Merge pull request #704 in HDFFV/hdf5 from optimize_superblock_read to develop

* commit '3dde6d0e32461f46630f814a2fdfbd4c813703bf':
  Updated the code and RELEASE.txt note per comments from John Mainzer
  Try to address most of the issues raised by Dana in the code review
  Made edits suggested by John as part of the code review
  Update the MANIFEST and release_docs/RELEASE files
  Add a test for parallel reads of independent files using MPI subgroups
  Edits to the file open optimization and associated test code to bring them closer to the HDF5 library's unwritten coding standards.  Also bug fix to repair a hang in testphdf5.
  The initial coding for the superblock read optization

1 files changed, 90 insertions, 43 deletions

diff --git a/src/H5Fsuper.c b/src/H5Fsuper.c
index 942a7ed..0c6f9cd 100644
--- a/src/H5Fsuper.c
+++ b/src/H5Fsuper.c
@@ -21,15 +21,15 @@
 /***********/
 /* Headers */
 /***********/
-#include "H5private.h"		/* Generic Functions                    */
+#include "H5private.h"          /* Generic Functions                    */
 #include "H5ACprivate.h"        /* Metadata cache                       */
-#include "H5Eprivate.h"		/* Error handling                       */
+#include "H5Eprivate.h"         /* Error handling                       */
 #include "H5Fpkg.h"             /* File access                          */
-#include "H5FDprivate.h"	/* File drivers                         */
-#include "H5Iprivate.h"		/* IDs                                  */
+#include "H5FDprivate.h"        /* File drivers                         */
+#include "H5Iprivate.h"         /* IDs                                  */
 #include "H5MFprivate.h"        /* File memory management               */
-#include "H5MMprivate.h"	/* Memory management			*/
-#include "H5Pprivate.h"		/* Property lists                       */
+#include "H5MMprivate.h"        /* Memory management                    */
+#include "H5Pprivate.h"         /* Property lists                       */
 #include "H5SMprivate.h"        /* Shared Object Header Messages        */
 
 
@@ -158,7 +158,7 @@ H5F_super_ext_open(H5F_t *f, haddr_t ext_addr, H5O_loc_t *ext_ptr)
 
     /* Open the superblock extension object header */
     if(H5O_open(ext_ptr) < 0)
-	HGOTO_ERROR(H5E_OHDR, H5E_CANTOPENOBJ, FAIL, "unable to open superblock extension")
+        HGOTO_ERROR(H5E_OHDR, H5E_CANTOPENOBJ, FAIL, "unable to open superblock extension")
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
@@ -224,12 +224,12 @@ done:
 /*-------------------------------------------------------------------------
  * Function:    H5F__update_super_ext_driver_msg
  *
- * Purpose:	Update the superblock extension file driver info message if 
- *		we are using a V 2 superblock.  Observe that the function
- *		is a NO-OP if the file driver info message does not exist.
+ * Purpose:     Update the superblock extension file driver info message if 
+ *              we are using a V 2 superblock.  Observe that the function
+ *              is a NO-OP if the file driver info message does not exist.
  *              This is necessary, as the function is called whenever the 
- *		EOA is updated, and were it to create the file driver info
- *		message, it would find itself in an infinite recursion.
+ *              EOA is updated, and were it to create the file driver info
+ *              message, it would find itself in an infinite recursion.
  *
  * Return:      Success:        SUCCEED
  *              Failure:        FAIL
@@ -267,7 +267,7 @@ H5F__update_super_ext_driver_msg(H5F_t *f, hid_t dxpl_id)
                 /* Check for driver info */
                 H5_CHECKED_ASSIGN(driver_size, size_t, H5FD_sb_size(f->shared->lf), hsize_t);
 
-		/* Nothing to do unless there is both driver info and 
+                /* Nothing to do unless there is both driver info and 
                  * the driver info superblock extension message has 
                  * already been created.
                  */
@@ -330,9 +330,13 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
     unsigned            sblock_flags = H5AC__NO_FLAGS_SET;       /* flags used in superblock unprotect call      */
     haddr_t             super_addr;         /* Absolute address of superblock */
     haddr_t             eof;                /* End of file address */
-    unsigned      	rw_flags;           /* Read/write permissions for file */
-    hbool_t 		skip_eof_check = FALSE; /* Whether to skip checking the EOF value */
+    unsigned            rw_flags;           /* Read/write permissions for file */
+    hbool_t             skip_eof_check = FALSE; /* Whether to skip checking the EOF value */
     herr_t              ret_value = SUCCEED; /* Return value */
+#ifdef H5_HAVE_PARALLEL
+    int                 mpi_rank = 0, mpi_size = 1;
+    int                 mpi_result;
+#endif /* H5_HAVE_PARALLEL */
 
