Release 1.5.0

CHANGELOG.rst

@@ -7,6 +7,14 @@ Changelog
 .. This document is user facing. Please word the changes in such a way
 .. that users understand how the changes affect the new version.
 
+version 1.5.0
+-----------------
++ Make a special case for threads==1 in ``igzip_threaded.open`` for writing
+  files. This now combines the writing and compression thread for less
+  overhead.
++ Maximize time spent outside the GIL for ``igzip_threaded.open`` writing.
+  This has decreased wallclock time significantly.
+
 version 1.4.1
 -----------------
 + Fix several errors related to unclosed files and buffers.

setup.py

@@ -135,7 +135,7 @@ def build_isa_l():
 
 setup(
     name="isal",
-    version="1.4.1",
+    version="1.5.0",
     description="Faster zlib and gzip compatible compression and "
                 "decompression by providing python bindings for the ISA-L "
                 "library.",

src/isal/__init__.py

@@ -27,4 +27,4 @@
     "__version__"
 ]
 
-__version__ = "1.4.1"
+__version__ = "1.5.0"

src/isal/igzip_threaded.py

@@ -20,7 +20,8 @@
 
 
 def open(filename, mode="rb", compresslevel=igzip._COMPRESS_LEVEL_TRADEOFF,
-         encoding=None, errors=None, newline=None, *, threads=1):
+         encoding=None, errors=None, newline=None, *, threads=1,
+         block_size=1024 * 1024):
     """
     Utilize threads to read and write gzip objects and escape the GIL.
     Comparable to gzip.open. This method is only usable for streamed reading
@@ -39,6 +40,8 @@ def open(filename, mode="rb", compresslevel=igzip._COMPRESS_LEVEL_TRADEOFF,
     :param threads: If 0 will defer to igzip.open, if < 0 will use all threads
                     available to the system. Reading gzip can only
                     use one thread.
+    :param block_size: Determines how large the blocks in the read/write
+                       queues are for threaded reading and writing.
     :return: An io.BufferedReader, io.BufferedWriter, or io.TextIOWrapper,
              depending on the mode.
     """
@@ -61,21 +64,27 @@ def open(filename, mode="rb", compresslevel=igzip._COMPRESS_LEVEL_TRADEOFF,
     else:
         raise TypeError("filename must be a str or bytes object, or a file")
     if "r" in mode:
-        gzip_file = io.BufferedReader(_ThreadedGzipReader(binary_file))
+        gzip_file = io.BufferedReader(
+            _ThreadedGzipReader(binary_file, block_size=block_size))
     else:
         gzip_file = io.BufferedWriter(
-            _ThreadedGzipWriter(binary_file, compresslevel, threads),
-            buffer_size=1024 * 1024
+            _ThreadedGzipWriter(
+                fp=binary_file,
+                block_size=block_size,
+                level=compresslevel,
+                threads=threads
+            ),
+            buffer_size=block_size
         )
     if "t" in mode:
         return io.TextIOWrapper(gzip_file, encoding, errors, newline)
     return gzip_file
 
 
 class _ThreadedGzipReader(io.RawIOBase):
-    def __init__(self, fp, queue_size=4, block_size=8 * 1024 * 1024):
+    def __init__(self, fp, queue_size=2, block_size=1024 * 1024):
         self.raw = fp
-        self.fileobj = igzip._IGzipReader(fp, buffersize=8 * 1024 * 1024)
+        self.fileobj = igzip._IGzipReader(fp, buffersize=8 * block_size)
         self.pos = 0
         self.read_file = False
         self.queue = queue.Queue(queue_size)
@@ -179,35 +188,53 @@ class _ThreadedGzipWriter(io.RawIOBase):
 
