Move leftover flags that seemed forgotten.

theano/compile/debugmode.py

@@ -17,13 +17,12 @@ from theano.compat import izip
 import numpy
 
 import theano
-from theano import gof
+from theano import gof, config
 from theano.compat import get_unbound_function
-from six import string_types, iteritems, itervalues
+from six import iteritems, itervalues
 from six.moves import StringIO, xrange
 from theano.gof import (graph, utils, link, ops_with_inner_function)
 from theano.gof.link import raise_with_op
-from theano.configparser import (config, AddConfigVar, IntParam, StrParam)
 from theano.compile.function_module import (
     FunctionMaker, Function, infer_reuse_pattern,
     SymbolicInputKit, SymbolicOutput, Supervisor, std_fgraph)
@@ -31,39 +30,6 @@ from theano.compile.mode import Mode, register_mode
 from theano.compile.ops import OutputGuard
 
 __docformat__ = "restructuredtext en"
-
-
-def is_valid_check_preallocated_output_param(param):
-    if not isinstance(param, string_types):
-        return False
-    valid = ["initial", "previous", "c_contiguous", "f_contiguous",
-             "strided", "wrong_size", "ALL", ""]
-    for p in param.split(":"):
-        if p not in valid:
-            return False
-    return True
-
-AddConfigVar('DebugMode.check_preallocated_output',
-             ('Test thunks with pre-allocated memory as output storage. '
-              'This is a list of strings separated by ":". Valid values are: '
-              '"initial" (initial storage in storage map, happens with Scan),'
-              '"previous" (previously-returned memory), '
-              '"c_contiguous", "f_contiguous", '
-              '"strided" (positive and negative strides), '
-              '"wrong_size" (larger and smaller dimensions), and '
-              '"ALL" (all of the above).'),
-             StrParam('', is_valid=is_valid_check_preallocated_output_param),
-             in_c_key=False)
-
-AddConfigVar('DebugMode.check_preallocated_output_ndim',
-             ('When testing with "strided" preallocated output memory, '
-              'test all combinations of strides over that number of '
-              '(inner-most) dimensions. You may want to reduce that number '
-              'to reduce memory or time usage, but it is advised to keep a '
-              'minimum of 2.'),
-             IntParam(4, lambda i: i > 0),
-             in_c_key=False)
-
 _logger = logging.getLogger("theano.compile.debugmode")
 
 

theano/compile/profiling.py

@@ -29,7 +29,6 @@ import numpy
 import theano
 from six import iteritems
 from theano.gof import graph
-from theano.configparser import AddConfigVar, BoolParam, IntParam, StrParam
 
 theano_imported_time = time.time()
 config = theano.config

theano/configdefaults.py

@@ -10,6 +10,8 @@ import socket
 import struct
 import warnings
 
+from six import string_types
+
 import theano
 from theano.configparser import (AddConfigVar, BoolParam, ConfigParam, EnumStr,
                                  FloatParam, IntParam, StrParam,
@@ -963,6 +965,38 @@ AddConfigVar('DebugMode.warn_input_not_reused',
              BoolParam(True),
              in_c_key=False)
 
+
+def is_valid_check_preallocated_output_param(param):
+    if not isinstance(param, string_types):
+        return False
+    valid = ["initial", "previous", "c_contiguous", "f_contiguous",
+             "strided", "wrong_size", "ALL", ""]
+    for p in param.split(":"):
+        if p not in valid:
+            return False
+    return True
+
+AddConfigVar('DebugMode.check_preallocated_output',
+             ('Test thunks with pre-allocated memory as output storage. '
+              'This is a list of strings separated by ":". Valid values are: '
+              '"initial" (initial storage in storage map, happens with Scan),'
+              '"previous" (previously-returned memory), '
+              '"c_contiguous", "f_contiguous", '
+              '"strided" (positive and negative strides), '
+              '"wrong_size" (larger and smaller dimensions), and '
+              '"ALL" (all of the above).'),
+             StrParam('', is_valid=is_valid_check_preallocated_output_param),
+             in_c_key=False)
+
+AddConfigVar('DebugMode.check_preallocated_output_ndim',
+             ('When testing with "strided" preallocated output memory, '
+              'test all combinations of strides over that number of '
+              '(inner-most) dimensions. You may want to reduce that number '
+              'to reduce memory or time usage, but it is advised to keep a '
+              'minimum of 2.'),
+             IntParam(4, lambda i: i > 0),
+             in_c_key=False)
+
 AddConfigVar('profiling.time_thunks',
              """Time individual thunks when profiling""",
              BoolParam(True),
@@ -1053,6 +1087,215 @@ AddConfigVar('cmodule.preload_cache',
              BoolParam(False, allow_override=False),
              in_c_key=False)
 
