Checkin of fixes for a number of bugs in reads to page 0, and in file

open in the VFD SWMR reader case.

Note that the following failures in testvfdswmr.sh:

1) Unable to find metadata file on VFD SWMR reader open.

2) Occasional sanity check failures in the page buffer on raw data write.

3) Filter failures on raw data read in VFD SWMR readers when compression
   is enabled.

4) Unexpected data errors in VFD SWMR readers when compression is
   disabled.

Note that I expect that items 3 & 4 two aspects of the same issues -- the
fact that we don't guarantee that raw data is consistent with metadata.

Item 2) must be addressed, but it is so infrequent that it isn't doesn't
affect the conclusion VFD SWMR seems to work, and thus it can wait until
phase 2.

I am given to understand that Vailin has largely addressed item 1),
and will be checking in her solution to this soon.

Tested on Charis and Jelly.

3 files changed, 160 insertions, 10 deletions

diff --git a/src/H5FDprivate.h b/src/H5FDprivate.h
index b40c9f0..10217bd 100644
--- a/src/H5FDprivate.h
+++ b/src/H5FDprivate.h
@@ -328,6 +328,7 @@ H5_DLL herr_t H5FD_vfd_swmr_get_tick_and_idx(H5FD_t *_file, hbool_t read_index,
 H5_DLL hbool_t H5FD_is_vfd_swmr_driver(H5FD_t *_file);
 H5_DLL H5FD_t *H5FD_vfd_swmr_get_underlying_vfd(H5FD_t *_file);
 H5_DLL void H5FD_vfd_swmr_dump_status(H5FD_t *_file, int64_t page);
+H5_DLL void H5FD_vfd_swmr_set_pb_configured(H5FD_t *_file);
 
 /* Function prototypes for MPI based VFDs*/
 #ifdef H5_HAVE_PARALLEL
diff --git a/src/H5FDvfd_swmr.c b/src/H5FDvfd_swmr.c
index 81b7fe7..eb659e1 100644
--- a/src/H5FDvfd_swmr.c
+++ b/src/H5FDvfd_swmr.c
@@ -48,6 +48,11 @@ typedef struct H5FD_vfd_swmr_t {
     char md_file_path[H5FD_MAX_FILENAME_LEN];   /* Name of the metadate file  */
     H5FD_vfd_swmr_md_header md_header;          /* Metadata file header       */
     H5FD_vfd_swmr_md_index md_index;            /* Metadata file index        */
+
+    hbool_t pb_configured;                      /* boolean flag set to TRUE   */
+                                                /* when the page buffer is    */
+                                                /* and to FALSE otherwise.    */
+                                                /* Used for sanity checking.  */
 } H5FD_vfd_swmr_t;
 
 #define MAXADDR (((haddr_t)1<<(8*sizeof(HDoff_t)-1))-1)
@@ -328,6 +333,17 @@ H5FD_vfd_swmr_open(const char *name, unsigned flags, hid_t fapl_id,
 
         HGOTO_ERROR(H5E_VFL, H5E_CANTOPENFILE, NULL, "can't set driver info")
 
+    /* set pb_configured to FALSE.  This field should not exist, but 
+     * until we modify the file open proceedure to create the page buffer
+     * before there is any file I/O when opening a file VFD SWMR reader, 
+     * we need to be able to turn off sanity checking in the read function
+     * until the page buffer is enabled.  This field exists for this 
+     * purpose, and should be remove when it is no longer necessary.
+     *
+     *                                            JRM -- 1/29/19
+     */
+    file->pb_configured = FALSE;
+
     /* Set return value */
     ret_value = (H5FD_t*)file;
 
