Merge pull request #2870 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:final_qak_parallel_bugfix_1_10 to hdf5_1_10

* commit 'b89f84ef34c07ae0b0db22f16b8c8bfd27812004':
  Fixed errant comma
  Brings Quincey's parallel collective MD write bugfix from develop

8 files changed, 26 insertions, 232 deletions

diff --git a/src/H5Cdbg.c b/src/H5Cdbg.c
index 775db4c..a5ff7bc 100644
--- a/src/H5Cdbg.c
+++ b/src/H5Cdbg.c
@@ -28,16 +28,12 @@
 
 #include "H5Cmodule.h"          /* This source code file is part of the H5C module */
 
-#define H5AC_FRIEND
-
-
-
 
 /***********/
 /* Headers */
 /***********/
 #include "H5private.h"      /* Generic Functions            */
-#include "H5ACpkg.h"        /* Metadata Cache               */
+#include "H5ACprivate.h"    /* Metadata Cache               */
 #include "H5Cpkg.h"         /* Cache                        */
 #include "H5Eprivate.h"     /* Error Handling               */
 
@@ -368,107 +364,6 @@ H5C_dump_cache_skip_list(H5C_t * cache_ptr, char * calling_fcn)
 
 
 /*-------------------------------------------------------------------------
- * Function:    H5C_dump_coll_write_list
- *
- * Purpose:     Debugging routine that prints a summary of the contents of
- *		the collective write skip list used by the metadata cache
- *              in the parallel case to maintain a list of entries to write
- *              collectively at a sync point.
- *
- * Return:      Non-negative on success/Negative on failure
- *
- * Programmer:  John Mainzer
- *              4/1/17
- *
- *-------------------------------------------------------------------------
- */
-#ifdef H5_HAVE_PARALLEL
-#ifndef NDEBUG
-herr_t
-H5C_dump_coll_write_list(H5C_t * cache_ptr, char * calling_fcn)
-{
-    herr_t              ret_value = SUCCEED;   /* Return value */
-    int                 i;
-    int                 list_len;
-    H5AC_aux_t *        aux_ptr = NULL;
-    H5C_cache_entry_t * entry_ptr = NULL;
-    H5SL_node_t *       node_ptr = NULL;
-
-    FUNC_ENTER_NOAPI_NOERR
-
-    HDassert(cache_ptr != NULL);
-    HDassert(cache_ptr->magic == H5C__H5C_T_MAGIC);
-    HDassert(cache_ptr->aux_ptr);
-
-    aux_ptr = (H5AC_aux_t *)cache_ptr->aux_ptr;
-
-    HDassert(aux_ptr->magic == H5AC__H5AC_AUX_T_MAGIC);
-
-    HDassert(calling_fcn != NULL);
-
-    list_len = (int)H5SL_count(cache_ptr->coll_write_list);
-
-    HDfprintf(stdout, "\n\nDumping MDC coll write list from %d:%s.\n",
-              aux_ptr->mpi_rank, calling_fcn);
-    HDfprintf(stdout, "	slist len = %u.\n", cache_ptr->slist_len);
-
-    if ( list_len > 0 ) {
-
-        /* scan the collective write list generating the desired output */
-        HDfprintf(stdout,
-                  "Num:    Addr:               Len: Prot/Pind: Dirty: Type:\n");
-
-        i = 0;
-
-        node_ptr = H5SL_first(cache_ptr->coll_write_list);
-
-        if ( node_ptr != NULL )
-
-            entry_ptr = (H5C_cache_entry_t *)H5SL_item(node_ptr);
-
-        else
-
-            entry_ptr = NULL;
-
-        while ( entry_ptr != NULL ) {
-
-            HDassert(entry_ptr->magic == H5C__H5C_CACHE_ENTRY_T_MAGIC);
-
-            HDfprintf(stdout,
-               "%s%d       0x%016llx  %4lld    %d/%d       %d    %s\n",
-               cache_ptr->prefix, i,
-               (long long)(entry_ptr->addr),
-               (long long)(entry_ptr->size),
-               (int)(entry_ptr->is_protected),
-               (int)(entry_ptr->is_pinned),
-               (int)(entry_ptr->is_dirty),
-               entry_ptr->type->name);
-
-            node_ptr = H5SL_next(node_ptr);
-
-            if ( node_ptr != NULL )
-
-                entry_ptr = (H5C_cache_entry_t *)H5SL_item(node_ptr);
-
-            else
-
-                entry_ptr = NULL;
-
-            i++;
-
-        } /* end while */
-    } /* end if */
-
-    HDfprintf(stdout, "\n\n");
-
-    FUNC_LEAVE_NOAPI(ret_value)
-
-} /* H5C_dump_coll_write_list() */
-#endif /* NDEBUG */
-#endif /* H5_HAVE_PARALLEL */
-
-
-/*-------------------------------------------------------------------------
  * Function:    H5C_set_prefix
  *
  * Purpose:     Set the values of the prefix field of H5C_t.  This
diff --git a/src/H5Cmpio.c b/src/H5Cmpio.c
index 3579bc2..e0b7f17 100644
--- a/src/H5Cmpio.c
+++ b/src/H5Cmpio.c
@@ -999,6 +999,7 @@ H5C__collective_write(H5F_t *f)
 {
     H5AC_t              *cache_ptr;
     H5FD_mpio_xfer_t    orig_xfer_mode = H5FD_MPIO_COLLECTIVE;
+    void                *base_buf;
     int                 count;
     int                 *length_array = NULL;
     MPI_Aint            *buf_array = NULL;
@@ -1008,6 +1009,8 @@ H5C__collective_write(H5F_t *f)
     MPI_Datatype        ftype;
     hbool_t             ftype_created = FALSE;
     int                 mpi_code;
+    char                unused = 0;             /* Unused, except for non-NULL pointer value */
+    size_t              buf_count;
     herr_t              ret_value = SUCCEED;
 
