[t:4502] Merged new Garbage Collection to main, one test, stat64-root-changes...

[t:4502] Merged new Garbage Collection to main, one test, stat64-root-changes fails, but just needs to be updated now that GC is removed from message application.

git-svn-id: file:///svn/toku/tokudb@40096 c7de825b-a66e-492c-adef-691d508d4ae1

newbrt/brt-internal.h

@@ -912,8 +912,6 @@ brt_leaf_apply_cmd_once (
     const BRT_MSG cmd,
     u_int32_t idx,
     LEAFENTRY le,
-    OMT snapshot_txnids,
-    OMT live_list_reverse,
     uint64_t *workdonep
     );
 
@@ -927,9 +925,7 @@ brt_leaf_put_cmd (
     BASEMENTNODE bn, 
     BRT_MSG cmd, 
     bool* made_change,
-    uint64_t *workdone,
-    OMT snapshot_txnids,
-    OMT live_list_reverse
+    uint64_t *workdone
     );
 
 void toku_apply_cmd_to_leaf(
@@ -939,9 +935,7 @@ void toku_apply_cmd_to_leaf(
     BRTNODE node, 
     BRT_MSG cmd, 
     bool *made_change, 
-    uint64_t *workdone, 
-    OMT snapshot_txnids, 
-    OMT live_list_reverse
+    uint64_t *workdone
     );
 
 // FIXME needs toku prefix
@@ -951,9 +945,7 @@ void brtnode_put_cmd (
     DESCRIPTOR desc,
     BRTNODE node, 
     BRT_MSG cmd, 
-    bool is_fresh, 
-    OMT snapshot_txnids, 
-    OMT live_list_reverse
+    bool is_fresh
     );
 
 void toku_reset_root_xid_that_created(BRT brt, TXNID new_root_xid_that_created);

newbrt/brt-test-helpers.c

@@ -143,9 +143,7 @@ int toku_testsetup_insert_to_leaf (BRT brt, BLOCKNUM blocknum, char *key, int ke
         &brt->h->descriptor,
         node,
         &cmd,
-        true, 
-        NULL, 
-        NULL
+        true
         );    
 
     toku_verify_or_set_counts(node);

newbrt/brt.c

@@ -1373,8 +1373,6 @@ brt_leaf_apply_cmd_once (
     const BRT_MSG cmd,
     u_int32_t idx,
     LEAFENTRY le,
-    OMT snapshot_txnids,
-    OMT live_list_reverse,
     uint64_t *workdone
     )
 // Effect: Apply cmd to leafentry (msn is ignored)
@@ -1397,18 +1395,19 @@ brt_leaf_apply_cmd_once (
     // That means le is guaranteed to not cause a sigsegv but it may point to a mempool that is 
     // no longer in use.  We'll have to release the old mempool later.
     {
-	int r = apply_msg_to_leafentry(cmd, le, &newsize, &new_le, bn->buffer, &bn->buffer_mempool, &maybe_free, snapshot_txnids, live_list_reverse, &numbytes_delta);
+	int r = apply_msg_to_leafentry(cmd, le, &newsize, &new_le, bn->buffer, &bn->buffer_mempool, &maybe_free, &numbytes_delta);
 	invariant(r==0);
     }
 
     if (new_le) assert(newsize == leafentry_disksize(new_le));
-
     if (le && new_le) {
 	bn->n_bytes_in_buffer -= oldsize;
 	bn->n_bytes_in_buffer += newsize;
 
-        // This mfree must occur after the mempool_malloc so that when the mempool is compressed everything is accounted for.
-        // But we must compute the size before doing the mempool mfree because otherwise the le pointer is no good.
+        // This mfree must occur after the mempool_malloc so that when
+        // the mempool is compressed everything is accounted for.  But
+        // we must compute the size before doing the mempool mfree
+        // because otherwise the le pointer is no good.
         toku_mempool_mfree(&bn->buffer_mempool, 0, oldsize); // Must pass 0, since le may be no good any more.
         
 	{ 
@@ -1467,8 +1466,6 @@ struct setval_extra_s {
     const DBT *key;
     u_int32_t idx;
     LEAFENTRY le;
-    OMT snapshot_txnids;
-    OMT live_list_reverse;
     bool made_change;
     uint64_t * workdone;  // set by brt_leaf_apply_cmd_once()
 };
@@ -1501,7 +1498,6 @@ static void setval_fun (const DBT *new_val, void *svextra_v) {
         }
         brt_leaf_apply_cmd_once(svextra->leafnode, svextra->bn, &msg,
                                 svextra->idx, svextra->le,
-                                svextra->snapshot_txnids, svextra->live_list_reverse,
                                 svextra->workdone);
         svextra->setval_r = 0;
     }
@@ -1513,7 +1509,7 @@ static void setval_fun (const DBT *new_val, void *svextra_v) {
 // would be to put a dummy msn in the messages created by setval_fun(), but preserving
 // the original msn seems cleaner and it preserves accountability at a lower layer.
 static int do_update(brt_update_func update_fun, DESCRIPTOR desc, BRTNODE leafnode, BASEMENTNODE bn, BRT_MSG cmd, int idx,
-                     LEAFENTRY le, OMT snapshot_txnids, OMT live_list_reverse, bool* made_change,
+                     LEAFENTRY le,  bool* made_change,
                      uint64_t * workdone) {
     LEAFENTRY le_for_update;
     DBT key;
@@ -1556,7 +1552,7 @@ static int do_update(brt_update_func update_fun, DESCRIPTOR desc, BRTNODE leafno
     }
 