     FUNC_ENTER_PACKAGE_TAG(meta_dxpl_id, H5AC__SUPERBLOCK_TAG, FAIL)
 
@@ -354,8 +358,51 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "can't get property list")
 
     /* Find the superblock */
-    if(H5FD_locate_signature(&fdio_info, &super_addr) < 0)
-        HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "unable to locate file signature")
+#ifdef H5_HAVE_PARALLEL
+    if(H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI)) {
+
+        if((mpi_rank = H5F_mpi_get_rank(f)) < 0)
+            HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "Can't get MPI rank")
+
+        if((mpi_size = H5F_mpi_get_size(f)) < 0)
+            HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't retrieve MPI communicator size")
+    }
+
+    /* If we are an MPI application with at least two processes, the
+     * following superblock signature location optimization is applicable.
+     *
+     * Note:: For parallel applications which don't setup for using the
+     * HDF5 MPIO driver, we will arrive here with mpi_size == 1.
+     * This occurs because of the variable initialization (above) and the
+     * fact that we have skipped actually calling MPI functions to determine
+     * our MPI rank and size.
+     */
+    if ( mpi_size > 1 ) {
+        MPI_Comm this_comm = MPI_COMM_NULL;
+
+        if ( mpi_rank == 0 ) {
+            if (H5FD_locate_signature(&fdio_info, &super_addr) < 0)
+                HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "unable to locate file signature")
+        }
+        HDassert(H5F_HAS_FEATURE(f, H5FD_FEAT_HAS_MPI));
+
+        if ( MPI_COMM_NULL == (this_comm = H5F_mpi_get_comm(f)) )
+            HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't get MPI communicator")
+        
+        if ( MPI_SUCCESS != 
+            (mpi_result = MPI_Bcast(&super_addr,sizeof(super_addr), MPI_BYTE, 0, this_comm)))
+            HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_result)
+    }
+    else {
+    /* Locate the signature as per per the serial library */
+#endif /* H5_HAVE_PARALLEL */
+
+        if (H5FD_locate_signature(&fdio_info, &super_addr) < 0)
+            HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "unable to locate file signature")
+
+#ifdef H5_HAVE_PARALLEL
+    }
+#endif /* H5_HAVE_PARALLEL */
     if(HADDR_UNDEF == super_addr)
         HGOTO_ERROR(H5E_FILE, H5E_NOTHDF5, FAIL, "file signature not found")
 
@@ -406,12 +453,12 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
         HGOTO_ERROR(H5E_FILE, H5E_CANTPROTECT, FAIL, "unable to load superblock")
 
     if(H5F_INTENT(f) & H5F_ACC_SWMR_WRITE)
-       	if(sblock->super_vers < HDF5_SUPERBLOCK_VERSION_3)
-	    HGOTO_ERROR(H5E_FILE, H5E_CANTPROTECT, FAIL, "invalid superblock version for SWMR_WRITE")
+        if(sblock->super_vers < HDF5_SUPERBLOCK_VERSION_3)
+            HGOTO_ERROR(H5E_FILE, H5E_CANTPROTECT, FAIL, "invalid superblock version for SWMR_WRITE")
 
     /* Enable all latest version support when file has v3 superblock */
     if(sblock->super_vers >= HDF5_SUPERBLOCK_VERSION_3)
-	f->shared->latest_flags |= H5F_LATEST_ALL_FLAGS;
+        f->shared->latest_flags |= H5F_LATEST_ALL_FLAGS;
 
     /* Pin the superblock in the cache */
     if(H5AC_pin_protected_entry(sblock) < 0)
@@ -511,15 +558,15 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
      * been flushed to disk by the SWMR writer process.
      */
     if(H5F_INTENT(f) & H5F_ACC_SWMR_READ) {
-	/* 
-	 * When the file is opened for SWMR read access, skip the check if:
-	 * --the file is already marked for SWMR writing and
-	 * --the file has version 3 superblock for SWMR support
-	 */
-	if((sblock->status_flags & H5F_SUPER_SWMR_WRITE_ACCESS) &&
+        /* 
+         * When the file is opened for SWMR read access, skip the check if:
+         * --the file is already marked for SWMR writing and
+         * --the file has version 3 superblock for SWMR support
+         */
+        if((sblock->status_flags & H5F_SUPER_SWMR_WRITE_ACCESS) &&
                (sblock->status_flags & H5F_SUPER_WRITE_ACCESS) &&
                 sblock->super_vers >= HDF5_SUPERBLOCK_VERSION_3)
-	    skip_eof_check = TRUE;
+            skip_eof_check = TRUE;
     } /* end if */
     if(!skip_eof_check && initial_read) {
         if(HADDR_UNDEF == (eof = H5FD_get_eof(f->shared->lf, H5FD_MEM_DEFAULT)))
@@ -593,7 +640,7 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
         H5O_loc_t ext_loc;      /* "Object location" for superblock extension */
         H5O_btreek_t btreek;    /* v1 B-tree 'K' value message from superblock extension */
         H5O_drvinfo_t drvinfo;  /* Driver info message from superblock extension */
-	size_t u; 		/* Local index variable */
+        size_t u;               /* Local index variable */
         htri_t status;          /* Status for message existing */
 
