[svn-r7993] Purpose:

    Code cleanup, bug fixes

Description:
    Wrap up rest of changes necessary for fixing the "short" MPI-I/O read
problem that Robb reported.

Platforms tested:
    FreeBSD 4.9 (sleipnir)
    too minor to require h5committest

10 files changed, 89 insertions, 98 deletions

diff --git a/configure b/configure
index 722a680..50cbb5a 100755
--- a/configure
+++ b/configure
@@ -32326,7 +32326,6 @@ fi
 rm -f conftest.$ac_objext conftest$ac_exeext conftest.$ac_ext
   fi
 
-
                MPE=yes
 
 # Check whether --with-mpe or --without-mpe was given.
diff --git a/configure.in b/configure.in
index 17669ee..c2e9ef8 100644
--- a/configure.in
+++ b/configure.in
@@ -2194,35 +2194,6 @@ if test -n "$PARALLEL"; then
     )
   fi
 
-dnl ----------------------------------------------------------------------
-dnl Block the MPI_Get_count code since it does not work
-dnl   dnl Check whether MPI_Get_count actually works correctly on this
-dnl   dnl platform.
-dnl   AC_MSG_CHECKING(whether a MPI_Get_count works correctly)
-dnl   AC_TRY_RUN([
-dnl #include <mpi.h>
-dnl 
-dnl int main(int argc, char **argv)
-dnl {
-dnl     MPI_Status mpi_stat;
-dnl     int bytes_read = 0, ret;
-dnl 
-dnl     MPI_Init(&argc, &argv);
-dnl     memset(&mpi_stat, 0, sizeof(MPI_Status)); /* zero out status */
-dnl     ret = MPI_Get_count(&mpi_stat, MPI_BYTE, &bytes_read);
-dnl     MPI_Finalize();
-dnl 
-dnl     /* this returns TRUE if bytes_read is 0...the shell thinks that the
-dnl      * program fails, but we want it to fail of course so switch the
-dnl      * "true"/"false" parts of the TRY_RUN macro */
-dnl     return bytes_read == 0;
-dnl }
-dnl   ],
-dnl   AC_MSG_RESULT(no),
-dnl   AC_MSG_RESULT(yes)
-dnl   CPPFLAGS="$CPPFLAGS -DMPI_GET_COUNT_WORKS",AC_MSG_RESULT(no))
-dnl ----------------------------------------------------------------------
-
   dnl --------------------------------------------------------------------
   dnl Do we want MPE instrumentation feature on?
   dnl
diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index ca689d9..c2e23dd 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -95,6 +95,9 @@ Bug Fixes since HDF5-1.6.0 release
     -------
         - Fixed bug with variable-length datatypes used in compound datatypes.
             SLU - 2003/12/29
+        - Fixed bug in parallel I/O routines that would cause reads from
+            "short datasets" (datasets which were only partially written out)
+            to return invalid data.  QAK & AKC - 2003/12/19
         - Fixed bug where scalar dataspaces for attributes were reporting as
             simple dataspaces.  QAK - 2003/12/13
         - Fixed problem with selection offsets of hyperslab selections in
diff --git a/src/H5FDfphdf5.c b/src/H5FDfphdf5.c
index 6ee76f6..8198165 100644
--- a/src/H5FDfphdf5.c
+++ b/src/H5FDfphdf5.c
@@ -1160,14 +1160,11 @@ H5FD_fphdf5_read(H5FD_t *_file, H5FD_mem_t mem_type, hid_t dxpl_id,
                  haddr_t addr, size_t size, void *buf)
 {
     H5FD_fphdf5_t      *file = (H5FD_fphdf5_t*)_file;
-    MPI_Offset          mpi_off;
     MPI_Status          status;
-    int                 mrc;
-    MPI_Datatype        buf_type;
-    int                 size_i;
-    int                 bytes_read;
-    int                 n;
-    unsigned            use_view_this_time = 0;
+    MPI_Offset          mpi_off;
+    int                 size_i;             /* Integer copy of 'size' to read */
+    int                 bytes_read;         /* Number of bytes read in */
+    int                 mrc;                /* MPI return code */
     herr_t              ret_value = SUCCEED;
 
