[SPARK-4897] [PySpark] Python 3 support

This PR update PySpark to support Python 3 (tested with 3.4).

Known issue: unpickle array from Pyrolite is broken in Python 3, those tests are skipped.

TODO: ec2/spark-ec2.py is not fully tested with python3.

Author: Davies Liu <davies@databricks.com>
Author: twneale <twneale@gmail.com>
Author: Josh Rosen <joshrosen@databricks.com>

Closes #5173 from davies/python3 and squashes the following commits:

d7d6323 [Davies Liu] fix tests
6c52a98 [Davies Liu] fix mllib test
99e334f [Davies Liu] update timeout
b716610 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
cafd5ec [Davies Liu] adddress comments from @mengxr
bf225d7 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
179fc8d [Davies Liu] tuning flaky tests
8c8b957 [Davies Liu] fix ResourceWarning in Python 3
5c57c95 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
4006829 [Davies Liu] fix test
2fc0066 [Davies Liu] add python3 path
71535e9 [Davies Liu] fix xrange and divide
5a55ab4 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
125f12c [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
ed498c8 [Davies Liu] fix compatibility with python 3
820e649 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
e8ce8c9 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
ad7c374 [Davies Liu] fix mllib test and warning
ef1fc2f [Davies Liu] fix tests
4eee14a [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
20112ff [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
59bb492 [Davies Liu] fix tests
1da268c [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
ca0fdd3 [Davies Liu] fix code style
9563a15 [Davies Liu] add imap back for python 2
0b1ec04 [Davies Liu] make python examples work with Python 3
d2fd566 [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
a716d34 [Davies Liu] test with python 3.4
f1700e8 [Davies Liu] fix test in python3
671b1db [Davies Liu] fix test in python3
692ff47 [Davies Liu] fix flaky test
7b9699f [Davies Liu] invalidate import cache for Python 3.3+
9c58497 [Davies Liu] fix kill worker
309bfbf [Davies Liu] keep compatibility
5707476 [Davies Liu] cleanup, fix hash of string in 3.3+
8662d5b [Davies Liu] Merge branch 'master' of github.com:apache/spark into python3
f53e1f0 [Davies Liu] fix tests
70b6b73 [Davies Liu] compile ec2/spark_ec2.py in python 3
a39167e [Davies Liu] support customize class in __main__
814c77b [Davies Liu] run unittests with python 3
7f4476e [Davies Liu] mllib tests passed
d737924 [Davies Liu] pass ml tests
375ea17 [Davies Liu] SQL tests pass
6cc42a9 [Davies Liu] rename
431a8de [Davies Liu] streaming tests pass
78901a7 [Davies Liu] fix hash of serializer in Python 3
24b2f2e [Davies Liu] pass all RDD tests
35f48fe [Davies Liu] run future again
1eebac2 [Davies Liu] fix conflict in ec2/spark_ec2.py
6e3c21d [Davies Liu] make cloudpickle work with Python3
2fb2db3 [Josh Rosen] Guard more changes behind sys.version; still doesn't run
1aa5e8f [twneale] Turned out `pickle.DictionaryType is dict` == True, so swapped it out
7354371 [twneale] buffer --> memoryview  I'm not super sure if this a valid change, but the 2.7 docs recommend using memoryview over buffer where possible, so hoping it'll work.
b69ccdf [twneale] Uses the pure python pickle._Pickler instead of c-extension _pickle.Pickler. It appears pyspark 2.7 uses the pure python pickler as well, so this shouldn't degrade pickling performance (?).
f40d925 [twneale] xrange --> range
e104215 [twneale] Replaces 2.7 types.InstsanceType with 3.4 `object`....could be horribly wrong depending on how types.InstanceType is used elsewhere in the package--see http://bugs.python.org/issue8206
79de9d0 [twneale] Replaces python2.7 `file` with 3.4 _io.TextIOWrapper
2adb42d [Josh Rosen] Fix up some import differences between Python 2 and 3
854be27 [Josh Rosen] Run `futurize` on Python code:
7c5b4ce [Josh Rosen] Remove Python 3 check in shell.py.