     FUNC_ENTER_STATIC
@@ -1022,20 +1025,17 @@ H5C__collective_write(H5F_t *f)
     if(H5CX_get_io_xfer_mode(&orig_xfer_mode) < 0)
         HGOTO_ERROR(H5E_CACHE, H5E_CANTGET, FAIL, "can't get MPI-I/O transfer mode")
 
+    /* Set transfer mode */
+    if(H5CX_set_io_xfer_mode(H5FD_MPIO_COLLECTIVE) < 0)
+        HGOTO_ERROR(H5E_CACHE, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode")
+
     /* Get number of entries in collective write list */
     count = (int)H5SL_count(cache_ptr->coll_write_list);
-
     if(count > 0) {
-        H5FD_mpio_xfer_t    xfer_mode = H5FD_MPIO_COLLECTIVE;
         H5SL_node_t         *node;
         H5C_cache_entry_t   *entry_ptr;
-        void                *base_buf;
         int                 i;
 
-        /* Set new transfer mode */
-        if(H5CX_set_io_xfer_mode(xfer_mode) < 0)
-            HGOTO_ERROR(H5E_CACHE, H5E_CANTSET, FAIL, "can't set MPI-I/O transfer mode")
-
         /* Allocate arrays */
         if(NULL == (length_array = (int *)H5MM_malloc((size_t)count * sizeof(int))) )
             HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "memory allocation failed for collective write table length array")
@@ -1059,7 +1059,6 @@ H5C__collective_write(H5F_t *f)
         node = H5SL_next(node);
         i = 1;
         while(node) {
-
             if(NULL == (entry_ptr = (H5C_cache_entry_t *)H5SL_item(node)))
                 HGOTO_ERROR(H5E_CACHE, H5E_NOTFOUND, FAIL, "can't retrieve skip list item")
 