     struct setval_extra_s setval_extra = {setval_tag, FALSE, 0, leafnode, bn, cmd->msn, cmd->xids,
-                                          keyp, idx, le_for_update, snapshot_txnids, live_list_reverse, 0, workdone};
+                                          keyp, idx, le_for_update, 0, workdone};
     // call handlerton's brt->update_fun(), which passes setval_extra to setval_fun()
     FAKE_DB(db, tmp_desc, desc);
     int r = update_fun(
@@ -1585,9 +1581,7 @@ brt_leaf_put_cmd (
     BASEMENTNODE bn, 
     BRT_MSG cmd, 
     bool* made_change,
-    uint64_t *workdone,
-    OMT snapshot_txnids,
-    OMT live_list_reverse
+    uint64_t *workdone
     )
 // Effect: 
 //   Put a cmd into a leaf.
@@ -1629,7 +1623,7 @@ brt_leaf_put_cmd (
 	    assert(r==0);
 	    storeddata=storeddatav;
 	}
-	brt_leaf_apply_cmd_once(leafnode, bn, cmd, idx, storeddata, snapshot_txnids, live_list_reverse, workdone);
+	brt_leaf_apply_cmd_once(leafnode, bn, cmd, idx, storeddata, workdone);
 
 	// if the insertion point is within a window of the right edge of
 	// the leaf then it is sequential
@@ -1661,7 +1655,7 @@ brt_leaf_put_cmd (
 	while (1) {
 	    u_int32_t num_leafentries_before = toku_omt_size(bn->buffer);
 
-	    brt_leaf_apply_cmd_once(leafnode, bn, cmd, idx, storeddata, snapshot_txnids, live_list_reverse, workdone);
+	    brt_leaf_apply_cmd_once(leafnode, bn, cmd, idx, storeddata, workdone);
 	    *made_change = 1;
 
 	    { 
@@ -1711,7 +1705,7 @@ brt_leaf_put_cmd (
 	    storeddata=storeddatav;
 	    int deleted = 0;
 	    if (!le_is_clean(storeddata)) { //If already clean, nothing to do.
-		brt_leaf_apply_cmd_once(leafnode, bn, cmd, idx, storeddata, snapshot_txnids, live_list_reverse, workdone);
+		brt_leaf_apply_cmd_once(leafnode, bn, cmd, idx, storeddata, workdone);
 		u_int32_t new_omt_size = toku_omt_size(bn->buffer);
 		if (new_omt_size != omt_size) {
 		    assert(new_omt_size+1 == omt_size);
@@ -1738,7 +1732,7 @@ brt_leaf_put_cmd (
 	    storeddata=storeddatav;
 	    int deleted = 0;
 	    if (le_has_xids(storeddata, cmd->xids)) {
-		brt_leaf_apply_cmd_once(leafnode, bn, cmd, idx, storeddata, snapshot_txnids, live_list_reverse, workdone);
+		brt_leaf_apply_cmd_once(leafnode, bn, cmd, idx, storeddata, workdone);
 		u_int32_t new_omt_size = toku_omt_size(bn->buffer);
 		if (new_omt_size != omt_size) {
 		    assert(new_omt_size+1 == omt_size);
@@ -1760,10 +1754,10 @@ brt_leaf_put_cmd (
 	r = toku_omt_find_zero(bn->buffer, toku_cmd_leafval_heaviside, &be,
 			       &storeddatav, &idx);
 	if (r==DB_NOTFOUND) {
-	    r = do_update(update_fun, desc, leafnode, bn, cmd, idx, NULL, snapshot_txnids, live_list_reverse, made_change, workdone);
+	    r = do_update(update_fun, desc, leafnode, bn, cmd, idx, NULL, made_change, workdone);
 	} else if (r==0) {
 	    storeddata=storeddatav;
-	    r = do_update(update_fun, desc, leafnode, bn, cmd, idx, storeddata, snapshot_txnids, live_list_reverse, made_change, workdone);
+	    r = do_update(update_fun, desc, leafnode, bn, cmd, idx, storeddata, made_change, workdone);
 	} // otherwise, a worse error, just return it
 	break;
     }
@@ -1775,7 +1769,7 @@ brt_leaf_put_cmd (
 	    r = toku_omt_fetch(bn->buffer, idx, &storeddatav);
 	    assert(r==0);
 	    storeddata=storeddatav;
-	    r = do_update(update_fun, desc, leafnode, bn, cmd, idx, storeddata, snapshot_txnids, live_list_reverse, made_change, workdone);
+	    r = do_update(update_fun, desc, leafnode, bn, cmd, idx, storeddata, made_change, workdone);
 	    // TODO(leif): This early return means get_leaf_reactivity()
 	    // and VERIFY_NODE() never get called.  Is this a problem?
 	    assert(r==0);
@@ -2104,6 +2098,126 @@ brt_handle_maybe_reactive_root (BRT brt, CACHEKEY *rootp, BRTNODE *nodep) {
     abort(); // cannot happen
 }
 