1 files changed, 69 insertions, 57 deletions

diff --git a/python/pyspark/shuffle.py b/python/pyspark/shuffle.py
index 8a6fc627eb..b54baa57ec 100644
--- a/python/pyspark/shuffle.py
+++ b/python/pyspark/shuffle.py
@@ -78,8 +78,8 @@ def _get_local_dirs(sub):
 
 
 # global stats
-MemoryBytesSpilled = 0L
-DiskBytesSpilled = 0L
+MemoryBytesSpilled = 0
+DiskBytesSpilled = 0
 
 
 class Aggregator(object):
@@ -126,7 +126,7 @@ class Merger(object):
         """ Merge the combined items by mergeCombiner """
         raise NotImplementedError
 
-    def iteritems(self):
+    def items(self):
         """ Return the merged items ad iterator """
         raise NotImplementedError
 
@@ -156,9 +156,9 @@ class InMemoryMerger(Merger):
         for k, v in iterator:
             d[k] = comb(d[k], v) if k in d else v
 
-    def iteritems(self):
-        """ Return the merged items as iterator """
-        return self.data.iteritems()
+    def items(self):
+        """ Return the merged items ad iterator """
+        return iter(self.data.items())
 
 
 def _compressed_serializer(self, serializer=None):
@@ -208,15 +208,15 @@ class ExternalMerger(Merger):
     >>> agg = SimpleAggregator(lambda x, y: x + y)
     >>> merger = ExternalMerger(agg, 10)
     >>> N = 10000
-    >>> merger.mergeValues(zip(xrange(N), xrange(N)))
+    >>> merger.mergeValues(zip(range(N), range(N)))
     >>> assert merger.spills > 0
-    >>> sum(v for k,v in merger.iteritems())
+    >>> sum(v for k,v in merger.items())
     49995000
 
     >>> merger = ExternalMerger(agg, 10)
-    >>> merger.mergeCombiners(zip(xrange(N), xrange(N)))
+    >>> merger.mergeCombiners(zip(range(N), range(N)))
     >>> assert merger.spills > 0
-    >>> sum(v for k,v in merger.iteritems())
+    >>> sum(v for k,v in merger.items())
     49995000
     """
 
@@ -335,10 +335,10 @@ class ExternalMerger(Merger):
             # above limit at the first time.
 
             # open all the files for writing
-            streams = [open(os.path.join(path, str(i)), 'w')
+            streams = [open(os.path.join(path, str(i)), 'wb')
                        for i in range(self.partitions)]
 
-            for k, v in self.data.iteritems():
+            for k, v in self.data.items():
                 h = self._partition(k)
                 # put one item in batch, make it compatible with load_stream
                 # it will increase the memory if dump them in batch
@@ -354,9 +354,9 @@ class ExternalMerger(Merger):
         else:
             for i in range(self.partitions):
                 p = os.path.join(path, str(i))
-                with open(p, "w") as f:
+                with open(p, "wb") as f:
                     # dump items in batch
-                    self.serializer.dump_stream(self.pdata[i].iteritems(), f)
+                    self.serializer.dump_stream(iter(self.pdata[i].items()), f)
                 self.pdata[i].clear()
                 DiskBytesSpilled += os.path.getsize(p)
 
@@ -364,10 +364,10 @@ class ExternalMerger(Merger):
         gc.collect()  # release the memory as much as possible
         MemoryBytesSpilled += (used_memory - get_used_memory()) << 20
 
-    def iteritems(self):
+    def items(self):
         """ Return all merged items as iterator """
         if not self.pdata and not self.spills:
-            return self.data.iteritems()
+            return iter(self.data.items())
         return self._external_items()
 
     def _external_items(self):
@@ -398,7 +398,8 @@ class ExternalMerger(Merger):
             path = self._get_spill_dir(j)
             p = os.path.join(path, str(index))
             # do not check memory during merging
-            self.mergeCombiners(self.serializer.load_stream(open(p)), 0)
+            with open(p, "rb") as f:
+                self.mergeCombiners(self.serializer.load_stream(f), 0)
 
