fbtl_posix_pwritev: add datasieving support for write

its however restricted to collective I/O operations, at this point
only from vulcan and dynamic_gen2. required some more infrastructure
to be added to recognize individual I/O and multi-threaded environments.

Signed-off-by: Edgar Gabriel <egabriel@central.uh.edu>

ompi/mca/common/ompio/common_ompio.h

@@ -67,6 +67,7 @@
 #define OMPIO_LOCK_NEVER             0x00000100
 #define OMPIO_LOCK_NOT_THIS_OP       0x00000200
 #define OMPIO_DATAREP_NATIVE         0x00000400
+#define OMPIO_COLLECTIVE_OP          0x00000800
 
 #define OMPIO_ROOT                    0
 

ompi/mca/fbtl/posix/fbtl_posix_preadv.c

@@ -158,6 +158,7 @@ ssize_t mca_fbtl_posix_preadv_datasieving (ompio_file_t *fh)
                         ret, strerror(errno));
             /* Just in case some part of the lock worked */
             mca_fbtl_posix_unlock ( &lock, fh);
+            free ( temp_buf);
             return OMPI_ERROR;
         }
         
@@ -165,6 +166,7 @@ ssize_t mca_fbtl_posix_preadv_datasieving (ompio_file_t *fh)
         mca_fbtl_posix_unlock ( &lock, fh);
         if ( ret_code == -1 ) {
             opal_output(1, "mca_fbtl_posix_preadv_datasieving: error in (p)read(v):%s", strerror(errno));
+            free ( temp_buf);
             return OMPI_ERROR;
         }
         

ompi/mca/fbtl/posix/fbtl_posix_pwritev.c

@@ -9,7 +9,7 @@
  *                         University of Stuttgart.  All rights reserved.
  * Copyright (c) 2004-2005 The Regents of the University of California.
  *                         All rights reserved.
- * Copyright (c) 2008-2017 University of Houston. All rights reserved.
+ * Copyright (c) 2008-2020 University of Houston. All rights reserved.
  * Copyright (c) 2015-2018 Research Organization for Information Science
  *                         and Technology (RIST). All rights reserved.
  * $COPYRIGHT$
@@ -30,7 +30,187 @@
 #include "ompi/constants.h"
 #include "ompi/mca/fbtl/fbtl.h"
 
