Fix bugs in selection I/O code.

2 files changed, 45 insertions, 30 deletions

diff --git a/src/H5FDint.c b/src/H5FDint.c
index 8deec48..65e090a 100644
--- a/src/H5FDint.c
+++ b/src/H5FDint.c
@@ -795,6 +795,12 @@ H5FD__read_selection_translate(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, uin
     /* Check if we're using vector I/O */
     use_vector = file->cls->read_vector != NULL;
 
+    /* Allocate sequence lists for memory and file spaces */
+    if (NULL == (file_iter = H5FL_MALLOC(H5S_sel_iter_t)))
+        HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, FAIL, "couldn't allocate file selection iterator")
+    if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t)))
+        HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, FAIL, "couldn't allocate memory selection iterator")
+
     /* Loop over dataspaces */
     for (i = 0; i < count; i++) {
 
@@ -827,12 +833,6 @@ H5FD__read_selection_translate(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, uin
             }
         }
 
-        /* Allocate sequence lists for memory and file spaces */
-        if (NULL == (file_iter = H5FL_MALLOC(H5S_sel_iter_t)))
-            HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, FAIL, "couldn't allocate file selection iterator")
-        if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t)))
-            HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, FAIL, "couldn't allocate memory selection iterator")
-
         /* Initialize sequence lists for memory and file spaces */
         if (H5S_select_iter_init(file_iter, file_spaces[i], element_size, 0) < 0)
             HGOTO_ERROR(H5E_VFL, H5E_CANTINIT, FAIL, "can't initialize sequence list for file space")
@@ -970,6 +970,14 @@ H5FD__read_selection_translate(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, uin
         /* Make sure both memory and file sequences terminated at the same time */
         if (mem_seq_i < mem_nseq)
             HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "file selection terminated before memory selection")
+
+        /* Terminate iterators */
+        if (H5S_SELECT_ITER_RELEASE(file_iter) < 0)
+            HGOTO_ERROR(H5E_INTERNAL, H5E_CANTFREE, FAIL, "can't release file selection iterator")
+        file_iter_init = FALSE;
+        if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
+            HGOTO_ERROR(H5E_INTERNAL, H5E_CANTFREE, FAIL, "can't release memory selection iterator")
+        mem_iter_init = FALSE;
     }
 
     /* Issue vector read call if appropriate */
@@ -981,7 +989,7 @@ H5FD__read_selection_translate(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, uin
     }
 
 done:
-    /* Terminate iterators */
+    /* Terminate and free iterators */
     if (file_iter) {
         if (file_iter_init && H5S_SELECT_ITER_RELEASE(file_iter) < 0)
             HGOTO_ERROR(H5E_INTERNAL, H5E_CANTFREE, FAIL, "can't release file selection iterator")
@@ -1430,6 +1438,12 @@ H5FD__write_selection_translate(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, ui
     /* Check if we're using vector I/O */
     use_vector = file->cls->write_vector != NULL;
 
+    /* Allocate sequence lists for memory and file spaces */
+    if (NULL == (file_iter = H5FL_MALLOC(H5S_sel_iter_t)))
+        HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, FAIL, "couldn't allocate file selection iterator")
+    if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t)))
+        HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, FAIL, "couldn't allocate memory selection iterator")
+
     /* Loop over dataspaces */
     for (i = 0; i < count; i++) {
 
@@ -1462,12 +1476,6 @@ H5FD__write_selection_translate(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, ui
             }
         }
 
-        /* Allocate sequence lists for memory and file spaces */
-        if (NULL == (file_iter = H5FL_MALLOC(H5S_sel_iter_t)))
-            HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, FAIL, "couldn't allocate file selection iterator")
-        if (NULL == (mem_iter = H5FL_MALLOC(H5S_sel_iter_t)))
-            HGOTO_ERROR(H5E_VFL, H5E_CANTALLOC, FAIL, "couldn't allocate memory selection iterator")
-
         /* Initialize sequence lists for memory and file spaces */
         if (H5S_select_iter_init(file_iter, file_spaces[i], element_size, 0) < 0)
             HGOTO_ERROR(H5E_VFL, H5E_CANTINIT, FAIL, "can't initialize sequence list for file space")
@@ -1605,6 +1613,14 @@ H5FD__write_selection_translate(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, ui
         /* Make sure both memory and file sequences terminated at the same time */
         if (mem_seq_i < mem_nseq)
             HGOTO_ERROR(H5E_INTERNAL, H5E_BADVALUE, FAIL, "file selection terminated before memory selection")
+
+        /* Terminate iterators */
+        if (H5S_SELECT_ITER_RELEASE(file_iter) < 0)
+            HGOTO_ERROR(H5E_INTERNAL, H5E_CANTFREE, FAIL, "can't release file selection iterator")
+        file_iter_init = FALSE;
+        if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
+            HGOTO_ERROR(H5E_INTERNAL, H5E_CANTFREE, FAIL, "can't release memory selection iterator")
+        mem_iter_init = FALSE;
     }
 