+
+def default_blas_ldflags():
+    global numpy
+    try:
+        if (hasattr(numpy.distutils, '__config__') and
+                numpy.distutils.__config__):
+            # If the old private interface is available use it as it
+            # don't print information to the user.
+            blas_info = numpy.distutils.__config__.blas_opt_info
+        else:
+            # We do this import only here, as in some setup, if we
+            # just import theano and exit, with the import at global
+            # scope, we get this error at exit: "Exception TypeError:
+            # "'NoneType' object is not callable" in <bound method
+            # Popen.__del__ of <subprocess.Popen object at 0x21359d0>>
+            # ignored"
+
+            # This happen with Python 2.7.3 |EPD 7.3-1 and numpy 1.8.1
+            import numpy.distutils.system_info  # noqa
+
+            # We need to catch warnings as in some cases NumPy print
+            # stuff that we don't want the user to see.
+            # I'm not able to remove all printed stuff
+            with warnings.catch_warnings(record=True):
+                numpy.distutils.system_info.system_info.verbosity = 0
+                blas_info = numpy.distutils.system_info.get_info("blas_opt")
+
+        # If we are in a EPD installation, mkl is available
+        if "EPD" in sys.version:
+            use_unix_epd = True
+            if sys.platform == 'win32':
+                return ' '.join(
+                    ['-L%s' % os.path.join(sys.prefix, "Scripts")] +
+                    # Why on Windows, the library used are not the
+                    # same as what is in
+                    # blas_info['libraries']?
+                    ['-l%s' % l for l in ["mk2_core", "mk2_intel_thread",
+                                          "mk2_rt"]])
+            elif sys.platform == 'darwin':
+                # The env variable is needed to link with mkl
+                new_path = os.path.join(sys.prefix, "lib")
+                v = os.getenv("DYLD_FALLBACK_LIBRARY_PATH", None)
+                if v is not None:
+                    # Explicit version could be replaced by a symbolic
+                    # link called 'Current' created by EPD installer
+                    # This will resolve symbolic links
+                    v = os.path.realpath(v)
+
+                # The python __import__ don't seam to take into account
+                # the new env variable "DYLD_FALLBACK_LIBRARY_PATH"
+                # when we set with os.environ['...'] = X or os.putenv()
+                # So we warn the user and tell him what todo.
+                if v is None or new_path not in v.split(":"):
+                    _logger.warning(
+                        "The environment variable "
+                        "'DYLD_FALLBACK_LIBRARY_PATH' does not contain "
+                        "the '%s' path in its value. This will make "
+                        "Theano use a slow version of BLAS. Update "
+                        "'DYLD_FALLBACK_LIBRARY_PATH' to contain the "
+                        "said value, this will disable this warning."
+                        % new_path)
+
+                    use_unix_epd = False
+            if use_unix_epd:
+                return ' '.join(
+                    ['-L%s' % os.path.join(sys.prefix, "lib")] +
+                    ['-l%s' % l for l in blas_info['libraries']])
+
+                # Canopy
+        if "Canopy" in sys.prefix:
+            subsub = 'lib'
+            if sys.platform == 'win32':
+                subsub = 'Scripts'
+            lib_path = os.path.join(sys.base_prefix, subsub)
+            if not os.path.exists(lib_path):
+                # Old logic to find the path. I don't think we still
+                # need it, but I don't have the time to test all
+                # installation configuration. So I keep this as a fall
+                # back in case the current expectation don't work.
+
+                # This old logic don't work when multiple version of
+                # Canopy is installed.
+                p = os.path.join(sys.base_prefix, "..", "..", "appdata")
+                assert os.path.exists(p), "Canopy changed the location of MKL"
+                lib_paths = os.listdir(p)
+                # Try to remove subdir that can't contain MKL
+                for sub in lib_paths:
+                    if not os.path.exists(os.path.join(p, sub, subsub)):
+                        lib_paths.remove(sub)
+                assert len(lib_paths) == 1, (
+                    "Unexpected case when looking for Canopy MKL libraries",
+                    p, lib_paths, [os.listdir(os.path.join(p, sub))
+                                   for sub in lib_paths])
+                lib_path = os.path.join(p, lib_paths[0], subsub)