     FUNC_ENTER_NOAPI(H5FD_fphdf5_read, FAIL)
@@ -1189,14 +1186,18 @@ H5FD_fphdf5_read(H5FD_t *_file, H5FD_mem_t mem_type, hid_t dxpl_id,
         HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from haddr_t to MPI offset")
 
     size_i = (int)size;
-
     if ((hsize_t)size_i != size)
         HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't convert from size_t to int")
 
-    /* Only look for MPI views for raw data transfers */
-    if (mem_type == H5FD_MEM_DRAW) {
+    /* Only do real MPI stuff for raw data transfers */
+    if(mem_type==H5FD_MEM_DRAW) {
         H5P_genplist_t     *plist;
-        H5FD_mpio_xfer_t    xfer_mode;  /* I/O tranfer mode */
+        H5FD_mpio_xfer_t            xfer_mode;   /* I/O tranfer mode */
+        MPI_Datatype buf_type;  /* MPI datatype for I/O operation */
+        int n;
+        int type_size;          /* MPI datatype used for I/O's size */
+        int io_size;            /* Actual number of bytes requested */
+        unsigned use_view_this_time = 0;        /* Flag to indicate we are using an MPI view */
 
         /* Obtain the data transfer properties */
         if ((plist = H5I_object(dxpl_id)) == NULL)
@@ -1239,6 +1240,13 @@ H5FD_fphdf5_read(H5FD_t *_file, H5FD_mem_t mem_type, hid_t dxpl_id,
             if ((mrc = MPI_File_read_at_all(file->f, mpi_off, buf, size_i,
                                             buf_type, &status)) != MPI_SUCCESS)
                 HMPI_GOTO_ERROR(FAIL, "MPI_File_read_at_all failed", mrc)
+
+            /*
+             * Reset the file view when we used MPI derived types
+             */
+            if ((mrc = MPI_File_set_view(file->f, (MPI_Offset)0, MPI_BYTE, MPI_BYTE,
+                                         H5FD_mpio_native,  file->info)) != MPI_SUCCESS)
+                HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mrc)
         } else {
             /*
              * Prepare for a simple xfer of a contiguous block of bytes. The
@@ -1252,21 +1260,33 @@ H5FD_fphdf5_read(H5FD_t *_file, H5FD_mem_t mem_type, hid_t dxpl_id,
                 HMPI_GOTO_ERROR(FAIL, "MPI_File_read_at failed", mrc)
         }
 
-        /*
-         * MPI_Get_count incorrectly returns negative count; fake a complete
-         * read.
+        /* How many bytes were actually read? */
+        /* [This works because the "basic elements" we use for all our MPI derived
+         *  types are MPI_BYTE.  We should be using the 'buf_type' for the MPI
+         *  datatype in this call though... (We aren't because using it causes
+         *  the LANL "qsc" machine to dump core - 12/19/03) - QAK]
          */
-        bytes_read = size_i;
+        if (MPI_SUCCESS != (mrc=MPI_Get_elements(&status, MPI_BYTE, &bytes_read)))
+            HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements failed", mrc)
+
+        /* Get the type's size */
+        if (MPI_SUCCESS != (mrc=MPI_Type_size(buf_type,&type_size)))
+            HMPI_GOTO_ERROR(FAIL, "MPI_Type_size failed", mrc)
+
+        /* Compute the actual number of bytes requested */
+        io_size=type_size*size_i;
+
+        /* Check for read failure */
+        if (bytes_read<0 || bytes_read>io_size)
+            HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed")
 