+
+// Garbage collect one leaf entry.
+static void
+brt_basement_node_gc_once(BASEMENTNODE bn,
+                          u_int32_t index,
+                          LEAFENTRY leaf_entry,
+                          OMT snapshot_xids,
+                          OMT live_list_reverse,
+                          STAT64INFO_S * delta)
+{
+    assert(leaf_entry);
+
+    // There is no point in running GC if there is only one committed
+    // leaf entry.
+    if (leaf_entry->type != LE_MVCC || leaf_entry->u.mvcc.num_cxrs <= 1) { // MAKE ACCESSOR
+        goto exit;
+    }
+
+    size_t oldsize = 0, newsize = 0;
+    LEAFENTRY new_leaf_entry = NULL;
+
+    // The mempool doesn't free itself.  When it allocates new memory,
+    // this pointer will be set to the older memory that must now be
+    // freed.
+    void * maybe_free = NULL;
+
+    // Cache the size of the leaf entry.
+    oldsize = leafentry_memsize(leaf_entry);
+    garbage_collect_leafentry(leaf_entry,
+                              &new_leaf_entry,
+                              &newsize,
+                              bn->buffer,
+                              &bn->buffer_mempool,
+                              &maybe_free,
+                              snapshot_xids,
+                              live_list_reverse);
+
+    // These will represent the number of bytes and rows changed as
+    // part of the garbage collection.
+    int64_t numbytes_delta = newsize - oldsize;
+    int64_t numrows_delta = 0;
+    if (new_leaf_entry) {
+        // If we have a new leaf entry, we must update the size of the
+        // memory object.
+        bn->n_bytes_in_buffer -= oldsize;
+        bn->n_bytes_in_buffer += newsize;
+        toku_mempool_mfree(&bn->buffer_mempool, 0, oldsize);
+        toku_omt_set_at(bn->buffer, new_leaf_entry, index);
+        numrows_delta = 0;
+    } else {
+        // Our garbage collection removed the leaf entry so we must
+        // remove it from the mempool.
+        brt_leaf_delete_leafentry (bn, index, leaf_entry);
+        numrows_delta = -1;
+    }
+
+    // If we created a new mempool buffer we must free the
+    // old/original buffer.
+    if (maybe_free) {
+        toku_free(maybe_free);
+    }
+
+    // Update stats.
+    bn->stat64_delta.numrows += numrows_delta;
+    bn->stat64_delta.numbytes += numbytes_delta;
+    delta->numrows += numrows_delta;
+    delta->numbytes += numbytes_delta;
+
+ exit:
+    return;
+}
+
+// Garbage collect all leaf entries for a given basement node.
+static void
+basement_node_gc_all_les(BASEMENTNODE bn,
+                         OMT snapshot_xids,
+                         OMT live_list_reverse,
+                         STAT64INFO_S * delta)
+{
+    int r = 0;
+    u_int32_t index = 0;
+    u_int32_t num_leafentries_before;
+    while (index < (num_leafentries_before = toku_omt_size(bn->buffer))) {
+        OMTVALUE storedatav = NULL;
+        LEAFENTRY leaf_entry;
+        r = toku_omt_fetch(bn->buffer, index, &storedatav);
+        assert(r == 0);
+        leaf_entry = storedatav;
+        brt_basement_node_gc_once(bn, index, leaf_entry, snapshot_xids, live_list_reverse, delta);
+        // Check if the leaf entry was deleted or not.
+        if (num_leafentries_before == toku_omt_size(bn->buffer)) {
+            ++index;
+        }
+    }
+}
+
+// Garbage collect all leaf entires.
+static void
+brt_leaf_gc_all_les(BRTNODE node,
+                    OMT snapshot_xids,
+                    OMT live_list_reverse)
+{
+    toku_assert_entire_node_in_memory(node);
+    assert(node->height == 0);
+    // Loop through each leaf entry, garbage collecting as we go.
+    for (int i = 0; i < node->n_children; ++i) {
+        // Perform the garbage collection.
+        BASEMENTNODE bn = BLB(node, i);
+        STAT64INFO_S delta;
+        delta.numrows = 0;
+        delta.numbytes = 0;
+        basement_node_gc_all_les(bn, snapshot_xids, live_list_reverse, &delta);
+        // Update the header stats, but only if the leaf node is
+        // dirty.
+        if (node->dirty) {
+            update_header_stats(&(node->h->in_memory_stats), &(delta));
+        }
+    }
+}
+
 int
 toku_bnc_flush_to_child(
     brt_compare_func compare_fun, 
@@ -2114,25 +2228,8 @@ toku_bnc_flush_to_child(
     BRTNODE child
     )
 {
-    assert(toku_fifo_n_entries(bnc->buffer)>0);
     assert(bnc);
-    OMT snapshot_txnids, live_list_reverse;
-    TOKULOGGER logger = toku_cachefile_logger(cf);
-    if (child->height == 0 && logger) {
-        toku_pthread_mutex_lock(&logger->txn_list_lock);
-        int r = toku_omt_clone_noptr(&snapshot_txnids, logger->snapshot_txnids);
-        assert_zero(r);
-        r = toku_omt_clone_pool(&live_list_reverse, logger->live_list_reverse, sizeof(XID_PAIR_S));
-        assert_zero(r);
-	size_t buffsize = bnc->n_bytes_in_buffer; 
-	STATUS_VALUE(BRT_MSG_BYTES_OUT) += buffsize;   // take advantage of surrounding mutex
-	STATUS_VALUE(BRT_MSG_BYTES_CURR) -= buffsize;  // may be misleading if there's a broadcast message in there
-	toku_pthread_mutex_unlock(&logger->txn_list_lock);
-    } else {
-        snapshot_txnids = NULL;
-        live_list_reverse = NULL;
-    }
-
+    assert(toku_fifo_n_entries(bnc->buffer)>0);
     FIFO_ITERATE(
         bnc->buffer, key, keylen, val, vallen, type, msn, xids, is_fresh,
         ({
@@ -2145,19 +2242,39 @@ toku_bnc_flush_to_child(
                 desc,
                 child, 
                 &brtcmd, 
-                is_fresh, 
-                snapshot_txnids, 
-                live_list_reverse
+                is_fresh
                 );
         }));
 
-    if (snapshot_txnids) {
+    // Run garbage collection, if we are a leaf entry.
+    TOKULOGGER logger = toku_cachefile_logger(cf);
+    if (child->height == 0 && logger) {
+        OMT snapshot_txnids = NULL;
+        OMT live_list_reverse = NULL;
+        toku_pthread_mutex_lock(&logger->txn_list_lock);
+        int r = toku_omt_clone_noptr(&snapshot_txnids,
+                                     logger->snapshot_txnids);
+        assert_zero(r);
+        r = toku_omt_clone_pool(&live_list_reverse, 
+                                logger->live_list_reverse,
+                                sizeof(XID_PAIR_S));
+        assert_zero(r);
+        // take advantage of surrounding mutex, update stats.
+	size_t buffsize = bnc->n_bytes_in_buffer;
+	STATUS_VALUE(BRT_MSG_BYTES_OUT) += buffsize;
+        // may be misleading if there's a broadcast message in there
+	STATUS_VALUE(BRT_MSG_BYTES_CURR) -= buffsize;
+	toku_pthread_mutex_unlock(&logger->txn_list_lock);
+
+        // Perform the garbage collection.
+        brt_leaf_gc_all_les(child, snapshot_txnids, live_list_reverse);
+
+        // Free the OMT's we used for garbage collecting.
         toku_omt_destroy(&snapshot_txnids);
-    }
-    if (live_list_reverse) {
         toku_omt_free_items_pool(live_list_reverse);
         toku_omt_destroy(&live_list_reverse);
     }
+
     return 0;
 }
 