             # limit the total partitions
             if (self.scale * self.partitions < self.MAX_TOTAL_PARTITIONS
@@ -408,7 +409,7 @@ class ExternalMerger(Merger):
                 gc.collect()  # release the memory as much as possible
                 return self._recursive_merged_items(index)
 
-        return self.data.iteritems()
+        return self.data.items()
 
     def _recursive_merged_items(self, index):
         """
@@ -426,7 +427,8 @@ class ExternalMerger(Merger):
         for j in range(self.spills):
             path = self._get_spill_dir(j)
             p = os.path.join(path, str(index))
-            m.mergeCombiners(self.serializer.load_stream(open(p)), 0)
+            with open(p, 'rb') as f:
+                m.mergeCombiners(self.serializer.load_stream(f), 0)
 
             if get_used_memory() > limit:
                 m._spill()
@@ -451,7 +453,7 @@ class ExternalSorter(object):
 
     >>> sorter = ExternalSorter(1)  # 1M
     >>> import random
-    >>> l = range(1024)
+    >>> l = list(range(1024))
     >>> random.shuffle(l)
     >>> sorted(l) == list(sorter.sorted(l))
     True
@@ -499,9 +501,16 @@ class ExternalSorter(object):
                 # sort them inplace will save memory
                 current_chunk.sort(key=key, reverse=reverse)
                 path = self._get_path(len(chunks))
-                with open(path, 'w') as f:
+                with open(path, 'wb') as f:
                     self.serializer.dump_stream(current_chunk, f)
-                chunks.append(self.serializer.load_stream(open(path)))
+
+                def load(f):
+                    for v in self.serializer.load_stream(f):
+                        yield v
+                    # close the file explicit once we consume all the items
+                    # to avoid ResourceWarning in Python3
+                    f.close()
+                chunks.append(load(open(path, 'rb')))
                 current_chunk = []
                 gc.collect()
                 limit = self._next_limit()
@@ -527,7 +536,7 @@ class ExternalList(object):
     ExternalList can have many items which cannot be hold in memory in
     the same time.
 
-    >>> l = ExternalList(range(100))
+    >>> l = ExternalList(list(range(100)))
     >>> len(l)
     100
     >>> l.append(10)
@@ -555,11 +564,11 @@ class ExternalList(object):
     def __getstate__(self):
         if self._file is not None:
             self._file.flush()
-            f = os.fdopen(os.dup(self._file.fileno()))
-            f.seek(0)
-            serialized = f.read()
+            with os.fdopen(os.dup(self._file.fileno()), "rb") as f:
+                f.seek(0)
+                serialized = f.read()
         else:
-            serialized = ''
+            serialized = b''
         return self.values, self.count, serialized
 
     def __setstate__(self, item):
@@ -575,7 +584,7 @@ class ExternalList(object):
         if self._file is not None:
             self._file.flush()
             # read all items from disks first
-            with os.fdopen(os.dup(self._file.fileno()), 'r') as f:
+            with os.fdopen(os.dup(self._file.fileno()), 'rb') as f:
                 f.seek(0)
                 for v in self._ser.load_stream(f):
                     yield v
@@ -598,11 +607,16 @@ class ExternalList(object):
         d = dirs[id(self) % len(dirs)]
         if not os.path.exists(d):
             os.makedirs(d)
-        p = os.path.join(d, str(id))
-        self._file = open(p, "w+", 65536)
+        p = os.path.join(d, str(id(self)))
+        self._file = open(p, "wb+", 65536)
         self._ser = BatchedSerializer(CompressedSerializer(PickleSerializer()), 1024)
         os.unlink(p)
 
+    def __del__(self):
+        if self._file:
+            self._file.close()
+            self._file = None
+
     def _spill(self):
         """ dump the values into disk """
         global MemoryBytesSpilled, DiskBytesSpilled
@@ -651,33 +665,28 @@ class GroupByKey(object):
     """
     Group a sorted iterator as [(k1, it1), (k2, it2), ...]
 