         /*
-         * Reset the file view when we used MPI derived types
+         * This gives us zeroes beyond end of physical MPI file.
          */
-        if (use_view_this_time)
-            if ((mrc = MPI_File_set_view(file->f, (MPI_Offset)0, MPI_BYTE, MPI_BYTE,
-                                         H5FD_mpio_native,  file->info)) != MPI_SUCCESS)
-                HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mrc)
-
-    } else {
+        if ((n=(io_size-bytes_read)) > 0)
+            HDmemset((char*)buf+bytes_read, 0, (size_t)n);
+    } /* end if */
+    else {
         /*
          * This is metadata - we want to try to read it from the SAP
          * first.
@@ -1276,7 +1296,7 @@ H5FD_fphdf5_read(H5FD_t *_file, H5FD_mem_t mem_type, hid_t dxpl_id,
 
         if (H5FP_request_read_metadata(_file, file->file_id, dxpl_id, mem_type,
                                        addr, size, (uint8_t**)&buf,
-                                       &bytes_read, &req_id, &sap_status) != SUCCEED) {
+                                       &req_id, &sap_status) != SUCCEED) {
             /* FIXME: The read failed, for some reason */
 HDfprintf(stderr, "%s:%d: Metadata cache read failed!\n", FUNC, __LINE__);
         }
@@ -1297,27 +1317,6 @@ HDfprintf(stderr, "%s:%d: Metadata cache read failed!\n", FUNC, __LINE__);
         }
     } /* end else */
 
-    /* Check for read failure */
-    if (bytes_read < 0 || bytes_read > size_i)
-        HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file read failed")
-
-    /*
-     * This gives us zeroes beyond end of physical MPI file. What about
-     * reading past logical end of HDF5 file???
-     */
-    n = size_i - bytes_read;
-
-    if (n > 0) {
-        if (use_view_this_time)
-            /*
-             * INCOMPLETE rky 1998-09-18
-             * Haven't implemented reading zeros beyond EOF. What to do???
-             */
-            HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "eof file read failed")
-
-        memset((char*)buf + bytes_read, 0, (size_t)n);
-    }
-
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 }
@@ -1440,6 +1439,8 @@ H5FD_fphdf5_write_real(H5FD_t *_file, H5FD_mem_t mem_type, H5P_genplist_t *plist
     MPI_Offset          mpi_off;
     int                 mrc;
     int                 bytes_written;
+    int                 type_size;      /* MPI datatype used for I/O's size */
+    int                 io_size;        /* Actual number of bytes requested */
     unsigned            use_view_this_time = 0;
     herr_t              ret_value = SUCCEED;
 
@@ -1504,28 +1505,38 @@ H5FD_fphdf5_write_real(H5FD_t *_file, H5FD_mem_t mem_type, H5P_genplist_t *plist
         if ((mrc = MPI_File_write_at_all(file->f, mpi_off, (void*)buf,
                                          size, buf_type, &status)) != MPI_SUCCESS)
             HMPI_GOTO_ERROR(FAIL, "MPI_File_write_at_all failed", mrc)
-    } else {
+
+        /* Reset the file view when we used MPI derived types */
+        if ((mrc = MPI_File_set_view(file->f, (MPI_Offset)0, MPI_BYTE, MPI_BYTE,
+                                     H5FD_mpio_native, file->info)) != MPI_SUCCESS)
+            HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mrc)
+    } /* end if */
+    else {
         /*OKAY: CAST DISCARDS CONST QUALIFIER*/
         if ((mrc = MPI_File_write_at(file->f, mpi_off, (void*)buf,
                                      size, buf_type, &status)) != MPI_SUCCESS)
             HMPI_GOTO_ERROR(FAIL, "MPI_File_write_at failed", mrc)
     }
 