@@ -2180,9 +2297,7 @@ brtnode_put_cmd (
     DESCRIPTOR desc,
     BRTNODE node, 
     BRT_MSG cmd, 
-    bool is_fresh, 
-    OMT snapshot_txnids, 
-    OMT live_list_reverse
+    bool is_fresh
     )
 // Effect: Push CMD into the subtree rooted at NODE.
 //   If NODE is a leaf, then
@@ -2207,9 +2322,7 @@ brtnode_put_cmd (
             node, 
             cmd, 
             &made_change, 
-            &workdone, 
-            snapshot_txnids, 
-            live_list_reverse
+            &workdone
             );
     } else {
         brt_nonleaf_put_cmd(compare_fun, desc, node, cmd, is_fresh);
@@ -2230,9 +2343,7 @@ void toku_apply_cmd_to_leaf(
     BRTNODE node, 
     BRT_MSG cmd, 
     bool *made_change, 
-    uint64_t *workdone, 
-    OMT snapshot_txnids, 
-    OMT live_list_reverse
+    uint64_t *workdone
     ) 
 {
     VERIFY_NODE(t, node);
@@ -2274,9 +2385,7 @@ void toku_apply_cmd_to_leaf(
                              BLB(node, childnum),
                              cmd,
                              made_change,
-                             workdone,
-                             snapshot_txnids,
-                             live_list_reverse);
+                             workdone);
         } else {
             STATUS_VALUE(BRT_MSN_DISCARDS)++;
         }
@@ -2293,9 +2402,7 @@ void toku_apply_cmd_to_leaf(
                                  BLB(node, childnum),
                                  cmd,
                                  &bn_made_change,
-                                 workdone,
-                                 snapshot_txnids,
-                                 live_list_reverse);
+                                 workdone);
                 if (bn_made_change) *made_change = 1;
             } else {
                 STATUS_VALUE(BRT_MSN_DISCARDS)++;
@@ -2314,9 +2421,6 @@ static void push_something_at_root (BRT brt, BRTNODE *nodep, BRT_MSG cmd)
 {
     BRTNODE node = *nodep;
     toku_assert_entire_node_in_memory(node);
-    TOKULOGGER logger = toku_cachefile_logger(brt->cf);
-    OMT snapshot_txnids = logger ? logger->snapshot_txnids : NULL;
-    OMT live_list_reverse = logger ? logger->live_list_reverse : NULL;
     MSN cmd_msn = cmd->msn;
     invariant(cmd_msn.msn > node->max_msn_applied_to_node_on_disk.msn);
     brtnode_put_cmd(
@@ -2325,9 +2429,7 @@ static void push_something_at_root (BRT brt, BRTNODE *nodep, BRT_MSG cmd)
         &brt->h->descriptor,
         node,
         cmd,
-        true,
-        snapshot_txnids,
-        live_list_reverse
+        true
         );
     //
     // assumption is that brtnode_put_cmd will
@@ -4470,7 +4572,7 @@ fifo_offset_msn_cmp(void *extrap, const void *va, const void *vb)
  * basement node.
  */
 static void
-do_brt_leaf_put_cmd(BRT t, BRTNODE leafnode, BASEMENTNODE bn, BRTNODE ancestor, int childnum, OMT snapshot_txnids, OMT live_list_reverse, const struct fifo_entry *entry)
+do_brt_leaf_put_cmd(BRT t, BRTNODE leafnode, BASEMENTNODE bn, BRTNODE ancestor, int childnum, const struct fifo_entry *entry)
 {
     // The messages are being iterated over in (key,msn) order or just in
     // msn order, so all the messages for one key, from one buffer, are in
@@ -4490,7 +4592,7 @@ do_brt_leaf_put_cmd(BRT t, BRTNODE leafnode, BASEMENTNODE bn, BRTNODE ancestor,
         DBT hv;
         BRT_MSG_S brtcmd = { type, msn, xids, .u.id = { &hk, toku_fill_dbt(&hv, val, vallen) } };
         bool made_change;
-        brt_leaf_put_cmd(t->compare_fun, t->update_fun, &t->h->descriptor, leafnode, bn, &brtcmd, &made_change, &BP_WORKDONE(ancestor, childnum), snapshot_txnids, live_list_reverse);
+        brt_leaf_put_cmd(t->compare_fun, t->update_fun, &t->h->descriptor, leafnode, bn, &brtcmd, &made_change, &BP_WORKDONE(ancestor, childnum));
     } else {
         STATUS_VALUE(BRT_MSN_DISCARDS)++;
     }
@@ -4502,8 +4604,6 @@ struct iterate_do_brt_leaf_put_cmd_extra {
     BASEMENTNODE bn;
     BRTNODE ancestor;
     int childnum;
-    OMT snapshot_txnids;
-    OMT live_list_reverse;
 };
 
 static int
@@ -4513,7 +4613,7 @@ iterate_do_brt_leaf_put_cmd(OMTVALUE v, u_int32_t UU(idx), void *extrap)
     const long offset = (long) v;
     NONLEAF_CHILDINFO bnc = BNC(e->ancestor, e->childnum);
     const struct fifo_entry *entry = toku_fifo_get_entry(bnc->buffer, offset);
-    do_brt_leaf_put_cmd(e->t, e->leafnode, e->bn, e->ancestor, e->childnum, e->snapshot_txnids, e->live_list_reverse, entry);
+    do_brt_leaf_put_cmd(e->t, e->leafnode, e->bn, e->ancestor, e->childnum, entry);
     return 0;
 }
 