+                assert os.path.exists(lib_path), "Canopy changed the location of MKL"
+
+            if sys.platform == "linux2" or sys.platform == "darwin":
+                return ' '.join(
+                    ['-L%s' % lib_path] +
+                    ['-l%s' % l for l in blas_info['libraries']])
+            elif sys.platform == 'win32':
+                return ' '.join(
+                    ['-L%s' % lib_path] +
+                    # Why on Windows, the library used are not the
+                    # same as what is in blas_info['libraries']?
+                    ['-l%s' % l for l in ["mk2_core", "mk2_intel_thread",
+                                          "mk2_rt"]])
+
+        # Anaconda
+        if "Anaconda" in sys.version and sys.platform == "win32":
+            # If the "mkl-service" conda package (available
+            # through Python package "mkl") is installed and
+            # importable, then the libraries (installed by conda
+            # package "mkl-rt") are actually available.  Using
+            # "conda install mkl" will install both, as well as
+            # optimized versions of numpy and scipy.
+            try:
+                import mkl  # noqa
+            except ImportError as e:
+                _logger.info('Conda mkl is not available: %s', e)
+            else:
+                # This branch is executed if no exception was raised
+                lib_path = os.path.join(sys.prefix, 'DLLs')
+                flags = ['-L%s' % lib_path]
+                flags += ['-l%s' % l for l in ["mkl_core",
+                                               "mkl_intel_thread",
+                                               "mkl_rt"]]
+                res = try_blas_flag(flags)
+                if res:
+                    return res
+
+        ret = (
+            # TODO: the Gemm op below should separate the
+            # -L and -l arguments into the two callbacks
+            # that CLinker uses for that stuff.  for now,
+            # we just pass the whole ldflags as the -l
+            # options part.
+            ['-L%s' % l for l in blas_info.get('library_dirs', [])] +
+            ['-l%s' % l for l in blas_info.get('libraries', [])] +
+            blas_info.get('extra_link_args', []))
+        res = try_blas_flag(ret)
+        if res:
+            return res
+
+        # Some environment don't have the lib dir in LD_LIBRARY_PATH.
+        # So add it.
+        ret.extend(['-Wl,-rpath,' + l for l in
+                    blas_info.get('library_dirs', [])])
+        res = try_blas_flag(ret)
+        if res:
+            return res
+
+        # Try to add the anaconda lib directory to runtime loading of lib.
+        # This fix some case with Anaconda 2.3 on Linux.
+        # Newer Anaconda still have this problem but only have
+        # Continuum in sys.version.
+        if (("Anaconda" in sys.version or
+             "Continuum" in sys.version) and
+                "linux" in sys.platform):
+            lib_path = os.path.join(sys.prefix, 'lib')
+            ret.append('-Wl,-rpath,' + lib_path)
+            res = try_blas_flag(ret)
+            if res:
+                return res
+
+    except KeyError:
+        pass
+
+    # Even if we could not detect what was used for numpy, or if these
+    # libraries are not found, most Linux systems have a libblas.so
+    # readily available. We try to see if that's the case, rather
+    # than disable blas. To test it correctly, we must load a program.
+    # Otherwise, there could be problem in the LD_LIBRARY_PATH.
+    return try_blas_flag(['-lblas'])
+
+
+def try_blas_flag(flags):
+    from theano.gof.cmodule import GCC_compiler
+    test_code = textwrap.dedent("""\
+        extern "C" double ddot_(int*, double*, int*, double*, int*);
+        int main(int argc, char** argv)
+        {
+            int Nx = 5;
+            int Sx = 1;
+            double x[5] = {0, 1, 2, 3, 4};
+            double r = ddot_(&Nx, x, &Sx, x, &Sx);
+
+            if ((r - 30.) > 1e-6 || (r - 30.) < -1e-6)
+            {
+                return -1;
+            }
+            return 0;
+        }
+        """)
+    cflags = flags + ['-L' + d for d in theano.gof.cmodule.std_lib_dirs()]
+    res = GCC_compiler.try_compile_tmp(
+        test_code, tmp_prefix='try_blas_',
+        flags=cflags, try_run=True)
+    # res[0]: shows successful compilation
+    # res[1]: shows successful execution
+    if res and res[0] and res[1]:
+        return ' '.join(flags)
+    else:
+        return ""
+
+AddConfigVar('blas.ldflags',
+             "lib[s] to include for [Fortran] level-3 blas implementation",
+             StrParam(default_blas_ldflags))
+
 AddConfigVar(
     'metaopt.verbose',
     "Enable verbose output for meta optimizers",

