Merge branch 'master' of gitlab.mpcdf.mpg.de:ift/D2O

.gitlab-ci.yml

+image: python:2.7-wheezy
+before_script:
+  - pip install nose
+  - pip install nose_parameterized
+  - pip install numpy
+  - chmod +x continuous_integration/*
+
+test_minimal:
+  script:
+  - python setup.py install
+  - nosetests
+
+test_mpi:
+  script:
+  - continuous_integration/install_mpi.sh
+  - python setup.py install
+  - nosetests
+  - mpirun -n 2 nosetests
+  - mpirun -n 5 nosetests
+
+test_mpi_fftw:
+  script:
+  - continuous_integration/install_mpi.sh
+  - continuous_integration/install_fftw.sh
+  - python setup.py install
+  - mpirun -n 2 nosetests
+
+test_mpi_fftw_hdf5:
+  script:
+  - continuous_integration/install_mpi.sh
+  - continuous_integration/install_fftw.sh
+  - continuous_integration/install_h5py.sh
+  - python setup.py install
+  - mpirun -n 2 nosetests
+

continuous_integration/install_fftw.sh

+#!/bin/bash
+
+pip install cython
+
+apt-get install -y libfftw3-3 libfftw3-bin libfftw3-dev libfftw3-mpi-dev libfftw3-mpi3
+git clone -b mpi https://github.com/fredRos/pyFFTW.git
+cd pyFFTW/
+#export LDFLAGS="-L/usr/include"
+#export CFLAGS="-I/usr/include"
+CC=mpicc python setup.py build_ext install
+cd ..

continuous_integration/install_h5py.sh

+#!/bin/bash
+pip install cython
+
+apt-get update -qy
+apt-get install -y libhdf5-openmpi-dev
+
+curl -s https://api.github.com/repos/h5py/h5py/tags | grep tarball_url | head -n 1 | cut -d '"' -f 4 | wget -i - -O h5py.tar.gz
+tar xzf h5py.tar.gz
+cd h5py-h5py*
+export CC=mpicc
+python setup.py configure --mpi
+python setup.py build
+python setup.py install
+cd ..

continuous_integration/install_mpi.sh

+#!/bin/bash
+
+apt-get update -qy
+apt-get install -y openmpi-bin libopenmpi-dev
+pip install mpi4py

d2o/config/d2o_config.py

@@ -22,7 +22,7 @@ import keepers
 dependency_injector = keepers.DependencyInjector(
                                     ['h5py',
                                      ('mpi4py.MPI', 'MPI'),
-                                     ('d2o.mpi_dummy.mpi_dummy', 'MPI_dummy')]
+                                     ('mpi_dummy', 'MPI_dummy')]
                                      )
 
 dependency_injector.register('pyfftw', lambda z: hasattr(z, 'FFTW_MPI'))

d2o/distributed_data_object.py

@@ -1288,6 +1288,7 @@ class distributed_data_object(Versionable, object):
             ('index', np.dtype('float'))])
         local_argmax_list = np.sort(local_argmax_list,
                                     order=['value', 'index'])
+
         # take the last entry here and correct the minus sign of the index
         return -np.int(local_argmax_list[-1][1])
 

d2o/mpi_dummy/__init__.py

-# D2O
-# Copyright (C) 2016  Theo Steininger
-#
-# Author: Theo Steininger
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-import mpi_dummy
\ No newline at end of file