@@ -4652,15 +4752,6 @@ bnc_apply_messages_to_basement_node(
     u_int32_t fresh_lbi, fresh_ube;
     find_bounds_within_message_tree(&t->h->descriptor, t->compare_fun, bnc->fresh_message_tree, bnc->buffer, bounds, &fresh_lbi, &fresh_ube);
 
-    // TOKULOGGER logger = toku_cachefile_logger(t->cf);
-    // Experimentally setting these to NULL to disable garbage collection
-    // on the query path, to let us remove the ydb lock from queries
-    // (ticket 4462).  We will need to find another solution in order to
-    // put this in production (probably either clone them or change when
-    // we do garbage collection, maybe on a background thread).
-    OMT snapshot_txnids = NULL;  //logger ? logger->snapshot_txnids : NULL;
-    OMT live_list_reverse = NULL;  //logger ? logger->live_list_reverse : NULL;
-
     // We now know where all the messages we must apply are, so one of the
     // following 4 cases will do the application, depending on which of
     // the lists contains relevant messages:
@@ -4697,20 +4788,20 @@ bnc_apply_messages_to_basement_node(
         // Apply the messages in MSN order.
         for (int i = 0; i < buffer_size; ++i) {
             const struct fifo_entry *entry = toku_fifo_get_entry(bnc->buffer, offsets[i]);
-            do_brt_leaf_put_cmd(t, leafnode, bn, ancestor, childnum, snapshot_txnids, live_list_reverse, entry);
+            do_brt_leaf_put_cmd(t, leafnode, bn, ancestor, childnum, entry);
         }
 
         toku_free(offsets);
     } else if (stale_lbi == stale_ube) {
         // No stale messages to apply, we just apply fresh messages.
-        struct iterate_do_brt_leaf_put_cmd_extra iter_extra = { .t = t, .leafnode = leafnode, .bn = bn, .ancestor = ancestor, .childnum = childnum, .snapshot_txnids = snapshot_txnids, .live_list_reverse = live_list_reverse };
+        struct iterate_do_brt_leaf_put_cmd_extra iter_extra = { .t = t, .leafnode = leafnode, .bn = bn, .ancestor = ancestor, .childnum = childnum };
 
         r = toku_omt_iterate_on_range(bnc->fresh_message_tree, fresh_lbi, fresh_ube, iterate_do_brt_leaf_put_cmd, &iter_extra);
         assert_zero(r);
     } else if (fresh_lbi == fresh_ube) {
         // No fresh messages to apply, we just apply stale messages.
 
-        struct iterate_do_brt_leaf_put_cmd_extra iter_extra = { .t = t, .leafnode = leafnode, .bn = bn, .ancestor = ancestor, .childnum = childnum, .snapshot_txnids = snapshot_txnids, .live_list_reverse = live_list_reverse };
+        struct iterate_do_brt_leaf_put_cmd_extra iter_extra = { .t = t, .leafnode = leafnode, .bn = bn, .ancestor = ancestor, .childnum = childnum };
 
         r = toku_omt_iterate_on_range(bnc->stale_message_tree, stale_lbi, stale_ube, iterate_do_brt_leaf_put_cmd, &iter_extra);
         assert_zero(r);
@@ -4742,7 +4833,7 @@ bnc_apply_messages_to_basement_node(
                 // but a smaller MSN.  We'll apply it, then get the next
                 // stale message into stale_i and stale_v.
                 const struct fifo_entry *stale_entry = toku_fifo_get_entry(bnc->buffer, stale_offset);
-                do_brt_leaf_put_cmd(t, leafnode, bn, ancestor, childnum, snapshot_txnids, live_list_reverse, stale_entry);
+                do_brt_leaf_put_cmd(t, leafnode, bn, ancestor, childnum, stale_entry);
                 stale_i++;
                 if (stale_i != stale_ube) {
                     invariant(stale_i < stale_ube);
@@ -4755,7 +4846,7 @@ bnc_apply_messages_to_basement_node(
                 // but a smaller MSN.  We'll apply it, then get the next
                 // fresh message into fresh_i and fresh_v.
                 const struct fifo_entry *fresh_entry = toku_fifo_get_entry(bnc->buffer, fresh_offset);
-                do_brt_leaf_put_cmd(t, leafnode, bn, ancestor, childnum, snapshot_txnids, live_list_reverse, fresh_entry);
+                do_brt_leaf_put_cmd(t, leafnode, bn, ancestor, childnum, fresh_entry);
                 fresh_i++;
                 if (fresh_i != fresh_ube) {
                     invariant(fresh_i < fresh_ube);
@@ -4774,7 +4865,7 @@ bnc_apply_messages_to_basement_node(
         while (stale_i < stale_ube) {
             const long stale_offset = (long) stale_v;
             const struct fifo_entry *stale_entry = toku_fifo_get_entry(bnc->buffer, stale_offset);
-            do_brt_leaf_put_cmd(t, leafnode, bn, ancestor, childnum, snapshot_txnids, live_list_reverse, stale_entry);
+            do_brt_leaf_put_cmd(t, leafnode, bn, ancestor, childnum, stale_entry);
             stale_i++;
             if (stale_i != stale_ube) {
                 r = toku_omt_fetch(bnc->stale_message_tree, stale_i, &stale_v);
@@ -4786,7 +4877,7 @@ bnc_apply_messages_to_basement_node(
         while (fresh_i < fresh_ube) {
             const long fresh_offset = (long) fresh_v;
             const struct fifo_entry *fresh_entry = toku_fifo_get_entry(bnc->buffer, fresh_offset);
-            do_brt_leaf_put_cmd(t, leafnode, bn, ancestor, childnum, snapshot_txnids, live_list_reverse, fresh_entry);
+            do_brt_leaf_put_cmd(t, leafnode, bn, ancestor, childnum, fresh_entry);
             fresh_i++;
             if (fresh_i != fresh_ube) {
                 r = toku_omt_fetch(bnc->fresh_message_tree, fresh_i, &fresh_v);