-    >>> k = [i/3 for i in range(6)]
+    >>> k = [i // 3 for i in range(6)]
     >>> v = [[i] for i in range(6)]
-    >>> g = GroupByKey(iter(zip(k, v)))
+    >>> g = GroupByKey(zip(k, v))
     >>> [(k, list(it)) for k, it in g]
     [(0, [0, 1, 2]), (1, [3, 4, 5])]
     """
 
     def __init__(self, iterator):
-        self.iterator = iter(iterator)
-        self.next_item = None
+        self.iterator = iterator
 
     def __iter__(self):
-        return self
-
-    def next(self):
-        key, value = self.next_item if self.next_item else next(self.iterator)
-        values = ExternalListOfList([value])
-        try:
-            while True:
-                k, v = next(self.iterator)
-                if k != key:
-                    self.next_item = (k, v)
-                    break
+        key, values = None, None
+        for k, v in self.iterator:
+            if values is not None and k == key:
                 values.append(v)
-        except StopIteration:
-            self.next_item = None
-        return key, values
+            else:
+                if values is not None:
+                    yield (key, values)
+                key = k
+                values = ExternalListOfList([v])
+        if values is not None:
+            yield (key, values)
 
 
 class ExternalGroupBy(ExternalMerger):
@@ -744,7 +753,7 @@ class ExternalGroupBy(ExternalMerger):
             # above limit at the first time.
 
             # open all the files for writing
-            streams = [open(os.path.join(path, str(i)), 'w')
+            streams = [open(os.path.join(path, str(i)), 'wb')
                        for i in range(self.partitions)]
 
             # If the number of keys is small, then the overhead of sort is small
@@ -756,7 +765,7 @@ class ExternalGroupBy(ExternalMerger):
                     h = self._partition(k)
                     self.serializer.dump_stream([(k, self.data[k])], streams[h])
             else:
-                for k, v in self.data.iteritems():
+                for k, v in self.data.items():
                     h = self._partition(k)
                     self.serializer.dump_stream([(k, v)], streams[h])
 
@@ -771,14 +780,14 @@ class ExternalGroupBy(ExternalMerger):
         else:
             for i in range(self.partitions):
                 p = os.path.join(path, str(i))
-                with open(p, "w") as f:
+                with open(p, "wb") as f:
                     # dump items in batch
                     if self._sorted:
                         # sort by key only (stable)
-                        sorted_items = sorted(self.pdata[i].iteritems(), key=operator.itemgetter(0))
+                        sorted_items = sorted(self.pdata[i].items(), key=operator.itemgetter(0))
                         self.serializer.dump_stream(sorted_items, f)
                     else:
-                        self.serializer.dump_stream(self.pdata[i].iteritems(), f)
+                        self.serializer.dump_stream(self.pdata[i].items(), f)
                 self.pdata[i].clear()
                 DiskBytesSpilled += os.path.getsize(p)
 
@@ -792,7 +801,7 @@ class ExternalGroupBy(ExternalMerger):
         # if the memory can not hold all the partition,
         # then use sort based merge. Because of compression,
         # the data on disks will be much smaller than needed memory
-        if (size >> 20) >= self.memory_limit / 10:
+        if size >= self.memory_limit << 17:  # * 1M / 8
             return self._merge_sorted_items(index)
 
         self.data = {}
@@ -800,15 +809,18 @@ class ExternalGroupBy(ExternalMerger):
             path = self._get_spill_dir(j)
             p = os.path.join(path, str(index))
             # do not check memory during merging
-            self.mergeCombiners(self.serializer.load_stream(open(p)), 0)
-        return self.data.iteritems()
+            with open(p, "rb") as f:
+                self.mergeCombiners(self.serializer.load_stream(f), 0)
+        return self.data.items()
 
     def _merge_sorted_items(self, index):
         """ load a partition from disk, then sort and group by key """
         def load_partition(j):
             path = self._get_spill_dir(j)
             p = os.path.join(path, str(index))
-            return self.serializer.load_stream(open(p, 'r', 65536))
+            with open(p, 'rb', 65536) as f:
+                for v in self.serializer.load_stream(f):
+                    yield v
 
         disk_items = [load_partition(j) for j in range(self.spills)]