diff --git a/ci/docker_images/ubuntu/bionic/Dockerfile b/ci/docker_images/ubuntu/bionic/Dockerfile
index 872147e972dbc3e5ca3e3f3cbe62baab1cc1442a..0bca021dbc3c8798dfe7d7469aa7c6411c40b13c 100644
--- a/ci/docker_images/ubuntu/bionic/Dockerfile
+++ b/ci/docker_images/ubuntu/bionic/Dockerfile
@@ -220,6 +220,20 @@ RUN cd /tmp \
&& cd - \
&& rm -Rf /tmp/pyFFTW
+# HPTT (tensor permutation library)
+RUN cd /tmp
+ && git clone https://gitlab.com/keckj/hptt \
+ && cd hptt \
+ && mkdir build \
+ && cd build \
+ && cmake -DCMAKE_BUILD_TYPE=Release .. \
+ && make -j8 \
+ && make install \
+ && cd ../pythonAPI \
+ && pip install --upgrade . \
+ && cd /tmp \
+ && rm -Rf /tmp/hptt
+
# ensure all libraries are known by the runtime linker
RUN ldconfig
diff --git a/hysop/backend/device/opencl/autotunable_kernels/transpose.py b/hysop/backend/device/opencl/autotunable_kernels/transpose.py
index d9a16ea93ab765e5921216fd3d3f5ae3a06a1eac..1dbd3fdb78a802c946817ba22653ef3b891f0d63 100644
--- a/hysop/backend/device/opencl/autotunable_kernels/transpose.py
+++ b/hysop/backend/device/opencl/autotunable_kernels/transpose.py
@@ -156,7 +156,8 @@ class OpenClAutotunableTransposeKernel(OpenClAutotunableKernel):
tile_sizes = tuple( int((2**i)*(3**j))
for (i,j) in it.product(range(0,imax+1), range(0,jmax+1)))
tile_sizes = (max_tile_size,) + tuple(sorted(tile_sizes, reverse=True))
- tile_sizes = tuple(filter(lambda x: (x>=8) and (x<=max_tile_size), tile_sizes))
+ tile_sizes = tuple(filter(lambda x: (x>=max_tile_size//8) and (x<=max_tile_size), tile_sizes))
+
params.register_extra_parameter('vectorization', vectorization)
params.register_extra_parameter('use_diagonal_coordinates', use_diagonal_coordinates)
diff --git a/hysop/backend/host/python/operator/transpose.py b/hysop/backend/host/python/operator/transpose.py
index e7e770609b9941397689e473b697edc5288ccd76..840ac9c97c7edcc481d596cee270ec8f094e6405 100644
--- a/hysop/backend/host/python/operator/transpose.py
+++ b/hysop/backend/host/python/operator/transpose.py
@@ -1,11 +1,21 @@
-from hysop.deps import np
-
from hysop.constants import MemoryOrdering
from hysop.tools.decorators import debug, profile
from hysop.backend.host.host_operator import HostOperator
from hysop.operator.base.transpose_operator import TransposeOperatorBase
from hysop.core.graph.graph import op_apply
+import numpy as np
+try:
+ import hptt
+ HAS_HPTT=True
+ # required version is: https://gitlab.com/keckj/hptt
+except ImportError:
+ HAS_HPTT=False
+ import warnings
+ from hysop.tools.warning import HysopPerformanceWarning
+ msg='Failed to import HPTT module, falling back to slow numpy transpose. Required version is available at https://gitlab.com/keckj/hptt.'
+ warnings.warn(msg, HysopPerformanceWarning)
+
class PythonTranspose(TransposeOperatorBase, HostOperator):
"""
Inplace and out of place field transposition and permutations in general.