@@ -1076,67 +1075,39 @@ H5C__collective_write(H5F_t *f)
         /* Create memory MPI type */
         if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed(count, length_array, buf_array, MPI_BYTE, &btype)))
             HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
-
         btype_created = TRUE;
-
         if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&btype)))
             HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
 
         /* Create file MPI type */
         if(MPI_SUCCESS != (mpi_code = MPI_Type_create_hindexed(count, length_array, offset_array, MPI_BYTE, &ftype)))
             HMPI_GOTO_ERROR(FAIL, "MPI_Type_create_hindexed failed", mpi_code)
-
         ftype_created = TRUE;
-
         if(MPI_SUCCESS != (mpi_code = MPI_Type_commit(&ftype)))
             HMPI_GOTO_ERROR(FAIL, "MPI_Type_commit failed", mpi_code)
 
-        /* Pass buf type, file type to the file driver */
-        if(H5CX_set_mpi_coll_datatypes(btype, ftype) < 0)
-            HGOTO_ERROR(H5E_CACHE, H5E_CANTSET, FAIL, "can't set MPI-I/O properties")
-
-        /* Write data */
-        if(H5F_block_write(f, H5FD_MEM_DEFAULT, (haddr_t)0, (size_t)1, base_buf) < 0)
-            HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to write entries collectively")
-
+        /* MPI count to write */
+        buf_count = 1;
     } /* end if */
     else {
-        MPI_Status mpi_stat;
-        MPI_File *mpi_fh_p;
-        MPI_File mpi_fh;
-        MPI_Info *info_p;
-        MPI_Info info;
-
-/* This should be rewritten to call H5F_block_write, with the correct
- *      buffer and file datatypes (null ones).  -QAK, 2018/02/21
- */
-        if(H5F_get_mpi_handle(f, (MPI_File **)&mpi_fh_p) < 0)
-            HGOTO_ERROR(H5E_CACHE, H5E_CANTGET, FAIL, "can't get mpi file handle")
-
-        mpi_fh = *(MPI_File*)mpi_fh_p;
-
-        if(H5F_get_mpi_info(f, &info_p) < 0)
-            HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't get mpi file info")
+        /* Pass trivial buf type, file type to the file driver */
+        btype = MPI_BYTE;
+        ftype = MPI_BYTE;
 
-        info = *info_p;
+        /* Set non-NULL pointer for I/O operation */
+        base_buf = &unused;
 
-        /* just to match up with the 1st MPI_File_set_view from
-         * H5FD_mpio_write()
-         */
-        if(MPI_SUCCESS != (mpi_code = MPI_File_set_view(mpi_fh, (MPI_Offset)0, MPI_BYTE, MPI_BYTE, "native", info)))
-            HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
+        /* MPI count to write */
+        buf_count = 0;
+    } /* end else */
 
-        /* just to match up with MPI_File_write_at_all from H5FD_mpio_write() */
-        HDmemset(&mpi_stat, 0, sizeof(MPI_Status));
-        if(MPI_SUCCESS != (mpi_code = MPI_File_write_at_all(mpi_fh, (MPI_Offset)0, NULL, 0, MPI_BYTE, &mpi_stat)))
-            HMPI_GOTO_ERROR(FAIL, "MPI_File_write_at_all failed", mpi_code)
+    /* Pass buf type, file type to the file driver */
+    if(H5CX_set_mpi_coll_datatypes(btype, ftype) < 0)
+        HGOTO_ERROR(H5E_CACHE, H5E_CANTSET, FAIL, "can't set MPI-I/O properties")
 