+static ssize_t mca_fbtl_posix_pwritev_datasieving (ompio_file_t *fh );
+static ssize_t mca_fbtl_posix_pwritev_generic (ompio_file_t *fh );
+
 ssize_t  mca_fbtl_posix_pwritev(ompio_file_t *fh )
+{
+    ssize_t bytes_written=0, ret_code=0;
+    struct flock lock;
+    int ret;
+
+    if (NULL == fh->f_io_array) {
+        return OMPI_ERROR;
+    }
+    
+    if ( fh->f_num_of_io_entries > 1 ) {
+        bool do_data_sieving = true;
+
+        size_t avg_gap_size=0;
+        size_t avg_block_size = 0;
+        off_t prev_offset = (off_t)fh->f_io_array[0].offset;
+        int i;
+        for ( i=0; i< fh->f_num_of_io_entries; i++ ) {
+            avg_block_size += fh->f_io_array[i].length;
+            avg_gap_size   += (size_t)((off_t)fh->f_io_array[i].offset - prev_offset);
+            prev_offset     = (off_t)fh->f_io_array[i].offset;
+        }
+        avg_block_size = avg_block_size / fh->f_num_of_io_entries;
+        avg_gap_size = avg_gap_size / fh->f_num_of_io_entries;
+
+        if ( false == mca_fbtl_posix_write_datasieving      ||
+             0     == avg_gap_size                          ||
+             avg_block_size > mca_fbtl_posix_max_block_size ||
+             avg_gap_size   > mca_fbtl_posix_max_gap_size   ||
+             ompi_mpi_thread_multiple                       ||
+             !(fh->f_flags & OMPIO_COLLECTIVE_OP)            ) {
+            do_data_sieving = false;
+        }
+                
+        if ( do_data_sieving) {
+            return mca_fbtl_posix_pwritev_datasieving (fh);
+        }
+        else {
+            return mca_fbtl_posix_pwritev_generic (fh);
+        }
+    }
+    else {
+        // i.e. fh->f_num_of_io_entries == 1
+        ret = mca_fbtl_posix_lock ( &lock, fh, F_WRLCK, (off_t)fh->f_io_array[0].offset,
+                                    (off_t)fh->f_io_array[0].length, OMPIO_LOCK_ENTIRE_REGION ); 
+        if ( 0 < ret ) {
+            opal_output(1, "mca_fbtl_posix_pwritev: error in mca_fbtl_posix_lock() ret=%d: %s",
+                        ret, strerror(errno));
+            /* Just in case some part of the lock worked */
+            mca_fbtl_posix_unlock ( &lock, fh);
+            return OMPI_ERROR;
+        }
+        
+        ret_code = pwrite(fh->fd, fh->f_io_array[0].memory_address, fh->f_io_array[0].length,
+                         (off_t)fh->f_io_array[0].offset );
+        mca_fbtl_posix_unlock ( &lock, fh );
+        if ( ret_code == -1 ) {
+            opal_output(1, "mca_fbtl_posix_pwritev: error in (p)write(v):%s", strerror(errno));
+	    return OMPI_ERROR;
+	}
+        
+        bytes_written += ret_code;
+    }
+        
+    return bytes_written;
+}
+
+ssize_t mca_fbtl_posix_pwritev_datasieving (ompio_file_t *fh)
+{
+    size_t start, end, len;
+    size_t bufsize = 0;
+    int ret, i, j;
+    ssize_t bytes_written=0, ret_code=0;
+    struct flock lock;
+    char *temp_buf = NULL;
+    
+    int startindex = 0;
+    int endindex   = 0;
+    bool done = false;
+    
+    while (!done) {
+        // Break the io_array into chunks such that the size of the temporary
+        // buffer does not exceed mca_fbtl_posix_max_tmpbuf_size bytes.
+        // Each iteration will thus work in the range (startindex, endindex[
+        startindex = endindex;
+        if ( startindex >= fh->f_num_of_io_entries  ) {
+            done = true;
+            break;
+        }
+        
+        size_t sstart = (size_t)fh->f_io_array[startindex].offset;
+        size_t slen=0;
+
+        for ( j = startindex; j < fh->f_num_of_io_entries; j++ ) {
+            endindex = j;
+            slen = ((size_t)fh->f_io_array[j].offset + fh->f_io_array[j].length) - sstart;            
+            if (slen > mca_fbtl_posix_max_tmpbuf_size ) {
+                endindex = j-1;
+                break;
+            }
+        }
+        // Need to increment the value of endindex
+        // by one for the loop syntax to work correctly.
+        endindex++;
+
+        start = (size_t)fh->f_io_array[startindex].offset;
+        end   = (size_t)fh->f_io_array[endindex-1].offset + fh->f_io_array[endindex-1].length;
+        len   = end - start;
+        
+        if ( len > bufsize ) {
+            if ( NULL != temp_buf ) {
+                free ( temp_buf);
+            }
+            temp_buf = (char *) malloc ( len );
+            if ( NULL == temp_buf ) {
+                opal_output(1, "OUT OF MEMORY\n");
+                return OMPI_ERR_OUT_OF_RESOURCE;
+            }
+            bufsize = len;
+        }
+        
+        // Read the entire block.
+        ret = mca_fbtl_posix_lock ( &lock, fh, F_WRLCK, start, len, OMPIO_LOCK_ENTIRE_REGION ); 
+        if ( 0 < ret ) {
+            opal_output(1, "mca_fbtl_posix_pwritev_datasieving: error in mca_fbtl_posix_lock() ret=%d: %s",
+                        ret, strerror(errno));
+            /* Just in case some part of the lock worked */
+            mca_fbtl_posix_unlock ( &lock, fh);
+            free ( temp_buf);
+            return OMPI_ERROR;
+        }
+        
+        ret_code = pread (fh->fd, temp_buf, len, start);
+        if ( ret_code == -1 ) {
+            //opal_output(1, "mca_fbtl_posix_pwritev_datasieving: error in pwrite:%s", strerror(errno));
+            opal_output(1, "mca_fbtl_posix_pwritev_datasieving: error in pwrite:%s", strerror(errno));
+            /* Just in case some part of the lock worked */
+            mca_fbtl_posix_unlock ( &lock, fh);
+            free ( temp_buf);
+            return OMPI_ERROR;
+        }
+        
+        // Copy out the elements to write into temporary buffer.
+        size_t pos = 0;
+        size_t num_bytes;
+        size_t start_offset = (size_t) fh->f_io_array[startindex].offset;
+        for ( i = startindex ; i < endindex ; i++) {
+            pos = (size_t) fh->f_io_array[i].offset - start_offset;
+            num_bytes = fh->f_io_array[i].length;          
+            memcpy (temp_buf + pos, fh->f_io_array[i].memory_address, num_bytes);
+            bytes_written += num_bytes;            
+        }
+        ret_code = pwrite (fh->fd, temp_buf, len, start);
+        if ( ret_code == -1 ) {
+            opal_output(1, "mca_fbtl_posix_pwritev_datasieving: error in pwrite:%s", strerror(errno));
+            /* Just in case some part of the lock worked */
+            mca_fbtl_posix_unlock ( &lock, fh);
+            free ( temp_buf);
+            return OMPI_ERROR;
+        }
+                        
+        mca_fbtl_posix_unlock ( &lock, fh);
+        if ( ret_code == -1 ) {
+            opal_output(1, "mca_fbtl_posix_pwritev_datasieving: error in pwrite:%s", strerror(errno));
+            /* Just in case some part of the lock worked */
+            mca_fbtl_posix_unlock ( &lock, fh);
+            free ( temp_buf);
+            return OMPI_ERROR;
+        }
+        
+    }
+    
+    free ( temp_buf);
+    return bytes_written;
+}
+
+
+ssize_t mca_fbtl_posix_pwritev_generic (ompio_file_t *fh )
 {
     /*int *fp = NULL;*/
     int i, block = 1, ret;