newbrt/brtloader.c

@@ -2788,7 +2788,7 @@ static void add_pair_to_leafnode (struct leaf_buf *lbuf, unsigned char *key, int
     DBT theval = { .data = val, .size = vallen };
     BRT_MSG_S cmd = { BRT_INSERT, ZERO_MSN, lbuf->xids, .u.id = { &thekey, &theval } };
     uint64_t workdone=0;
-    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode,0), &cmd, idx, NULL, NULL, NULL, &workdone);
+    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode,0), &cmd, idx, NULL, &workdone);
 }
 
 static int write_literal(struct dbout *out, void*data,  size_t len) {

newbrt/tests/make-tree.c

@@ -39,7 +39,7 @@ append_leaf(BRTNODE leafnode, void *key, size_t keylen, void *val, size_t vallen
 
     // apply an insert to the leaf node
     BRT_MSG_S cmd = { BRT_INSERT, msn, xids_get_root_xids(), .u.id = { &thekey, &theval } };
-    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode,0), &cmd, idx, NULL, NULL, NULL, NULL);
+    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode,0), &cmd, idx, NULL, NULL);
 
     leafnode->max_msn_applied_to_node_on_disk = msn;
 

newbrt/tests/msnfilter.c

@@ -48,7 +48,7 @@ append_leaf(BRT brt, BRTNODE leafnode, void *key, size_t keylen, void *val, size
 
     bool made_change;
     u_int64_t workdone=0;
-    toku_apply_cmd_to_leaf(brt->compare_fun, brt->update_fun, &brt->h->descriptor, leafnode, &cmd, &made_change, &workdone, NULL, NULL);
+    toku_apply_cmd_to_leaf(brt->compare_fun, brt->update_fun, &brt->h->descriptor, leafnode, &cmd, &made_change, &workdone);
     {
 	int r = toku_brt_lookup(brt, &thekey, lookup_checkf, &pair);
 	assert(r==0);
@@ -56,7 +56,7 @@ append_leaf(BRT brt, BRTNODE leafnode, void *key, size_t keylen, void *val, size
     }
 
     BRT_MSG_S badcmd = { BRT_INSERT, msn, xids_get_root_xids(), .u.id = { &thekey, &badval } };
-    toku_apply_cmd_to_leaf(brt->compare_fun, brt->update_fun, &brt->h->descriptor, leafnode, &badcmd, &made_change, &workdone, NULL, NULL);
+    toku_apply_cmd_to_leaf(brt->compare_fun, brt->update_fun, &brt->h->descriptor, leafnode, &badcmd, &made_change, &workdone);
 
     
     // message should be rejected for duplicate msn, row should still have original val
@@ -69,7 +69,7 @@ append_leaf(BRT brt, BRTNODE leafnode, void *key, size_t keylen, void *val, size
     // now verify that message with proper msn gets through
     msn = next_dummymsn();
     BRT_MSG_S cmd2 = { BRT_INSERT, msn, xids_get_root_xids(), .u.id = { &thekey, &val2 } };
-    toku_apply_cmd_to_leaf(brt->compare_fun, brt->update_fun, &brt->h->descriptor, leafnode, &cmd2, &made_change, &workdone, NULL, NULL);
+    toku_apply_cmd_to_leaf(brt->compare_fun, brt->update_fun, &brt->h->descriptor, leafnode, &cmd2, &made_change, &workdone);
     
     // message should be accepted, val should have new value
     {
@@ -81,7 +81,7 @@ append_leaf(BRT brt, BRTNODE leafnode, void *key, size_t keylen, void *val, size
     // now verify that message with lesser (older) msn is rejected
     msn.msn = msn.msn - 10;
     BRT_MSG_S cmd3 = { BRT_INSERT, msn, xids_get_root_xids(), .u.id = { &thekey, &badval } };
-    toku_apply_cmd_to_leaf(brt->compare_fun, brt->update_fun, &brt->h->descriptor, leafnode, &cmd3, &made_change, &workdone, NULL, NULL);
+    toku_apply_cmd_to_leaf(brt->compare_fun, brt->update_fun, &brt->h->descriptor, leafnode, &cmd3, &made_change, &workdone);
     