theano/sandbox/cuda/__init__.py

@@ -14,8 +14,7 @@ from theano.compile import optdb
 from theano.gof import EquilibriumDB, SequenceDB
 from theano.gof.cmodule import get_lib_extension
 from theano.gof.compilelock import get_lock, release_lock
-from theano.configparser import (
-    config, AddConfigVar, BoolParam, FloatParam, StrParam)
+from theano import config
 from . import nvcc_compiler
 
 from theano.tensor.basic import register_transfer

theano/sandbox/gpuarray/__init__.py

@@ -4,7 +4,7 @@ import sys
 import warnings
 
 import theano
-from theano.configparser import config, AddConfigVar, BoolParam
+from theano import config
 from theano.compile import optdb
 
 from theano.tensor.basic import register_transfer

theano/scan_module/scan_op.py

@@ -87,9 +87,6 @@ from theano.scan_module.scan_utils import safe_new, forced_replace
 _logger = logging.getLogger('theano.scan_module.scan_op')
 
 
-from theano.configparser import AddConfigVar, BoolParam
-
-
 class Scan(PureOp):
     """
 

theano/tensor/blas.py

@@ -128,10 +128,7 @@ from __future__ import print_function
 import copy
 import logging
 import os
-import sys
-import textwrap
 import time
-import warnings
 
 import numpy
 import numpy.distutils
@@ -140,15 +137,14 @@ try:
 except ImportError:
     pass
 
-from theano.configparser import config, AddConfigVar, StrParam
 from six import iteritems
 from six.moves import reduce, xrange
+from theano import config
 from theano.gof import (utils, Op, view_roots,
                         local_optimizer, Optimizer,
                         InconsistencyError, toolbox, SequenceDB,
                         EquilibriumOptimizer, Apply,
                         ReplacementDidntRemovedError)
-from theano.gof.cmodule import GCC_compiler
 from theano.printing import pprint, FunctionPrinter, debugprint
 from theano.compile.mode import optdb
 import theano.scalar
@@ -159,219 +155,6 @@ from theano.tensor.opt import in2out, local_dimshuffle_lift
 
 _logger = logging.getLogger('theano.tensor.blas')
 
