Backport PR #55518 on branch 2.1.x (CoW: Use exponential backoff when clearing dead references)

doc/source/whatsnew/v2.1.2.rst

@@ -17,6 +17,7 @@ Fixed regressions
 - Fixed regression in :meth:`DataFrame.join` where result has missing values and dtype is arrow backed string (:issue:`55348`)
 - Fixed regression in :meth:`DataFrame.resample` which was extrapolating back to ``origin`` when ``origin`` was outside its bounds (:issue:`55064`)
 - Fixed regression in :meth:`DataFrame.sort_index` which was not sorting correctly when the index was a sliced :class:`MultiIndex` (:issue:`55379`)
+- Fixed performance regression with wide DataFrames, typically involving methods where all columns were accessed individually (:issue:`55256`, :issue:`55245`)
 
 .. ---------------------------------------------------------------------------
 .. _whatsnew_212.bug_fixes:

pandas/_libs/internals.pyx

@@ -944,17 +944,29 @@ cdef class BlockValuesRefs:
     """
     cdef:
         public list referenced_blocks
+        public int clear_counter
 
     def __cinit__(self, blk: SharedBlock | None = None) -> None:
         if blk is not None:
             self.referenced_blocks = [weakref.ref(blk)]
         else:
             self.referenced_blocks = []
-
-    def _clear_dead_references(self) -> None:
-        self.referenced_blocks = [
-            ref for ref in self.referenced_blocks if ref() is not None
-        ]
+        self.clear_counter = 500  # set reasonably high
+
+    def _clear_dead_references(self, force=False) -> None:
+        # Use exponential backoff to decide when we want to clear references
+        # if force=False. Clearing for every insertion causes slowdowns if
+        # all these objects stay alive, e.g. df.items() for wide DataFrames
+        # see GH#55245 and GH#55008
+        if force or len(self.referenced_blocks) > self.clear_counter:
+            self.referenced_blocks = [
+                ref for ref in self.referenced_blocks if ref() is not None
+            ]
+            nr_of_refs = len(self.referenced_blocks)
+            if nr_of_refs < self.clear_counter // 2:
+                self.clear_counter = max(self.clear_counter // 2, 500)
+            elif nr_of_refs > self.clear_counter:
+                self.clear_counter = max(self.clear_counter * 2, nr_of_refs)
 
     def add_reference(self, blk: SharedBlock) -> None:
         """Adds a new reference to our reference collection.
@@ -988,6 +1000,6 @@ cdef class BlockValuesRefs:
         -------
         bool
         """
-        self._clear_dead_references()
+        self._clear_dead_references(force=True)
         # Checking for more references than block pointing to itself
         return len(self.referenced_blocks) > 1

pandas/tests/copy_view/test_internals.py

@@ -119,3 +119,33 @@ def test_iset_splits_blocks_inplace(using_copy_on_write, locs, arr, dtype):
     else:
         for col in df.columns:
             assert not np.shares_memory(get_array(df, col), get_array(df2, col))
+
+
+def test_exponential_backoff():
+    # GH#55518
+    df = DataFrame({"a": [1, 2, 3]})
+    for i in range(490):
+        df.copy(deep=False)
+
+    assert len(df._mgr.blocks[0].refs.referenced_blocks) == 491
+
+    df = DataFrame({"a": [1, 2, 3]})
+    dfs = [df.copy(deep=False) for i in range(510)]
+
+    for i in range(20):
+        df.copy(deep=False)
+    assert len(df._mgr.blocks[0].refs.referenced_blocks) == 531
+    assert df._mgr.blocks[0].refs.clear_counter == 1000
+
+    for i in range(500):
+        df.copy(deep=False)
+
+    # Don't reduce since we still have over 500 objects alive
+    assert df._mgr.blocks[0].refs.clear_counter == 1000
+
+    dfs = dfs[:300]
+    for i in range(500):
+        df.copy(deep=False)
+
+    # Reduce since there are less than 500 objects alive
+    assert df._mgr.blocks[0].refs.clear_counter == 500