     // message should be rejected, val should still have value in pair2
     {

newbrt/tests/orthopush-flush.c

@@ -125,10 +125,10 @@ insert_random_message_to_leaf(BRT t, BRTNODE leafnode, BASEMENTNODE blb, LEAFENT
     msg.u.id.val = valdbt;
     size_t memsize;
     int64_t numbytes;
-    int r = apply_msg_to_leafentry(&msg, NULL, &memsize, save, NULL, NULL, NULL, NULL, NULL, &numbytes);
+    int r = apply_msg_to_leafentry(&msg, NULL, &memsize, save, NULL, NULL, NULL, &numbytes);
     assert_zero(r);
     bool made_change;
-    brt_leaf_put_cmd(t->compare_fun, t->update_fun, NULL, leafnode, blb, &msg, &made_change, NULL, NULL, NULL);
+    brt_leaf_put_cmd(t->compare_fun, t->update_fun, NULL, leafnode, blb, &msg, &made_change, NULL);
     if (msn.msn > blb->max_msn_applied.msn) {
         blb->max_msn_applied = msn;
     }
@@ -167,14 +167,14 @@ insert_same_message_to_leaves(BRT t, BRTNODE child1, BASEMENTNODE blb1, BRTNODE
     msg.u.id.val = valdbt;
     size_t memsize;
     int64_t numbytes;
-    int r = apply_msg_to_leafentry(&msg, NULL, &memsize, save, NULL, NULL, NULL, NULL, NULL, &numbytes);
+    int r = apply_msg_to_leafentry(&msg, NULL, &memsize, save, NULL, NULL, NULL, &numbytes);
     assert_zero(r);
     bool made_change;
-    brt_leaf_put_cmd(t->compare_fun, t->update_fun, NULL, child1, blb1, &msg, &made_change, NULL, NULL, NULL);
+    brt_leaf_put_cmd(t->compare_fun, t->update_fun, NULL, child1, blb1, &msg, &made_change, NULL);
     if (msn.msn > blb1->max_msn_applied.msn) {
         blb1->max_msn_applied = msn;
     }
-    brt_leaf_put_cmd(t->compare_fun, t->update_fun, NULL, child2, blb2, &msg, &made_change, NULL, NULL, NULL);
+    brt_leaf_put_cmd(t->compare_fun, t->update_fun, NULL, child2, blb2, &msg, &made_change, NULL);
     if (msn.msn > blb2->max_msn_applied.msn) {
         blb2->max_msn_applied = msn;
     }
@@ -587,7 +587,7 @@ flush_to_leaf(BRT t, bool make_leaf_up_to_date, bool use_flush) {
         for (i = 0; i < num_parent_messages; ++i) {
             if (!parent_messages_is_fresh[i]) {
                 bool made_change;
-                toku_apply_cmd_to_leaf(t->compare_fun, t->update_fun, &t->h->descriptor, child, parent_messages[i], &made_change, NULL, NULL, NULL);
+                toku_apply_cmd_to_leaf(t->compare_fun, t->update_fun, &t->h->descriptor, child, parent_messages[i], &made_change, NULL);
             }
         }
         for (i = 0; i < 8; ++i) {
@@ -811,7 +811,7 @@ flush_to_leaf_with_keyrange(BRT t, bool make_leaf_up_to_date) {
             if (dummy_cmp(NULL, parent_messages[i]->u.id.key, &childkeys[7]) <= 0 &&
                 !parent_messages_is_fresh[i]) {
                 bool made_change;
-                toku_apply_cmd_to_leaf(t->compare_fun, t->update_fun, &t->h->descriptor, child, parent_messages[i], &made_change, NULL, NULL, NULL);
+                toku_apply_cmd_to_leaf(t->compare_fun, t->update_fun, &t->h->descriptor, child, parent_messages[i], &made_change, NULL);
             }
         }
         for (i = 0; i < 8; ++i) {
@@ -998,8 +998,8 @@ compare_apply_and_flush(BRT t, bool make_leaf_up_to_date) {
         for (i = 0; i < num_parent_messages; ++i) {
             if (!parent_messages_is_fresh[i]) {
                 bool made_change;
-                toku_apply_cmd_to_leaf(t->compare_fun, t->update_fun, &t->h->descriptor, child1, parent_messages[i], &made_change, NULL, NULL, NULL);
-                toku_apply_cmd_to_leaf(t->compare_fun, t->update_fun, &t->h->descriptor, child2, parent_messages[i], &made_change, NULL, NULL, NULL);
+                toku_apply_cmd_to_leaf(t->compare_fun, t->update_fun, &t->h->descriptor, child1, parent_messages[i], &made_change, NULL);
+                toku_apply_cmd_to_leaf(t->compare_fun, t->update_fun, &t->h->descriptor, child2, parent_messages[i], &made_change, NULL);
             }
         }
         for (i = 0; i < 8; ++i) {

newbrt/tests/test-leafentry-nested.c

@@ -398,7 +398,7 @@ test_le_apply(ULE ule_initial, BRT_MSG msg, ULE ule_expected) {
                                le_initial,
                                &result_memsize,
                                &le_result,
-                               NULL, NULL, NULL, 
+                               NULL, 
                                NULL, NULL, &ignoreme);
     CKERR(r);
 

newbrt/tests/verify-bad-msn.c

@@ -42,7 +42,7 @@ append_leaf(BRTNODE leafnode, void *key, size_t keylen, void *val, size_t vallen
 
     // apply an insert to the leaf node
     BRT_MSG_S cmd = { BRT_INSERT, msn, xids_get_root_xids(), .u.id = { &thekey, &theval } };
-    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL, NULL, NULL);
+    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL);
 
     // Create bad tree (don't do following):
     // leafnode->max_msn_applied_to_node = msn;

newbrt/tests/verify-bad-pivots.c

@@ -30,7 +30,7 @@ append_leaf(BRTNODE leafnode, void *key, size_t keylen, void *val, size_t vallen
     // apply an insert to the leaf node
     MSN msn = next_dummymsn();
     BRT_MSG_S cmd = { BRT_INSERT, msn, xids_get_root_xids(), .u.id = { &thekey, &theval } };
-    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL, NULL, NULL);
+    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL);
 
     // dont forget to dirty the node
     leafnode->dirty = 1;

newbrt/tests/verify-dup-in-leaf.c

@@ -31,7 +31,7 @@ append_leaf(BRTNODE leafnode, void *key, size_t keylen, void *val, size_t vallen
     // apply an insert to the leaf node
     MSN msn = next_dummymsn();
     BRT_MSG_S cmd = { BRT_INSERT, msn, xids_get_root_xids(), .u.id = { &thekey, &theval } };
-    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL, NULL, NULL);
+    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL);
 
     // dont forget to dirty the node
     leafnode->dirty = 1;

newbrt/tests/verify-dup-pivots.c

@@ -30,7 +30,7 @@ append_leaf(BRTNODE leafnode, void *key, size_t keylen, void *val, size_t vallen
     // apply an insert to the leaf node
     MSN msn = next_dummymsn();
     BRT_MSG_S cmd = { BRT_INSERT, msn, xids_get_root_xids(), .u.id = { &thekey, &theval } };
-    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL, NULL, NULL);
+    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL);
 