ompi/mca/fcoll/dynamic_gen2/fcoll_dynamic_gen2_file_write_all.c

@@ -736,11 +736,15 @@ static int write_init (ompio_file_t *fh, int aggregator, mca_io_ompio_aggregator
         
 
     if ( aggregator == fh->f_rank && aggr_data->prev_num_io_entries) {
-        while ( aggr_data->prev_bytes_to_write > 0 ) {                    
+        while ( aggr_data->prev_bytes_to_write > 0 ) {
+            ssize_t tret;
             aggr_data->prev_bytes_to_write -= mca_fcoll_dynamic_gen2_split_iov_array (fh, aggr_data->prev_io_array, 
                                                                                       aggr_data->prev_num_io_entries, 
                                                                                       &last_array_pos, &last_pos );
-            if ( 0 >  fh->f_fbtl->fbtl_pwritev (fh)) {
+            fh->f_flags |= OMPIO_COLLECTIVE_OP;
+            tret = fh->f_fbtl->fbtl_pwritev (fh);
+            fh->f_flags &= ~OMPIO_COLLECTIVE_OP;            
+            if ( 0 > tret ) {
                 free ( aggr_data->prev_io_array);
                 opal_output (1, "dynamic_gen2_write_all: fbtl_pwritev failed\n");
                 ret = OMPI_ERROR;

ompi/mca/fcoll/vulcan/fcoll_vulcan_file_write_all.c

@@ -771,7 +771,9 @@ static int write_init (ompio_file_t *fh,
             }
         }
         else {
+            fh->f_flags |= OMPIO_COLLECTIVE_OP;
             ret_temp = fh->f_fbtl->fbtl_pwritev(fh);
+            fh->f_flags &= ~OMPIO_COLLECTIVE_OP;
             if(0 > ret_temp) {
                 opal_output (1, "vulcan_write_all: fbtl_pwritev failed\n");
                 ret = ret_temp;