@@ -603,7 +619,31 @@ done:
 /*-------------------------------------------------------------------------
  * Function:    H5FD_vfd_swmr_read
  *
- * Purpose:     TBD
+ * Purpose:     If the target page or multi-page metadata entry is 
+ *              defined in the current metadata file index, satisfy 
+ *              the read from the metadata file.  Otherwise, pass the
+ *              read through to the underlying VFD.
+ *
+ *              Under normal operating conditions, the size of the 
+ *              read must always match the size supplied in the 
+ *              metadata file index.  However, until we modify the 
+ *              file open process for VFD SWMR readers to create the 
+ *              page buffer before any reads, we must allow non 
+ *              full page / non full multi-page metadata entry reads
+ *              until the page buffer is created.
+ *
+ *              This is tracked by the pb_configured flag in 
+ *              H5FD_vfd_swmr_t.  If this field is FALSE, the function 
+ *              must allow reads smaller than the size listed in the 
+ *              index, and possibly starting anywhere in the page.  
+ *              Note, however, that these reads must not cross page 
+ *              boundaries.
+ *
+ *              Once we modify the file open code to start up the 
+ *              page buffer before we attempt any reads, this exception
+ *              will not longer be necessary, and should be removed.
+ *
+ *                                            JRM -- 1/29/19
  *
  * Return:      Success:    SUCCEED. Result is stored in caller-supplied
  *                          buffer BUF.
@@ -723,7 +763,35 @@ H5FD_vfd_swmr_read(H5FD_t *_file, H5FD_mem_t type,
 #endif /* JRM */
 
     /* Found in index, read from the metadata file */
+#if 0 /* JRM */
     if( (cmp == 0) && ( target_page != 0)) {
+#else /* JRM */
+    if ( cmp == 0 ) {
+#endif /* JRM */
+
+        haddr_t page_offset;
+        haddr_t init_addr = addr;
+        size_t init_size = size;
+
+        HDassert(addr >= target_page * fs_page_size);
+        
+        page_offset = addr - (target_page * fs_page_size);
+
+#if 0 /* JRM */
+        if ( ( page_offset != 0 ) &&
+             ( ( file->pb_configured ) ||
+               ( page_offset + size > fs_page_size ) ) ) {
+
+            HDfprintf(stderr, 
+                      "page_offset = %lld, size = %lld, page_size = %lld\b",
+                      (uint64_t)page_offset, (uint64_t)size, 
+                      (uint64_t)fs_page_size);
+        }
+#endif /* JRM */
+
+        HDassert( ( page_offset == 0 ) ||
+                  ( ( ! file->pb_configured ) &&
+                    ( page_offset + size <= fs_page_size ) ) );
 
 #if 0 /* JRM */
         HDfprintf(stderr, "addr = %lld, page = %lld, len = %lld\n", 
@@ -750,14 +818,28 @@ H5FD_vfd_swmr_read(H5FD_t *_file, H5FD_mem_t type,
                       (int64_t)(index[my_idx].length));
         }
 #endif /* JRM */
-        HDassert((size == 8) ||
-                 (size == index[my_idx].length));
+
+#if 0 /* JRM */
+        if ( ( init_size != 8 ) &&
+             ( init_size != index[my_idx].length ) ) {
+
+            HDfprintf(stderr, "ERROR: addr = %lld, page = %lld, len = %lld\n", 
+                      (int64_t)init_addr, (int64_t)(init_addr / fs_page_size),
+                      (int64_t)init_size);
+        }
+
+        HDassert((init_size == 8) ||
+                 (init_size == index[my_idx].length));
+#endif /* JRM */
+
+        HDassert( ( ! file->pb_configured ) ||
+                  ( init_size == index[my_idx].length ) );
 
         do {
 
-            if(HDlseek(file->md_fd, 
-                     (HDoff_t)index[my_idx].md_file_page_offset * fs_page_size,
-                      SEEK_SET) < 0)
+            if(HDlseek(file->md_fd, (HDoff_t)
+                       ((index[my_idx].md_file_page_offset * fs_page_size)
+                        + page_offset), SEEK_SET) < 0)
 
                 HGOTO_ERROR(H5E_VFL, H5E_SEEKERROR, FAIL, \
                             "unable to seek in metadata file")
@@ -805,9 +887,10 @@ H5FD_vfd_swmr_read(H5FD_t *_file, H5FD_mem_t type,
              * signature -- clean this up.   
              *                                   JRM -- 1/14/19
              */
-            if ( size != 8 ) {
-                computed_chksum = H5_checksum_metadata(buf, 
-                                                       index[my_idx].length,0);
+            if ( file->pb_configured ) {
+
+                computed_chksum = 
+                    H5_checksum_metadata(buf, index[my_idx].length,0);
             } else {
                 computed_chksum = index[my_idx].chksum;
             }
@@ -832,10 +915,23 @@ H5FD_vfd_swmr_read(H5FD_t *_file, H5FD_mem_t type,
         } while(--entry_retries);
 