     // dont forget to dirty the node
     leafnode->dirty = 1;

newbrt/tests/verify-misrouted-msgs.c

@@ -31,7 +31,7 @@ append_leaf(BRTNODE leafnode, void *key, size_t keylen, void *val, size_t vallen
     // apply an insert to the leaf node
     MSN msn = next_dummymsn();
     BRT_MSG_S cmd = { BRT_INSERT, msn, xids_get_root_xids(), .u.id = { &thekey, &theval } };
-    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode,0), &cmd, idx, NULL, NULL, NULL, NULL);
+    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode,0), &cmd, idx, NULL, NULL);
 
     // dont forget to dirty the node
     leafnode->dirty = 1;

newbrt/tests/verify-unsorted-leaf.c

@@ -31,7 +31,7 @@ append_leaf(BRTNODE leafnode, void *key, size_t keylen, void *val, size_t vallen
     // apply an insert to the leaf node
     MSN msn = next_dummymsn();
     BRT_MSG_S cmd = { BRT_INSERT, msn, xids_get_root_xids(), .u.id = { &thekey, &theval } };
-    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL, NULL, NULL);
+    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL);
 
     // dont forget to dirty the node
     leafnode->dirty = 1;

newbrt/tests/verify-unsorted-pivots.c

@@ -30,7 +30,7 @@ append_leaf(BRTNODE leafnode, void *key, size_t keylen, void *val, size_t vallen
     // apply an insert to the leaf node
     MSN msn = next_dummymsn();
     BRT_MSG_S cmd = { BRT_INSERT, msn, xids_get_root_xids(), .u.id = { &thekey, &theval } };
-    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL, NULL, NULL);
+    brt_leaf_apply_cmd_once(leafnode, BLB(leafnode, 0), &cmd, idx, NULL, NULL);
 
     // dont forget to dirty the node
     leafnode->dirty = 1;

newbrt/ule.c

@@ -336,8 +336,6 @@ apply_msg_to_leafentry(BRT_MSG   msg,		// message to apply to leafentry
 		       OMT omt, 
 		       struct mempool *mp, 
 		       void **maybe_free,
-                       OMT snapshot_xids,
-                       OMT live_list_reverse,
                        int64_t * numbytes_delta_p) {  // change in total size of key and val, not including any overhead
     ULE_S ule;
     int rval;
@@ -351,9 +349,6 @@ apply_msg_to_leafentry(BRT_MSG   msg,		// message to apply to leafentry
 	oldnumbytes = ule_get_innermost_numbytes(&ule);
     }
     msg_modify_ule(&ule, msg);          // modify unpacked leafentry
-    if (snapshot_xids && live_list_reverse) {
-        garbage_collection(&ule, snapshot_xids, live_list_reverse);
-    }
     rval = le_pack(&ule,                // create packed leafentry
 		   new_leafentry_memorysize, 
 		   new_leafentry_p,
@@ -368,6 +363,49 @@ apply_msg_to_leafentry(BRT_MSG   msg,		// message to apply to leafentry
 }
 
 
+// Garbage collect one leaf entry, using the given OMT's.
+// Parameters:
+// -- old_leaf_entry : the leaf we intend to clean up through garbage
+// collecting.
+// -- new_leaf_entry (OUTPUT) : a pointer to the leaf entry after
+// garbage collection.
+// -- new_leaf_entry_memory_size : after this call, our leaf entry
+// should be empty or smaller.  This number represents that and is
+// used in a previous call to truncate the existing size.
+// -- omt : the memory where our leaf entry resides.
+// -- mp : our memory pool.
+// -- maybe_free (OUTPUT) : in a previous call, we may be able to free
+// the memory completely, if we removed the leaf entry.
+// -- snapshot_xids : we use these in memory transaction ids to
+// determine what to garbage collect.
+// -- live_list_reverse : list of in memory active transactions.
+// NOTE: it is not a good idea to garbage collect a leaf
+// entry with only one committed value.
+int
+garbage_collect_leafentry(LEAFENTRY old_leaf_entry,
+                          LEAFENTRY *new_leaf_entry,
+                          size_t *new_leaf_entry_memory_size,
+                          OMT omt,
+                          struct mempool *mp,
+                          void **maybe_free,
+                          OMT snapshot_xids,
+                          OMT live_list_reverse) {
+    int r = 0;
+    ULE_S ule;
+    le_unpack(&ule, old_leaf_entry);
+    assert(snapshot_xids);
+    assert(live_list_reverse);
+    garbage_collection(&ule, snapshot_xids, live_list_reverse);
+    r = le_pack(&ule,
+                new_leaf_entry_memory_size,
+                new_leaf_entry,
+                omt,
+                mp,
+                maybe_free);
+    assert(r == 0);
+    ule_cleanup(&ule);
+    return r;
+}
 
 /////////////////////////////////////////////////////////////////////////////////
 // This layer of abstraction (msg_xxx)

newbrt/ule.h

@@ -59,10 +59,16 @@ int apply_msg_to_leafentry(BRT_MSG   msg,
 			   OMT omt, 
 			   struct mempool *mp, 
 			   void **maybe_free,
-                           OMT snapshot_xids,
-                           OMT live_list_reverse,
                            int64_t * numbytes_delta_p);
 
+int garbage_collect_leafentry(LEAFENTRY old_leaf_entry,
+                              LEAFENTRY *new_leaf_entry,
+                              size_t *new_leaf_entry_memory_size,
+                              OMT omt,
+                              struct mempool *mp,
+                              void **maybe_free,
+                              OMT snapshot_xids,
+                              OMT live_list_reverse);
 
 TXNID toku_get_youngest_live_list_txnid_for(TXNID xc, OMT live_list_reverse);