         /* Sanity check - superblock extension should only be defined for
@@ -614,7 +661,7 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
         } /* end if */
 
         /* Open the superblock extension */
-	if(H5F_super_ext_open(f, sblock->ext_addr, &ext_loc) < 0)
+        if(H5F_super_ext_open(f, sblock->ext_addr, &ext_loc) < 0)
             HGOTO_ERROR(H5E_FILE, H5E_CANTOPENOBJ, FAIL, "unable to open file's superblock extension")
 
         /* Check for the extension having a 'driver info' message */
@@ -637,8 +684,8 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
                 /* Reset driver info message */
                 H5O_msg_reset(H5O_DRVINFO_ID, &drvinfo);
 
-		HDassert(FALSE == f->shared->drvinfo_sb_msg_exists);
-		f->shared->drvinfo_sb_msg_exists = TRUE;
+                HDassert(FALSE == f->shared->drvinfo_sb_msg_exists);
+                f->shared->drvinfo_sb_msg_exists = TRUE;
             } /* end else */
         } /* end if */
 
@@ -764,37 +811,37 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
             } /* end if not marked "unknown" */
         } /* end if */
 
-	/* Check for the extension having a 'metadata cache image' message */
+        /* Check for the extension having a 'metadata cache image' message */
         if((status = H5O_msg_exists(&ext_loc, H5O_MDCI_MSG_ID, meta_dxpl_id)) < 0)
             HGOTO_ERROR(H5E_FILE, H5E_EXISTS, FAIL, "unable to read object header")
         if(status) {
-            hbool_t 	rw = ((rw_flags & H5AC__READ_ONLY_FLAG) == 0);
-	    H5O_mdci_t  mdci_msg;
+            hbool_t     rw = ((rw_flags & H5AC__READ_ONLY_FLAG) == 0);
+            H5O_mdci_t  mdci_msg;
 
-	    /* if the metadata cache image superblock extension message exists,
+            /* if the metadata cache image superblock extension message exists,
              * read its contents and pass the data on to the metadata cache.
              * Given this data, the cache will load and decode the metadata
- 	     * cache image block, decoded it and load its contents into the 
-	     * the cache on the test protect call.  
+             * cache image block, decoded it and load its contents into the 
+             * the cache on the test protect call.  
              *
              * Further, if the file is opened R/W, the metadata cache will 
-	     * delete the metadata cache image superblock extension and free
-	     * the cache image block.  Don't do this now as f->shared 
-	     * is not fully setup, which complicates matters.
+             * delete the metadata cache image superblock extension and free
+             * the cache image block.  Don't do this now as f->shared 
+             * is not fully setup, which complicates matters.
              */
 
             /* Retrieve the 'metadata cache image message' structure */
-	    if(NULL == H5O_msg_read(&ext_loc, H5O_MDCI_MSG_ID, &mdci_msg, meta_dxpl_id))
+            if(NULL == H5O_msg_read(&ext_loc, H5O_MDCI_MSG_ID, &mdci_msg, meta_dxpl_id))
                 HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "unable to get metadata cache image message")
 
             /* Indicate to the cache that there's an image to load on first protect call */
             if(H5AC_load_cache_image_on_next_protect(f, mdci_msg.addr, mdci_msg.size, rw) < 0)
-		HGOTO_ERROR(H5E_FILE, H5E_CANTLOAD, FAIL, "call to H5AC_load_cache_image_on_next_protect failed");
+                HGOTO_ERROR(H5E_FILE, H5E_CANTLOAD, FAIL, "call to H5AC_load_cache_image_on_next_protect failed");
         } /* end if */
 
         /* Close superblock extension */
         if(H5F_super_ext_close(f, &ext_loc, meta_dxpl_id, FALSE) < 0)
-	    HGOTO_ERROR(H5E_FILE, H5E_CANTCLOSEOBJ, FAIL, "unable to close file's superblock extension")
+            HGOTO_ERROR(H5E_FILE, H5E_CANTCLOSEOBJ, FAIL, "unable to close file's superblock extension")
     } /* end if */
 
     /* Update the driver info if VFD indicated to do so */