-        /* just to match up with the 2nd MPI_File_set_view (reset) in
-         * H5FD_mpio_write()
-         */
-        if(MPI_SUCCESS != (mpi_code = MPI_File_set_view(mpi_fh, (MPI_Offset)0, MPI_BYTE, MPI_BYTE, "native", info)))
-            HMPI_GOTO_ERROR(FAIL, "MPI_File_set_view failed", mpi_code)
-    } /* end else */
+    /* Write data */
+    if(H5F_block_write(f, H5FD_MEM_DEFAULT, (haddr_t)0, buf_count, base_buf) < 0)
+        HGOTO_ERROR(H5E_CACHE, H5E_WRITEERROR, FAIL, "unable to write entries collectively")
 
 done:
     /* Free arrays */
diff --git a/src/H5Cprivate.h b/src/H5Cprivate.h
index 3203da6..6411375 100644
--- a/src/H5Cprivate.h
+++ b/src/H5Cprivate.h
@@ -2338,12 +2338,9 @@ H5_DLL herr_t H5C_dump_cache_LRU(H5C_t *cache_ptr, const char *cache_name);
 H5_DLL hbool_t H5C_get_serialization_in_progress(const H5C_t *cache_ptr);
 H5_DLL hbool_t H5C_cache_is_clean(const H5C_t *cache_ptr, H5C_ring_t inner_ring);
 H5_DLL herr_t H5C_dump_cache_skip_list(H5C_t *cache_ptr, char *calling_fcn);
-#ifdef H5_HAVE_PARALLEL
-H5_DLL herr_t H5C_dump_coll_write_list(H5C_t * cache_ptr, char * calling_fcn);
-#endif /* H5_HAVE_PARALLEL */
 H5_DLL herr_t H5C_get_entry_ptr_from_addr(H5C_t *cache_ptr, haddr_t addr,
     void **entry_ptr_ptr);
-H5_DLL herr_t H5C_flush_dependency_exists(H5C_t *cache_ptr, haddr_t parent_addr,
+H5_DLL herr_t H5C_flush_dependency_exists(H5C_t *cache_ptr, haddr_t parent_addr, 
     haddr_t child_addr, hbool_t *fd_exists_ptr);
 H5_DLL herr_t H5C_verify_entry_type(H5C_t *cache_ptr, haddr_t addr,
     const H5C_class_t *expected_type, hbool_t *in_cache_ptr,
diff --git a/src/H5FDmpi.c b/src/H5FDmpi.c
index 38096f9..82af11a 100644
--- a/src/H5FDmpi.c
+++ b/src/H5FDmpi.c
@@ -141,42 +141,6 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5FD_get_mpi_info
- *
- * Purpose:	Retrieves the file's mpi info
- *
- * Return:	Success:	SUCCEED
- *
- *		Failure:	FAIL
- *
- * Programmer:	John Mainzer
- *              4/4/17
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5FD_get_mpi_info(H5FD_t *file, void** mpi_info)
-{
-    const H5FD_class_mpi_t *cls;
-    herr_t  ret_value = SUCCEED;
-
-    FUNC_ENTER_NOAPI_NOINIT
-
-    HDassert(file);
-    cls = (const H5FD_class_mpi_t *)(file->cls);
-    HDassert(cls);
-    HDassert(cls->get_mpi_info);    /* All MPI drivers must implement this */
-
-    /* Dispatch to driver */
-    if((ret_value = (cls->get_mpi_info)(file, mpi_info)) < 0)
-        HGOTO_ERROR(H5E_VFL, H5E_CANTGET, FAIL, "driver get_mpi_info request failed")
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5FD_get_mpi_info() */
-
-
-/*-------------------------------------------------------------------------
  * Function:    H5FD_mpi_MPIOff_to_haddr
  *
  * Purpose:     Convert an MPI_Offset value to haddr_t.
diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c
index ec1ca87..c1e1198 100644
--- a/src/H5FDmpio.c
+++ b/src/H5FDmpio.c
@@ -94,7 +94,6 @@ static herr_t H5FD_mpio_truncate(H5FD_t *_file, hid_t dxpl_id, hbool_t closing);
 static int H5FD_mpio_mpi_rank(const H5FD_t *_file);
 static int H5FD_mpio_mpi_size(const H5FD_t *_file);
 static MPI_Comm H5FD_mpio_communicator(const H5FD_t *_file);
-static herr_t  H5FD_mpio_get_info(H5FD_t *_file, void** mpi_info);
 
