh );
+    /* (char*) name is okay since MPI_File_open will not change it. */
+    mpierr = MPI_File_open( MPI_COMM_SELF, (char*) name, mpi_mode, MPI_INFO_NULL, &fh );
     if (mpierr == MPI_SUCCESS) {
 	mpierr = MPI_File_close( &fh );
     	if (mpierr != MPI_SUCCESS)
-	    HRETURN_ERROR(H5E_IO, H5E_ARGS, FAIL, "MPI_File_open failed");
+	    HRETURN_ERROR(H5E_IO, H5E_CLOSEERROR, FAIL, "MPI_File_close failed");
 	ret_val = TRUE;
     } else if (mode == F_OK) {
 	/* to see if it exists, this time try to open for write */
-	mpierr = MPI_File_open( MPI_COMM_SELF, name, MPI_MODE_WRONLY,
+	mpierr = MPI_File_open( MPI_COMM_SELF, (char*)name, MPI_MODE_WRONLY,
 				MPI_INFO_NULL, &fh );
 	if (mpierr == MPI_SUCCESS) {
 	    mpierr = MPI_File_close( &fh );
 	    if (mpierr != MPI_SUCCESS)
-		HRETURN_ERROR(H5E_IO, H5E_INTERNAL, FAIL, "MPI_File_close failed");
+		HRETURN_ERROR(H5E_IO, H5E_CLOSEERROR, FAIL, "MPI_File_close failed");
 	    ret_val = TRUE;
 	}
     }
@@ -214,7 +215,7 @@ H5F_mpio_access(char *name, int mode, H5F_search_t *key /*out */ )
  *-------------------------------------------------------------------------
  */
 static H5F_low_t       *
-H5F_mpio_open(char *name, uintn flags, H5F_search_t *key /*out */ )
+H5F_mpio_open(const char *name, uintn flags, H5F_search_t *key /*out */ )
 {
     H5F_low_t              *lf = NULL;
     MPI_File                fh;
@@ -234,7 +235,7 @@ H5F_mpio_open(char *name, uintn flags, H5F_search_t *key /*out */ )
     if (flags&H5F_ACC_CREAT)	mpi_amode |= MPI_MODE_CREATE;
     if (flags&H5F_ACC_EXCL)	mpi_amode |= MPI_MODE_EXCL;
 
-    mpierr = MPI_File_open(MPI_COMM_WORLD, name, mpi_amode, MPI_INFO_NULL, &fh);
+    mpierr = MPI_File_open(MPI_COMM_WORLD, (char*)name, mpi_amode, MPI_INFO_NULL, &fh);
     if (mpierr != MPI_SUCCESS) {
         MPI_Error_string( mpierr, mpierrmsg, &msglen );
 	HRETURN_ERROR(H5E_IO, H5E_CANTOPENFILE, NULL, mpierrmsg );
@@ -391,6 +392,7 @@ H5F_mpio_read(H5F_low_t *lf, const haddr_t *addr, size_t size, uint8 *buf)
 	HRETURN_ERROR(H5E_IO, H5E_READERROR, FAIL, mpierrmsg );
     }
 
+#define MPI_KLUGE0202
 #ifdef MPI_KLUGE0202
     /* KLUGE rky 980202 MPI_Get_count incorrectly returns negative count;
        fake a complete read */
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index 76ca1f6..3f71055 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -22,7 +22,7 @@
 
 /* This is a near top-level header! Try not to include much! */
 #include <H5private.h>
-#ifdef PHDF5
+#ifdef HAVE_PARALLEL
 #ifndef MPI_SUCCESS
 #include <mpi.h>
 #include <mpio.h>
@@ -231,6 +231,17 @@ typedef struct H5F_create_t {
 } H5F_create_t;
 
 /*
+ * File-access template.
+ */
+typedef struct H5F_access_t {
+    uintn	access_mode;	/* file access mode                     */
+#ifdef HAVE_PARALLEL
+    MPI_Comm    comm;           /* communicator for file access         */
+    MPI_Info    info;           /* optional info for MPI-IO             */
+#endif /*HAVE_PARALLEL*/
+} H5F_access_t;
+
+/*
  * These things make a file unique.
  */
 typedef struct H5F_search_t {
@@ -304,7 +315,7 @@ typedef struct H5F_low_t {
 	    size_t	alloc;	/* Current size of MEM buffer		*/
 	} core;
 
-#ifdef PHDF5
+#ifdef HAVE_PARALLEL
 	/* MPI-IO */
 	struct {
 	    MPI_File	f;	/* MPI-IO file handle			*/
@@ -323,10 +334,8 @@ extern const H5F_low_class_t H5F_LOW_STDIO[];	/* Posix stdio		*/
 extern const H5F_low_class_t H5F_LOW_CORE[];	/* In-core temp file	*/
 extern const H5F_low_class_t H5F_LOW_FAM[];	/* File family		*/
 extern const H5F_low_class_t H5F_LOW_SPLIT[];	/* Split meta/raw data	*/
-#ifdef PHDF5
+#ifdef HAVE_PARALLEL
   extern const H5F_low_class_t H5F_LOW_MPIO[];	/* MPI-IO		*/
-# undef  H5F_LOW_DFLT
-# define H5F_LOW_DFLT	H5F_LOW_MPIO	        /* The default type     */
 #endif
 