     The writer thread reads from output queues and uses the crc32_combine
     function to calculate the total crc. It also writes the compressed block.
+
+    When only one thread is requested, only the input queue is used and
+    compressing and output is handled in one thread.
     """
     def __init__(self,
                  fp: BinaryIO,
                  level: int = isal_zlib.ISAL_DEFAULT_COMPRESSION,
                  threads: int = 1,
-                 queue_size: int = 2):
-        if level < 0 or level > 3:
-            raise ValueError(
-                f"Invalid compression level, "
-                f"level should be between 0 and 3: {level}")
+                 queue_size: int = 1,
+                 block_size: int = 1024 * 1024,
+                 ):
         self.lock = threading.Lock()
         self.exception: Optional[Exception] = None
         self.raw = fp
         self.level = level
         self.previous_block = b""
-        self.input_queues: List[queue.Queue[Tuple[bytes, memoryview]]] = [
-            queue.Queue(queue_size) for _ in range(threads)]
-        self.output_queues: List[queue.Queue[Tuple[bytes, int, int]]] = [
-            queue.Queue(queue_size) for _ in range(threads)]
-        self.index = 0
+        # Deflating random data results in an output a little larger than the
+        # input. Making the output buffer 10% larger is sufficient overkill.
+        compress_buffer_size = block_size + max(block_size // 10, 500)
+        self.block_size = block_size
+        self.compressors: List[isal_zlib._ParallelCompress] = [
+            isal_zlib._ParallelCompress(buffersize=compress_buffer_size,
+                                        level=level) for _ in range(threads)
+        ]
+        if threads > 1:
+            self.input_queues: List[queue.Queue[Tuple[bytes, memoryview]]] = [
+                queue.Queue(queue_size) for _ in range(threads)]
+            self.output_queues: List[queue.Queue[Tuple[bytes, int, int]]] = [
+                queue.Queue(queue_size) for _ in range(threads)]
+            self.output_worker = threading.Thread(target=self._write)
+            self.compression_workers = [
+                threading.Thread(target=self._compress, args=(i,))
+                for i in range(threads)
+            ]
+        elif threads == 1:
+            self.input_queues = [queue.Queue(queue_size)]
+            self.output_queues = []
+            self.compression_workers = []
+            self.output_worker = threading.Thread(
+                target=self._compress_and_write)
+        else:
+            raise ValueError(f"threads should be at least 1, got {threads}")
         self.threads = threads
+        self.index = 0
         self._crc = 0
         self.running = False
         self._size = 0
-        self.output_worker = threading.Thread(target=self._write)
-        self.compression_workers = [
-            threading.Thread(target=self._compress, args=(i,))
-            for i in range(threads)
-        ]
         self._closed = False
         self._write_gzip_header()
         self.start()
@@ -246,8 +273,19 @@ def write(self, b) -> int:
         with self.lock:
             if self.exception:
                 raise self.exception
-        index = self.index
+        length = b.nbytes if isinstance(b, memoryview) else len(b)
+        if length > self.block_size:
+            # write smaller chunks and return the result
+            memview = memoryview(b)
+            start = 0
+            total_written = 0
+            while start < length:
+                total_written += self.write(
+                    memview[start:start+self.block_size])
+                start += self.block_size
+            return total_written
         data = bytes(b)
+        index = self.index
         zdict = memoryview(self.previous_block)[-DEFLATE_WINDOW_SIZE:]
         self.previous_block = data
         self.index += 1
@@ -289,6 +327,7 @@ def closed(self) -> bool:
     def _compress(self, index: int):
         in_queue = self.input_queues[index]
         out_queue = self.output_queues[index]
+        compressor: isal_zlib._ParallelCompress = self.compressors[index]
         while True:
             try:
                 data, zdict = in_queue.get(timeout=0.05)
@@ -297,23 +336,11 @@ def _compress(self, index: int):
                     return
                 continue
             try:
-                compressor = isal_zlib.compressobj(
-                    self.level, wbits=-15, zdict=zdict)
-                compressed = compressor.compress(data) + compressor.flush(
-                    isal_zlib.Z_SYNC_FLUSH)
-                crc = isal_zlib.crc32(data)
+                compressed, crc = compressor.compress_and_crc(data, zdict)
             except Exception as e:
-                with self.lock:
-                    self.exception = e
-                    # Abort everything and empty the queue
-                    in_queue.task_done()
-                    self.running = False
-                    while True:
-                        try:
-                            _ = in_queue.get(timeout=0.05)
-                            in_queue.task_done()
-                        except queue.Empty:
-                            return
+                in_queue.task_done()
+                self._set_error_and_empty_queue(e, in_queue)
+                return
             data_length = len(data)
             out_queue.put((compressed, crc, data_length))
             in_queue.task_done()
@@ -341,5 +368,46 @@ def _write(self):
             output_queue.task_done()
             index += 1
 
+    def _compress_and_write(self):
+        if not self.threads == 1:
+            raise SystemError("Compress_and_write is for one thread only")
+        fp = self.raw
+        total_crc = 0
+        size = 0
+        in_queue = self.input_queues[0]
+        compressor = self.compressors[0]
+        while True:
+            try:
+                data, zdict = in_queue.get(timeout=0.05)
+            except queue.Empty:
+                if not self.running:
+                    self._crc = total_crc
+                    self._size = size
+                    return
+                continue
+            try:
+                compressed, crc = compressor.compress_and_crc(data, zdict)
+            except Exception as e:
+                in_queue.task_done()
+                self._set_error_and_empty_queue(e, in_queue)
+                return
+            data_length = len(data)
+            total_crc = isal_zlib.crc32_combine(total_crc, crc, data_length)
+            size += data_length
+            fp.write(compressed)
+            in_queue.task_done()
+
+    def _set_error_and_empty_queue(self, error, q):
+        with self.lock:
+            self.exception = error
+            # Abort everything and empty the queue
+            self.running = False
+            while True:
+                try:
+                    _ = q.get(timeout=0.05)
+                    q.task_done()
+                except queue.Empty:
+                    return
+
     def writable(self) -> bool:
         return True

src/isal/isal_zlib.pyi

@@ -38,6 +38,10 @@ def adler32(__data, __value: int = 1) -> int: ...
 def crc32(__data, __value: int = 0) -> int: ...
 def crc32_combine(__crc1: int, __crc2: int, __crc2_length: int) -> int: ...
 
+class _ParallelCompress:
+    def __init__(self, buffersize: int, level: int): ...
+    def compress_and_crc(self, __data, __zdict) -> typing.Tuple[bytes, int]: ...
+
 def compress(__data,
              level: int = ISAL_DEFAULT_COMPRESSION,
              wbits: int = MAX_WBITS) -> bytes: ...