@@ -17,6 +27,21 @@ class PythonTranspose(TransposeOperatorBase, HostOperator):
"""Initialize a Transpose operator on the python backend."""
super(PythonTranspose, self).__init__(**kwds)
+
+ def discretize(self):
+ super(PythonTranspose, self).discretize()
+ assert self.din.dtype == self.dout.dtype
+ dtype = self.din.dtype
+ if HAS_HPTT and (dtype in (np.float32, np.float64, np.complex64, np.complex128)):
+ if self.is_inplace:
+ self.exec_transpose = self.transpose_hptt_inplace
+ else:
+ self.exec_transpose = self.transpose_hptt_outofplace
+ else:
+ if self.is_inplace:
+ self.exec_transpose = self.transpose_np_inplace
+ else:
+ self.exec_transpose = self.transpose_np_outofplace
@debug
def get_field_requirements(self):
@@ -27,26 +52,44 @@ class PythonTranspose(TransposeOperatorBase, HostOperator):
(field, td, req) = reqs
req.memory_order = MemoryOrdering.ANY
return requirements
+
+ @classmethod
+ def supports_mpi(cls):
+ return True
@op_apply
def apply(self, **kwds):
""" Transpose in or out of place."""
super(PythonTranspose,self).apply(**kwds)
+ self.exec_transpose(**kwds)
+
+ def transpose_hptt_inplace(self, **kwds):
+ axes = self.axes
+ din, dout, dtmp = self.din, self.dout, self.dtmp.handle.view(np.ndarray)
+ assert self.din.dfield is self.dout.dfield
+ for i in xrange(din.nb_components):
+ hptt.transpose(a=din.buffers[i], out=dtmp, axes=axes)
+ dout.buffers[i][...] = dtmp
+
+ def transpose_hptt_outofplace(self, **kwds):
+ axes = self.axes
+ din, dout = self.din, self.dout
+ assert self.din.dfield is not self.dout.dfield
+ for i in xrange(din.nb_components):
+ hptt.transpose(a=din.buffers[i], out=dout.buffers[i], axes=axes)
+ def transpose_np_inplace(self, **kwds):
axes = self.axes
-
- if self.is_inplace:
- din, dout, dtmp = self.din, self.dout, self.dtmp.handle.view(np.ndarray)
- assert self.din.dfield is self.dout.dfield
- for i in xrange(din.nb_components):
- dtmp[...] = np.transpose(din.buffers[i], axes=axes)
- dout.buffers[i][...] = dtmp
- else:
- din, dout = self.din, self.dout
- assert self.din.dfield is not self.dout.dfield
- for i in xrange(din.nb_components):
- dout.buffers[i][...] = np.transpose(din.buffers[i], axes=axes)
-
- @classmethod
- def supports_mpi(cls):
- return True
+ din, dout, dtmp = self.din, self.dout, self.dtmp.handle.view(np.ndarray)
+ assert self.din.dfield is self.dout.dfield
+ for i in xrange(din.nb_components):
+ dtmp[...] = np.transpose(din.buffers[i], axes=axes)
+ dout.buffers[i][...] = dtmp
+
+ def transpose_np_outofplace(self, **kwds):
+ axes = self.axes
+ din, dout = self.din, self.dout
+ assert self.din.dfield is not self.dout.dfield
+ for i in xrange(din.nb_components):
+ dout.buffers[i][...] = np.transpose(din.buffers[i], axes=axes)
+
diff --git a/hysop/operator/tests/test_transpose.py b/hysop/operator/tests/test_transpose.py
index 655f2a73b110f083eeaebd47c5a330aba4183304..ce3da5a76ea3fd88d7d025805abbebf4c66c4279 100644
--- a/hysop/operator/tests/test_transpose.py
+++ b/hysop/operator/tests/test_transpose.py
@@ -21,10 +21,10 @@ class TestTransposeOperator(object):
IO.set_default_path('/tmp/hysop_tests/test_transpose')