 /* The MPIO file driver information */
 static const H5FD_class_mpi_t H5FD_mpio_g = {
@@ -134,8 +133,7 @@ static const H5FD_class_mpi_t H5FD_mpio_g = {
     },  /* End of superclass information */
     H5FD_mpio_mpi_rank,                         /*get_rank              */
     H5FD_mpio_mpi_size,                         /*get_size              */
-    H5FD_mpio_communicator,                     /*get_comm              */
-    H5FD_mpio_get_info                          /*get_info              */
+    H5FD_mpio_communicator                      /*get_comm              */
 };
 
 #ifdef H5FDmpio_DEBUG
diff --git a/src/H5FDprivate.h b/src/H5FDprivate.h
index c5bc043..d659a34 100644
--- a/src/H5FDprivate.h
+++ b/src/H5FDprivate.h
@@ -51,7 +51,6 @@ typedef struct H5FD_class_mpi_t {
     int  (*get_rank)(const H5FD_t *file);     /* Get the MPI rank of a process */
     int  (*get_size)(const H5FD_t *file);     /* Get the MPI size of a communicator */
     MPI_Comm (*get_comm)(const H5FD_t *file); /* Get the communicator for a file */
-    herr_t (*get_mpi_info)(H5FD_t *file, void** mpi_info); /* get MPI_Info for a file */
 } H5FD_class_mpi_t;
 #endif
 
@@ -174,7 +173,6 @@ H5_DLL herr_t H5FD_get_mpio_atomicity(H5FD_t *file, hbool_t *flag);
 H5_DLL int H5FD_mpi_get_rank(const H5FD_t *file);
 H5_DLL int H5FD_mpi_get_size(const H5FD_t *file);
 H5_DLL MPI_Comm H5FD_mpi_get_comm(const H5FD_t *_file);
-H5_DLL herr_t H5FD_get_mpi_info(H5FD_t *file, void** file_info);
 #endif /* H5_HAVE_PARALLEL */
 
 #endif /* !_H5FDprivate_H */
diff --git a/src/H5Fmpi.c b/src/H5Fmpi.c
index b6cf3a3..fe85c89 100644
--- a/src/H5Fmpi.c
+++ b/src/H5Fmpi.c
@@ -343,33 +343,5 @@ H5F_mpi_retrieve_comm(hid_t loc_id, hid_t acspl_id, MPI_Comm *mpi_comm)
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5F_mpi_retrieve_comm */
-
-
-/*-------------------------------------------------------------------------
- * Function:    H5F_get_mpi_info
- *
- * Purpose:     Retrieves MPI File info.
- *
- * Return:      Success:        The size (positive)
- *              Failure:        Negative
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5F_get_mpi_info(const H5F_t *f, MPI_Info **f_info)
-{
-    herr_t ret_value = SUCCEED;
-
-    FUNC_ENTER_NOAPI(FAIL)
-
-    HDassert(f && f->shared);
-
-    /* Dispatch to driver */
-    if ((ret_value = H5FD_get_mpi_info(f->shared->lf, (void **)f_info)) < 0)
-        HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "can't get mpi file info")
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5F_get_mpi_info() */
 #endif /* H5_HAVE_PARALLEL */
 
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index 469a37c..cb6e6fe 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -855,7 +855,6 @@ H5_DLL int H5F_mpi_get_rank(const H5F_t *f);
 H5_DLL MPI_Comm H5F_mpi_get_comm(const H5F_t *f);
 H5_DLL int H5F_mpi_get_size(const H5F_t *f);
 H5_DLL herr_t H5F_mpi_retrieve_comm(hid_t loc_id, hid_t acspl_id, MPI_Comm *mpi_comm);
-H5_DLL herr_t H5F_get_mpi_info(const H5F_t *f, MPI_Info **f_info);
 #endif /* H5_HAVE_PARALLEL */
 
 /* External file cache routines */