     /* Issue vector write call if appropriate */
@@ -1616,7 +1632,7 @@ H5FD__write_selection_translate(H5FD_t *file, H5FD_mem_t type, hid_t dxpl_id, ui
     }
 
 done:
-    /* Terminate iterators */
+    /* Terminate and free iterators */
     if (file_iter) {
         if (file_iter_init && H5S_SELECT_ITER_RELEASE(file_iter) < 0)
             HGOTO_ERROR(H5E_INTERNAL, H5E_CANTFREE, FAIL, "can't release file selection iterator")
diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c
index 1d96979..5a279d0 100644
--- a/src/H5FDmpio.c
+++ b/src/H5FDmpio.c
@@ -1711,7 +1711,9 @@ H5FD__mpio_vector_build_types(uint32_t count, H5FD_mem_t types[], haddr_t addrs[
         *file_type     = MPI_BYTE;
         *mpi_bufs_base = bufs[0];
 
-        /* Setup s_sizes and s_bufs (needed for incomplete read filling code) */
+        /* Setup s_addrs, s_sizes and s_bufs (needed for incomplete read filling code and eof
+         * calculation code) */
+        *s_addrs = addrs;
         *s_sizes = sizes;
         *s_bufs  = bufs;
 
@@ -1792,8 +1794,9 @@ H5FD__mpio_vector_build_types(uint32_t count, H5FD_mem_t types[], haddr_t addrs[
             /* Determine size of this vector element */
             if (!fixed_size) {
                 if ((*s_sizes)[i] == 0) {
+                    HDassert(vector_was_sorted);
                     fixed_size = TRUE;
-                    size       = (*s_sizes)[i - 1];
+                    size       = sizes[i - 1];
                 }
                 else {
                     size = (*s_sizes)[i];
@@ -2369,11 +2372,6 @@ done:
         }
     }
 
-    /* Make sure we cleaned up */
-    HDassert(!s_addrs);
-    HDassert(!s_sizes);
-    HDassert(!s_bufs);
-
 #ifdef H5FDmpio_DEBUG
     if (H5FD_mpio_debug_t_flag)
         HDfprintf(stdout, "%s: Leaving, proc %d: ret_value = %d\n", __func__, file->mpi_rank, ret_value);
@@ -2428,7 +2426,7 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co
     hbool_t                    vector_was_sorted = TRUE;
     haddr_t *                  s_addrs           = NULL;
     size_t *                   s_sizes           = NULL;
-    void **                    s_bufs            = NULL;
+    const void **              s_bufs            = NULL;
     char                       unused            = 0; /* Unused, except for non-NULL pointer value */
     const void *               mpi_bufs_base     = NULL;
     MPI_Datatype               buf_type          = MPI_BYTE; /* MPI description of the selection in memory */
@@ -2495,7 +2493,8 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co
             HGOTO_ERROR(H5E_VFL, H5E_CANTGET, FAIL, "can't build MPI datatypes for I/O")
 
         /* Compute max addr writted to */
-        max_addr = s_addrs[count - 1] + (haddr_t)(s_sizes[count - 1]);
+        if (count > 0)
+            max_addr = s_addrs[count - 1] + (haddr_t)(s_sizes[count - 1]);
 
         /* free sorted vectors if they exist */
         if (!vector_was_sorted) {
@@ -2516,10 +2515,6 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co
         /* Portably initialize MPI status variable */
         HDmemset(&mpi_stat, 0, sizeof(MPI_Status));
 
-        /* some numeric conversions */
-        if (H5FD_mpi_haddr_to_MPIOff((haddr_t)0, &mpi_off) < 0)
-            HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't set MPI off to 0")
-
 #ifdef H5FDmpio_DEBUG
         if (H5FD_mpio_debug_w_flag)
             HDfprintf(stdout, "%s: mpi_off = %ld  size_i = %d\n", __func__, (long)mpi_off, size_i);
@@ -2530,6 +2525,10 @@ H5FD__mpio_write_vector(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, uint32_t co
                                                          H5FD_mpi_native_g, file->info)))
             HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
 
+        /* Reset mpi_off to 0 since the view now starts at the data offset */
+        if (H5FD_mpi_haddr_to_MPIOff((haddr_t)0, &mpi_off) < 0)
+            HGOTO_ERROR(H5E_INTERNAL, H5E_BADRANGE, FAIL, "can't set MPI off to 0")
+
         /* Get the collective_opt property to check whether the application wants to do IO individually.
          */
         if (H5CX_get_mpio_coll_opt(&coll_opt_mode) < 0)
@@ -2668,9 +2667,9 @@ done:
     }
 
     /* Make sure we cleaned up */
-    HDassert(!s_addrs);
-    HDassert(!s_sizes);
-    HDassert(!s_bufs);
+    HDassert(vector_was_sorted || !s_addrs);
+    HDassert(vector_was_sorted || !s_sizes);
+    HDassert(vector_was_sorted || !s_bufs);
 
 #ifdef H5FDmpio_DEBUG
     if (H5FD_mpio_debug_t_flag)