         /* Exhaust all retries for reading the page/multi-page entry */
-        if(entry_retries == 0)
+        if(entry_retries == 0) {
+
+            HDfprintf(stderr, "ERROR: addr = %lld, page = %lld, len = %lld\n", 
+                      (int64_t)init_addr, (int64_t)(init_addr / fs_page_size),
+                      (int64_t)init_size);
+            HDfprintf(stderr, " type = %d\n", type);
+            HDfprintf(stderr, 
+            "reading index[%d]  fo/mdfo/l/chksum/fc/lc = %lld/%lld/%ld/%llx\n",
+                      my_idx,
+                      index[my_idx].hdf5_page_offset,
+                      index[my_idx].md_file_page_offset,
+                      index[my_idx].length,
+                      (uint64_t)(index[my_idx].chksum));
 
             HGOTO_ERROR(H5E_VFL, H5E_CANTLOAD, FAIL, \
                         "error in reading the page/multi-page entry")
+        }
 
     } else { /* Cannot find addr in index, read from the underlying hdf5 file */
 
@@ -1618,6 +1714,42 @@ H5FD_vfd_swmr_dump_status(H5FD_t *_file, int64_t page)
 
 }  /* H5FD_vfd_swmr_dump_status() */
 
+
+/*-------------------------------------------------------------------------
+ * Function:    H5FD_vfd_swmr_set_pb_configured
+ *
+ * Purpose:     Set the pb_configured field.  
+ *
+ *              This notifies the VFD that the page buffer is configured,
+ *              and that therefore all reads to the metadata file should
+ *              read complete pages or multi-page metadata entries.
+ *
+ *              This function in necessary because we haven't modified
+ *              the file open code to configure the page buffer prior 
+ *              to any file I/O when opening a file VFD SWMR reader.
+ *              Once this is done, this function should be removed.
+ *
+ * Return:      VOID
+ *
+ * Programmer:  JRM -- 1/29/19
+ *
+ *-------------------------------------------------------------------------
+ */
+void
+H5FD_vfd_swmr_set_pb_configured(H5FD_t *_file)
+{
+    H5FD_vfd_swmr_t *file = (H5FD_vfd_swmr_t *)_file; /* VFD SWMR file struct */
+
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+    HDassert(file);
+
+    file->pb_configured = TRUE;
+
+    FUNC_LEAVE_NOAPI_VOID
+
+}  /* H5FD_vfd_swmr_set_pb_configured() */
+
 
 
 
diff --git a/src/H5PB.c b/src/H5PB.c
index 920341e..b6db93a 100644
--- a/src/H5PB.c
+++ b/src/H5PB.c
@@ -621,6 +621,23 @@ H5PB_create(H5F_t *f, size_t size, unsigned page_buf_min_meta_perc,
 
     f->shared->pb_ptr = pb_ptr;
 
+    /* if this is a VFD SWMR reader, inform the reader VFD that the 
+     * page buffer is configured.  Note that this is for sanity 
+     * checking, and only needed until we modify the file open 
+     * code to create the page buffer before any file reads in 
+     * the VFD SWMR reader case.  After that, this code should be
+     * removed.
+     *                               JRM -- 1/29/19
+     */
+    if ( ( H5F_VFD_SWMR_CONFIG(f) ) && 
+         ( 0 == (H5F_INTENT(f) & H5F_ACC_RDWR) ) ) {
+
+        HDassert(f->shared->lf);
+        HDassert(! f->shared->vfd_swmr_config.vfd_swmr_writer);
+
+        H5FD_vfd_swmr_set_pb_configured(f->shared->lf);
+    }
+
 done:
 
     if ( ret_value < 0 ) {