if enable_debug_mode:
- cls.size_min = 2
- cls.size_max = 6
+ cls.size_min = 3
+ cls.size_max = 4
else:
- cls.size_min = 2
+ cls.size_min = 4
cls.size_max = 23
cls.enable_extra_tests = enable_extra_tests
@@ -59,12 +59,9 @@ class TestTransposeOperator(object):
random.shuffle(all_axes)
all_axes = all_axes[:min(naxes,len(all_axes))]
- if dtype is None:
- types = [#np.int8, np.int16, np.int32, np.int64,
- #np.uint8, np.uint16, np.uint32, np.uint64,
- #np.float32, np.float64,
+ if (dtype is None):
+ types = [np.float32, np.float64,
np.complex64, np.complex128]
- random.shuffle(types)
dtype = types[0]
domain = Box(length=(1.0,)*dim)
@@ -129,8 +126,15 @@ class TestTransposeOperator(object):
refout = tuple(df.copy() for df in dfout.buffers)
- for in_,out_ in zip(refin, refout):
- assert np.all(out_ == np.transpose(in_, axes=axes))
+ for i,(in_,out_) in enumerate(zip(refin, refout)):
+ ref = np.transpose(in_, axes=axes)
+ if (ref!=out_).any():
+ print
+ print np.transpose(in_, axes=axes)
+ print
+ print out_
+ msg = 'Reference did not match numpy for component {}.'.format(i)
+ raise RuntimeError(msg)
def iter_impl(impl):
base_kwds = dict(fields=fin, output_fields=fout, variables=variables,
@@ -196,37 +200,37 @@ class TestTransposeOperator(object):
raise RuntimeError(msg)
- def test_2d_out_of_place(self):
- self._test(dim=2, dtype=None, is_inplace=False)
- def test_3d_out_of_place(self):
- self._test(dim=3, dtype=None, is_inplace=False)
- def test_4d_out_of_place(self):
- self._test(dim=4, dtype=None, is_inplace=False)
+ def test_2d_out_of_place(self, **kwds):
+ self._test(dim=2, is_inplace=False, **kwds)
+ def test_3d_out_of_place(self, **kwds):
+ self._test(dim=3, is_inplace=False, **kwds)
+ def test_4d_out_of_place(self, **kwds):
+ self._test(dim=4, is_inplace=False, **kwds)
def test_upper_dimensions_out_of_place(self):
for i in xrange(5,9):
self._test(dim=i, dtype=None, is_inplace=False,
size_min=3, size_max=4, naxes=1)
- def test_2d_inplace(self):
- self._test(dim=2, dtype=None, is_inplace=True)
- def test_3d_inplace(self):
- self._test(dim=3, dtype=None, is_inplace=True)
- def test_4d_inplace(self):
- self._test(dim=4, dtype=None, is_inplace=True)
+ def test_2d_inplace(self, **kwds):
+ self._test(dim=2, is_inplace=True, **kwds)
+ def test_3d_inplace(self, **kwds):
+ self._test(dim=3, is_inplace=True, **kwds)
+ def test_4d_inplace(self, **kwds):
+ self._test(dim=4, is_inplace=True, **kwds)
def test_upper_dimensions_inplace(self):
for i in xrange(5,9):
self._test(dim=i, dtype=None, is_inplace=True,
size_min=3, size_max=4, naxes=1)
def perform_tests(self):
- self.test_2d_out_of_place()
- self.test_3d_out_of_place()
+ self.test_2d_out_of_place(dtype=np.float32)
+ self.test_3d_out_of_place(dtype=np.complex64)
if __ENABLE_LONG_TESTS__:
self.test_4d_out_of_place()
self.test_upper_dimensions_out_of_place()
- self.test_2d_inplace()
- self.test_3d_inplace()
+ self.test_2d_inplace(dtype=np.float64)
+ self.test_3d_inplace(dtype=np.complex128)
if __ENABLE_LONG_TESTS__:
self.test_4d_inplace()
self.test_upper_dimensions_inplace()