d2o/mpi_dummy/mpi_dummy.py

-# D2O
-# Copyright (C) 2016  Theo Steininger
-#
-# Author: Theo Steininger
-#
-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-
-import copy
-import numpy as np
-
-
-class Op(object):
-    @classmethod
-    def Create(cls, function, commute=False):
-        pass
-
-MIN = Op()
-MAX = Op()
-SUM = Op()
-PROD = Op()
-LAND = Op()
-LOR = Op()
-BAND = Op()
-BOR = Op()
-
-
-class Comm(object):
-    pass
-
-
-class Intracomm(Comm):
-    def __init__(self, name):
-        if not running_single_threadedQ():
-            raise RuntimeError("ERROR: MPI_dummy module is running in a " +
-                               "mpirun with n>1.")
-        self.name = name
-        self.rank = 0
-        self.size = 1
-
-    def Get_rank(self):
-        return self.rank
-
-    def Get_size(self):
-        return self.size
-
-    def _scattergather_helper(self, sendbuf, recvbuf=None, **kwargs):
-        sendbuf = self._unwrapper(sendbuf)
-        recvbuf = self._unwrapper(recvbuf)
-        if recvbuf is not None:
-            recvbuf[:] = sendbuf
-            return recvbuf
-        else:
-            recvbuf = np.copy(sendbuf)
-            return recvbuf
-
-    def bcast(self, sendbuf, *args, **kwargs):
-        return sendbuf
-
-    def Bcast(self, sendbuf, *args, **kwargs):
-        return sendbuf
-
-    def scatter(self, sendbuf, *args, **kwargs):
-        return sendbuf[0]
-
-    def Scatter(self, *args, **kwargs):
-        return self._scattergather_helper(*args, **kwargs)
-
-    def Scatterv(self, *args, **kwargs):
-        return self._scattergather_helper(*args, **kwargs)
-
-    def gather(self, sendbuf, *args, **kwargs):
-        return [sendbuf]
-
-    def Gather(self, *args, **kwargs):
-        return self._scattergather_helper(*args, **kwargs)
-
-    def Gatherv(self, *args, **kwargs):
-        return self._scattergather_helper(*args, **kwargs)
-
-    def allgather(self, sendbuf, *args, **kwargs):
-        return [sendbuf]
-
-    def Allgather(self, *args, **kwargs):
-        return self._scattergather_helper(*args, **kwargs)
-
-    def Allgatherv(self, *args, **kwargs):
-        return self._scattergather_helper(*args, **kwargs)
-
-    def Allreduce(self, sendbuf, recvbuf, op, **kwargs):
-        sendbuf = self._unwrapper(sendbuf)
-        recvbuf = self._unwrapper(recvbuf)
-        recvbuf[:] = sendbuf
-        return recvbuf
-
-    def allreduce(self, sendobj, op=SUM, **kwargs):
-        if np.isscalar(sendobj):
-            return sendobj
-        return copy.copy(sendobj)
-
-    def sendrecv(self, sendobj, **kwargs):
-        return sendobj
-
-    def _unwrapper(self, x):
-        if isinstance(x, list):
-            return x[0]
-        else:
-            return x
-
-    def Barrier(self):
-        pass
-
-
-class _datatype():
-    def __init__(self, name):
-        self.name = str(name)
-
-
-def running_single_threadedQ():
-    try:
-        from mpi4py import MPI
-    except ImportError:
-        return True
-    else:
-        if MPI.COMM_WORLD.size != 1:
-            return False
-        else:
-            return True
-
-
-BYTE = _datatype('MPI_BYTE')
-SHORT = _datatype('MPI_SHORT')
-UNSIGNED_SHORT = _datatype("MPI_UNSIGNED_SHORT")
-UNSIGNED_INT = _datatype("MPI_UNSIGNED_INT")
-INT = _datatype("MPI_INT")
-LONG = _datatype("MPI_LONG")
-UNSIGNED_LONG = _datatype("MPI_UNSIGNED_LONG")
-LONG_LONG = _datatype("MPI_LONG_LONG")
-UNSIGNED_LONG_LONG = _datatype("MPI_UNSIGNED_LONG_LONG")
-FLOAT = _datatype("MPI_FLOAT")
-DOUBLE = _datatype("MPI_DOUBLE")
-LONG_DOUBLE = _datatype("MPI_LONG_DOUBLE")
-COMPLEX = _datatype("MPI_COMPLEX")
-DOUBLE_COMPLEX = _datatype("MPI_DOUBLE_COMPLEX")
-
-
-class _comm_wrapper(Intracomm):
-    def __init__(self, name):
-        self.cache = None
-        self.name = name
-        self.size = 1
-        self.rank = 0
-
-    @property
-    def comm(self):
-        if self.cache is None:
-            self.cache = Intracomm(self.name)
-        return self.cache
-
-    def __getattr__(self, x):
-        return self.comm.__getattribute__(x)
-
-
-COMM_WORLD = _comm_wrapper('MPI_dummy_COMM_WORLD')
-#COMM_WORLD.__class__ = COMM_WORLD.comm.__class__