-    /* Reset the file view when we used MPI derived types */
-    if (use_view_this_time)
-        if ((mrc = MPI_File_set_view(file->f, (MPI_Offset)0, MPI_BYTE, MPI_BYTE,
-                                     H5FD_mpio_native, file->info)) != MPI_SUCCESS)
-            HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mrc)
-
-    /*
-     * MPI_Get_count incorrectly returns negative count; fake a complete
-     * write (use size for both parameters).
+    /* How many bytes were actually written? */
+    /* [This works because the "basic elements" we use for all our MPI derived
+     *  types are MPI_BYTE.  We should be using the 'buf_type' for the MPI
+     *  datatype in this call though... (We aren't because using it causes
+     *  the LANL "qsc" machine to dump core - 12/19/03) - QAK]
      */
-    bytes_written = size;
+    if (MPI_SUCCESS != (mrc=MPI_Get_elements(&status, MPI_BYTE, &bytes_written)))
+        HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements failed", mrc)
+
+    /* Get the type's size */
+    if (MPI_SUCCESS != (mrc=MPI_Type_size(buf_type,&type_size)))
+        HMPI_GOTO_ERROR(FAIL, "MPI_Type_size failed", mrc)
+
+    /* Compute the actual number of bytes requested */
+    io_size=type_size*size;
 
     /* Check for write failure */
-    if (bytes_written < 0 || bytes_written > size)
-        HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "file write failed")
+    if (bytes_written!=io_size)
+        HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "file write failed")
 
     /* Forget the EOF value (see H5FD_fphdf5_get_eof()) */
     file->eof = HADDR_UNDEF;
diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c
index 1b0f461..61d97da 100644
--- a/src/H5FDmpio.c
+++ b/src/H5FDmpio.c
@@ -40,8 +40,7 @@
 /*
  * The driver identification number, initialized at runtime if H5_HAVE_PARALLEL
  * is defined. This allows applications to still have the H5FD_MPIO
- * "constants" in their source code (it also makes this file strictly ANSI
- * compliant when H5_HAVE_PARALLEL isn't defined)
+ * "constants" in their source code.
  */
 static hid_t H5FD_MPIO_g = 0;
 
@@ -1323,6 +1322,10 @@ done:
  *		to HADDR_UNDEF which is the error return value of this
  *		function.
  *
+ *              Keeping the EOF updated (during write calls) is expensive
+ *              because any process may extend the physical end of the
+ *              file. -QAK
+ *
  * Return:	Success:	The end-of-address marker.
  *
  *		Failure:	HADDR_UNDEF
@@ -1563,7 +1566,9 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t dxpl_id, haddr_t add
 
     /* How many bytes were actually read? */
     /* [This works because the "basic elements" we use for all our MPI derived
-     *  types are MPI_BYTE - QAK]
+     *  types are MPI_BYTE.  We should be using the 'buf_type' for the MPI
+     *  datatype in this call though... (We aren't because using it causes
+     *  the LANL "qsc" machine to dump core - 12/19/03) - QAK]
      */
     if (MPI_SUCCESS != (mpi_code=MPI_Get_elements(&mpi_stat, MPI_BYTE, &bytes_read)))
         HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements failed", mpi_code)
@@ -1879,7 +1884,9 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t dxpl_id, haddr_t addr,
 
     /* How many bytes were actually written? */
     /* [This works because the "basic elements" we use for all our MPI derived
-     *  types are MPI_BYTE - QAK]
+     *  types are MPI_BYTE.  We should be using the 'buf_type' for the MPI
+     *  datatype in this call though... (We aren't because using it causes
+     *  the LANL "qsc" machine to dump core - 12/19/03) - QAK]
      */
     if (MPI_SUCCESS != (mpi_code=MPI_Get_elements(&mpi_stat, MPI_BYTE, &bytes_written)))
         HMPI_GOTO_ERROR(FAIL, "MPI_Get_elements failed", mpi_code)
@@ -1903,7 +1910,7 @@ done:
     /* if only p<round> writes, need to broadcast the ret_value to other processes */
     if ((type!=H5FD_MEM_DRAW) && H5_mpi_1_metawrite_g) {
 	if (MPI_SUCCESS != (mpi_code=MPI_Bcast(&ret_value, sizeof(ret_value), MPI_BYTE, H5_PAR_META_WRITE, file->comm)))
-	    HMPI_GOTO_ERROR(FAIL, "MPI_Bcast failed", mpi_code)
+	    HMPI_DONE_ERROR(FAIL, "MPI_Bcast failed", mpi_code)
     } /* end if */
 #endif /* OLD_METADATA_WRITE */
 
