Merge pull request #14 from kiyo-masui/thread_blocks

Paralellization of blocked functions.
kiyo-masui · Dec 5, 2014 · d60b215 · d60b215
2 parents 2854e9d + f3cbe33
commit d60b215
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Showing 5 changed files with 281 additions and 113 deletions.
diff --git a/bitshuffle/tests/test_ext.py b/bitshuffle/tests/test_ext.py
@@ -8,7 +8,7 @@
 from bitshuffle import ext
 
 
-# If we are doing timeings and by what factor in increase workload.
+# If we are doing timeings by what factor to increase workload.
 # Remember to change `ext.REPEATC`.
 TIME = 0
 #TIME = 8    # 8kB blocks same as final blocking. 
@@ -528,8 +528,8 @@ class TestBitShuffleCircle(unittest.TestCase):
     any length buffer."""
 
     def test_circle(self):
-        nmax = 10000
-        reps = 100
+        nmax = 100000
+        reps = 20
         for dtype in TEST_DTYPES:
             itemsize = np.dtype(dtype).itemsize
             nbyte_max = nmax * itemsize
@@ -545,8 +545,8 @@ def test_circle(self):
                                        == out.view(np.uint8)))
 
     def test_circle_with_compression(self):
-        nmax = 10000
-        reps = 100
+        nmax = 100000
+        reps = 20
         for dtype in TEST_DTYPES:
             itemsize = np.dtype(dtype).itemsize
             nbyte_max = nmax * itemsize

diff --git a/setup.py b/setup.py
@@ -54,7 +54,8 @@
                    include_dirs=INCLUDE_DIRS + [np.get_include(), "src/",
                                                 "lz4/"],
                    library_dirs = LIBRARY_DIRS,
-                   depends=["src/bitshuffle.h", "lz4/lz4.h"],
+                   depends=["src/bitshuffle.h", "src/iochain.h", "lz4/lz4.h"],
+                   libraries = ['gomp'],
                    extra_compile_args=COMPILE_FLAGS,
                    define_macros=MACROS,
                    )
@@ -65,9 +66,9 @@
                     "src/bitshuffle.c", "lz4/lz4.c"],
                    include_dirs=INCLUDE_DIRS + ["src/", "lz4/"],
                    library_dirs = LIBRARY_DIRS,
-                   depends=["src/bitshuffle.h", 'src/bshuf_h5filter.h', 
-                            "lz4/lz4.h"],
-                   libraries = ['hdf5'],
+                   depends=["src/bitshuffle.h", "src/iochain.h",
+                            'src/bshuf_h5filter.h', "lz4/lz4.h"],
+                   libraries = ['hdf5', 'gomp'],
                    extra_compile_args=COMPILE_FLAGS,
                    define_macros=MACROS,
                    )
@@ -78,9 +79,9 @@
                     "src/bitshuffle.c", "lz4/lz4.c"],
                    include_dirs=INCLUDE_DIRS +["src/", "lz4/"] ,
                    library_dirs = LIBRARY_DIRS,
-                   depends=["src/bitshuffle.h", 'src/bshuf_h5filter.h',
-                            "lz4/lz4.h"],
-                   libraries = ['hdf5'],
+                   depends=["src/bitshuffle.h", "src/iochain.h",
+                            'src/bshuf_h5filter.h', "lz4/lz4.h"],
+                   libraries = ['hdf5', 'gomp'],
                    extra_compile_args=['-fPIC', '-g'] + COMPILE_FLAGS,
                    define_macros=MACROS,
                    )