setup.py

@@ -37,11 +37,12 @@ setup(
                    "computing in Python"),
     keywords = "parallelization, numerics, MPI",
     url = "https://gitlab.mpcdf.mpg.de/ift/D2O",
-    packages=['d2o', 'd2o.config', 'd2o.mpi_dummy', 'test'],
+    packages=['d2o', 'd2o.config', 'test'],
     zip_safe=False,
     dependency_links = [
-        "git+https://gitlab.mpcdf.mpg.de/ift/keepers.git#egg=keepers-0.3.4"],
-    install_requires=['keepers>=0.3.4'],
+        "git+https://gitlab.mpcdf.mpg.de/ift/keepers.git#egg=keepers-0.3.4",
+        "git+https://gitlab.mpcdf.mpg.de/ift/mpi_dummy.git#egg=mpi_dummy-1.0.0"],
+    install_requires=['keepers>=0.3.4', 'mpi_dummy>=1.0.0'],
     long_description=read('README.rst'),
     license = "GPLv3",
     classifiers=[

test/test_distributed_data_object.py

@@ -18,7 +18,8 @@
 
 from numpy.testing import assert_equal,\
     assert_almost_equal,\
-    assert_raises
+    assert_raises,\
+    assert_allclose
 
 from nose_parameterized import parameterized
 import unittest
@@ -140,9 +141,9 @@ def generate_data(global_shape, dtype, distribution_strategy,
             local_shape[0] = 0
         else:
             local_shape[0] = global_shape[0] // np.ceil(size / 2.)
-            number_of_extras = global_shape[
-                0] - local_shape[0] * np.ceil(size / 2.)
-            if number_of_extras > rank:
+            number_of_extras = (global_shape[0] -
+                                local_shape[0] * np.ceil(size / 2.))
+            if number_of_extras > rank//2:
                 local_shape[0] += 1
         local_shape = tuple(local_shape)
 
@@ -1536,8 +1537,8 @@ class Test_contractions(unittest.TestCase):
         (a, obj) = generate_data(global_shape, dtype,
                                  distribution_strategy,
                                  strictly_positive=True)
-        assert_almost_equal(getattr(obj, function)(), getattr(np, function)(a),
-                            decimal=4)
+        assert_allclose(getattr(obj, function)(), getattr(np, function)(a),
+                        rtol=1e-4)
 
 ###############################################################################
 
@@ -1553,8 +1554,8 @@ class Test_contractions(unittest.TestCase):
         (a, obj) = generate_data(global_shape, dtype,
                                  distribution_strategy,
                                  strictly_positive=True)
-        assert_almost_equal(getattr(obj, function)(), getattr(np, function)(a),
-                            decimal=4)
+        assert_allclose(getattr(obj, function)(), getattr(np, function)(a),
+                        rtol=1e-4)
 
 ###############################################################################
 
@@ -1563,9 +1564,13 @@ class Test_contractions(unittest.TestCase):
                           all_distribution_strategies
                           ))
     def test_argmin_argmax(self, dtype, distribution_strategy):
+        print (dtype, distribution_strategy)
         global_shape = (8, 8)
         (a, obj) = generate_data(global_shape, dtype,
-                                 distribution_strategy)
+                                 distribution_strategy,
+                                 strictly_positive=True)
+        o_full = obj.get_full_data()
+        print (a, o_full)
         assert_equal(obj.argmax(), np.argmax(a))
         assert_equal(obj.argmin(), np.argmin(a))
         assert_equal(obj.argmin_nonflat(),