@@ -1912,6 +1919,7 @@ done:
     	fprintf(stdout, "proc %d: Leaving H5FD_mpio_write with ret_value=%d\n",
 	    file->mpi_rank, ret_value );
 #endif
+
     FUNC_LEAVE_NOAPI(ret_value)
 }
 
diff --git a/src/H5FDmpiposix.c b/src/H5FDmpiposix.c
index 647fb35..4dadb1b 100644
--- a/src/H5FDmpiposix.c
+++ b/src/H5FDmpiposix.c
@@ -1209,7 +1209,7 @@ H5FD_mpiposix_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id,
         if (0==nbytes) {
             /* end of file but not end of format address space */
             HDmemset(buf, 0, size);
-            size = 0;
+            break;
         } /* end if */
         assert(nbytes>=0);
         assert((size_t)nbytes<=size);
diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c
index 5b73475..5924c0a 100644
--- a/src/H5FDsec2.c
+++ b/src/H5FDsec2.c
@@ -682,7 +682,7 @@ H5FD_sec2_read(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, hadd
         if (0==nbytes) {
             /* end of file but not end of format address space */
             HDmemset(buf, 0, size);
-            size = 0;
+            break;
         }
         assert(nbytes>=0);
         assert((size_t)nbytes<=size);
diff --git a/src/H5FPclient.c b/src/H5FPclient.c
index e80288d..cdc22e0 100644
--- a/src/H5FPclient.c
+++ b/src/H5FPclient.c
@@ -286,7 +286,7 @@ done:
 herr_t
 H5FP_request_read_metadata(H5FD_t *file, unsigned file_id, hid_t dxpl_id,
                            H5FD_mem_t UNUSED mem_type, haddr_t addr,
-                           size_t size, uint8_t **buf, int *bytes_read,
+                           size_t size, uint8_t **buf,
                            unsigned *req_id, H5FP_status_t *status)
 {
     H5FP_request_t req;
@@ -300,7 +300,6 @@ H5FP_request_read_metadata(H5FD_t *file, unsigned file_id, hid_t dxpl_id,
     /* check args */
     assert(file);
     assert(buf);
-    assert(bytes_read);
     assert(req_id);
     assert(status);
 
@@ -352,7 +351,6 @@ HDfprintf(stderr, "Buffer not big enough to hold metadata!!!!\n");
 assert(0);
         }
 
-        *bytes_read = size;
         break;
     case H5FP_STATUS_DUMPING:
         /*
diff --git a/src/H5FPprivate.h b/src/H5FPprivate.h
index 0abd9cf..aa85969 100644
--- a/src/H5FPprivate.h
+++ b/src/H5FPprivate.h
@@ -305,7 +305,7 @@ extern herr_t H5FP_request_release_lock(unsigned sap_file_id, hobj_ref_t oid,
                                         H5FP_status_t *status);
 extern herr_t H5FP_request_read_metadata(H5FD_t *file, unsigned sap_file_id, hid_t dxpl_id,
                                          H5FD_mem_t mem_type, haddr_t addr,
-                                         size_t size, uint8_t **buf, int *bytes_read,
+                                         size_t size, uint8_t **buf,
                                          unsigned *req_id, H5FP_status_t *status);
 extern herr_t H5FP_request_write_metadata(H5FD_t *file, unsigned file_id, hid_t dxpl_id,
                                           H5FD_mem_t mem_type, haddr_t addr,
diff --git a/testpar/testphdf5.h b/testpar/testphdf5.h
index 711d189..bb5164a 100644
--- a/testpar/testphdf5.h
+++ b/testpar/testphdf5.h
@@ -187,6 +187,7 @@ void extend_readInd(char *filename);
 void extend_readAll(char *filename);
 void compact_dataset(char *filename);
 void big_dataset(const char *filename);
+void short_dataset(const char *filename);
 int dataset_vrfy(hssize_t start[], hsize_t count[], hsize_t stride[],
                  hsize_t block[], DATATYPE *dataset, DATATYPE *original);