 /*
@@ -346,8 +355,8 @@ typedef struct H5F_file_t {
     haddr_t	hdf5_eof;	/* Relative addr of end of all hdf5 data*/
     struct H5AC_t *cache;	/* The object cache			*/
     H5F_create_t create_parms;	/* File-creation template		*/
-#ifdef LATER
-    file_access_temp_t file_access_parms; /* File-access template	*/
+#ifdef HAVE_PARALLEL
+    H5F_access_t access_parms;  /* File-access template	*/
 #endif
     struct H5G_entry_t *root_ent; /* Root symbol table entry		*/
 } H5F_file_t;
@@ -414,11 +423,12 @@ struct H5O_layout_t;		/*forward decl for prototype arguments */
 
 /* library variables */
 extern const H5F_create_t H5F_create_dflt;
+extern const H5F_access_t H5F_access_dflt;
 
 /* Private functions, not part of the publicly documented API */
 void H5F_encode_length_unusual(const H5F_t *f, uint8 **p, uint8 *l);
 H5F_t *H5F_open(const H5F_low_class_t *type, const char *name, uintn flags,
-		const H5F_create_t *create_parms);
+		const H5F_create_t *create_parms, const H5F_access_t *access_parms);
 herr_t H5F_close(H5F_t *f);
 herr_t H5F_debug(H5F_t *f, const haddr_t *addr, FILE * stream, intn indent,
 		 intn fwidth);
diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h
index 885277d..538b07b 100644
--- a/src/H5Fpublic.h
+++ b/src/H5Fpublic.h
@@ -24,6 +24,11 @@
 #define H5ACC_DEFAULT       0x0000/*use in H5Fopen & H5Fcreate to open a file with default access*/
 #define H5ACC_WRITE         0x0001/*use in H5Fopen to open a file with write access*/
 #define H5ACC_OVERWRITE     0x0002/*use in H5Fcreate truncate an existing file*/
+#ifdef HAVE_PARALLEL
+#define H5ACC_INDEPENDENT   0x0010/*use in H5Cset_mpi for MPI independent access*/
+#define H5ACC_COLLECTIVE    0x0011/*use in H5Cset_mpi for MPI collective access*/
+#endif
+
 
 #ifdef __cplusplus
 extern "C" {
diff --git a/src/H5M.c b/src/H5M.c
index 5466a1e..a9dc02b 100644
--- a/src/H5M.c
+++ b/src/H5M.c
@@ -76,6 +76,23 @@ static meta_func_t      meta_func_arr[] =
         NULL,                   /* File-Creation Template GetFile */
         H5Cclose                /* File-Creation Template Release */
     },
+    {                           /* Template object meta-functions (defined in H5C.c) */
+        H5_TEMPLATE_1,          /* File-Access Template Type ID */
+        NULL,                   /* File-Access Template Create */
+        NULL,                   /* File-Access Template Access */
+        H5Ccopy,                /* File-Access Template Copy */
+        NULL,                   /* File-Access Template FindName */
+        NULL,                   /* File-Access Template NameLen */
+        NULL,                   /* File-Access Template GetName */
+        NULL,                   /* File-Access Template SetName */
+        NULL,                   /* File-Access Template Search */
+        NULL,                   /* File-Access Template Index */
+        NULL,                   /* File-Access Template Flush */
+        NULL,                   /* File-Access Template Delete */
+        NULL,                   /* File-Access Template GetParent */
+        NULL,                   /* File-Access Template GetFile */
+        H5Cclose                /* File-Access Template Release */
+    },
     {                           /* Datatype object meta-functions (defined in H5T.c) */
         H5_DATATYPE,            /* Datatype Type ID */
         NULL,                   /* Datatype Create */
diff --git a/src/H5private.h b/src/H5private.h
index 995b53d..a2d5d49 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -46,6 +46,15 @@
 #  include <unistd.h>
 #endif
 
+#ifdef HAVE_PARALLEL
+/*
+ * MPIO headers
+ */
+#  include <mpi.h>
+#  include <mpio.h>
+#endif
+
+
 /*
  * Pablo support files.
  */
diff --git a/src/H5public.h b/src/H5public.h
index 7436cc2..9d7eee8 100644
--- a/src/H5public.h
+++ b/src/H5public.h
@@ -18,6 +18,10 @@
 
 #include <H5config.h>           /*from configure                             */
 #include <sys/types.h>
+#ifdef HAVE_PARALLEL
+#include <mpi.h>
+#include <mpio.h>
+#endif
 
 /*
  * Data types