-
-# We need to define blas.ldflag before we try to import scipy.
-# Otherwise, we give an optimization warning for no reason in some cases.
-def default_blas_ldflags():
-    global numpy
-    try:
-        if (hasattr(numpy.distutils, '__config__') and
-                numpy.distutils.__config__):
-            # If the old private interface is available use it as it
-            # don't print information to the user.
-            blas_info = numpy.distutils.__config__.blas_opt_info
-        else:
-            # We do this import only here, as in some setup, if we
-            # just import theano and exit, with the import at global
-            # scope, we get this error at exit: "Exception TypeError:
-            # "'NoneType' object is not callable" in <bound method
-            # Popen.__del__ of <subprocess.Popen object at 0x21359d0>>
-            # ignored"
-
-            # This happen with Python 2.7.3 |EPD 7.3-1 and numpy 1.8.1
-            import numpy.distutils.system_info  # noqa
-
-            # We need to catch warnings as in some cases NumPy print
-            # stuff that we don't want the user to see like this:
-            """
-SOMEPATH/Canopy_64bit/User/lib/python2.7/site-packages/numpy/distutils/system_info.py:564: UserWarning: Specified path /home/vagrant/src/master-env/lib is invalid.
-  warnings.warn('Specified path %s is invalid.' % d)
-"""
-            # I'm not able to remove all printed stuff
-            with warnings.catch_warnings(record=True):
-                numpy.distutils.system_info.system_info.verbosity = 0
-                blas_info = numpy.distutils.system_info.get_info("blas_opt")
-
-        # If we are in a EPD installation, mkl is available
-        if "EPD" in sys.version:
-            use_unix_epd = True
-            if sys.platform == 'win32':
-                return ' '.join(
-                    ['-L%s' % os.path.join(sys.prefix, "Scripts")] +
-                    # Why on Windows, the library used are not the
-                    # same as what is in
-                    # blas_info['libraries']?
-                    ['-l%s' % l for l in ["mk2_core", "mk2_intel_thread",
-                                          "mk2_rt"]])
-            elif sys.platform == 'darwin':
-                # The env variable is needed to link with mkl
-                new_path = os.path.join(sys.prefix, "lib")
-                v = os.getenv("DYLD_FALLBACK_LIBRARY_PATH", None)
-                if v is not None:
-                    # Explicit version could be replaced by a symbolic
-                    # link called 'Current' created by EPD installer
-                    # This will resolve symbolic links
-                    v = os.path.realpath(v)
-
-                # The python __import__ don't seam to take into account
-                # the new env variable "DYLD_FALLBACK_LIBRARY_PATH"
-                # when we set with os.environ['...'] = X or os.putenv()
-                # So we warn the user and tell him what todo.
-                if v is None or new_path not in v.split(":"):
-                    _logger.warning(
-                        "The environment variable "
-                        "'DYLD_FALLBACK_LIBRARY_PATH' does not contain "
-                        "the '%s' path in its value. This will make "
-                        "Theano use a slow version of BLAS. Update "
-                        "'DYLD_FALLBACK_LIBRARY_PATH' to contain the "
-                        "said value, this will disable this warning."
-                        % new_path)
-
-                    use_unix_epd = False
-            if use_unix_epd:
-                return ' '.join(
-                    ['-L%s' % os.path.join(sys.prefix, "lib")] +
-                    ['-l%s' % l for l in blas_info['libraries']])
-        # Canopy
-        if "Canopy" in sys.prefix:
-            subsub = 'lib'
-            if sys.platform == 'win32':
-                subsub = 'Scripts'
-            lib_path = os.path.join(sys.base_prefix, subsub)
-            if not os.path.exists(lib_path):
-                # Old logic to find the path. I don't think we still
-                # need it, but I don't have the time to test all
-                # installation configuration. So I keep this as a fall
-                # back in case the current expectation don't work.
-
-                # This old logic don't work when multiple version of
-                # Canopy is installed.
-                p = os.path.join(sys.base_prefix, "..", "..", "appdata")
-                assert os.path.exists(p), "Canopy changed the location of MKL"
-                lib_paths = os.listdir(p)
-                # Try to remove subdir that can't contain MKL
-                for sub in lib_paths:
-                    if not os.path.exists(os.path.join(p, sub, subsub)):
-                        lib_paths.remove(sub)
-                assert len(lib_paths) == 1, (
-                    "Unexpected case when looking for Canopy MKL libraries",
-                    p, lib_paths, [os.listdir(os.path.join(p, sub))
-                                   for sub in lib_paths])
-                lib_path = os.path.join(p, lib_paths[0], subsub)
-                assert os.path.exists(lib_path), "Canopy changed the location of MKL"
-            if sys.platform == "linux2" or sys.platform == "darwin":
-                return ' '.join(
-                    ['-L%s' % lib_path] +
-                    ['-l%s' % l for l in blas_info['libraries']])
-            elif sys.platform == 'win32':
-                return ' '.join(
-                    ['-L%s' % lib_path] +
-                    # Why on Windows, the library used are not the
-                    # same as what is in blas_info['libraries']?
-                    ['-l%s' % l for l in ["mk2_core", "mk2_intel_thread",
-                                          "mk2_rt"]])
-        # Anaconda
-        if "Anaconda" in sys.version and sys.platform == "win32":
-            # If the "mkl-service" conda package (available
-            # through Python package "mkl") is installed and
-            # importable, then the libraries (installed by conda
-            # package "mkl-rt") are actually available.  Using
-            # "conda install mkl" will install both, as well as
-            # optimized versions of numpy and scipy.
-            try:
-                import mkl  # noqa
-            except ImportError as e:
-                _logger.info('Conda mkl is not available: %s', e)
-            else:
-                # This branch is executed if no exception was raised
-                lib_path = os.path.join(sys.prefix, 'DLLs')
-                flags = ['-L%s' % lib_path]
-                flags += ['-l%s' % l for l in ["mkl_core",
-                                               "mkl_intel_thread",
-                                               "mkl_rt"]]
-                res = try_blas_flag(flags)
-                if res:
-                    return res
-
-        ret = (
-            # TODO: the Gemm op below should separate the
-            # -L and -l arguments into the two callbacks
-            # that CLinker uses for that stuff.  for now,
-            # we just pass the whole ldflags as the -l
-            # options part.
-            ['-L%s' % l for l in blas_info.get('library_dirs', [])] +
-            ['-l%s' % l for l in blas_info.get('libraries', [])] +
-            blas_info.get('extra_link_args', []))
-        res = try_blas_flag(ret)
-        if res:
-            return res
-
-        # Some environment don't have the lib dir in LD_LIBRARY_PATH.
-        # So add it.
-        ret.extend(['-Wl,-rpath,' + l for l in
-                    blas_info.get('library_dirs', [])])
-        res = try_blas_flag(ret)
-        if res:
-            return res
-
-        # Try to add the anaconda lib directory to runtime loading of lib.
-        # This fix some case with Anaconda 2.3 on Linux.
-        # Newer Anaconda still have this problem but only have
-        # Continuum in sys.version.
-        if (("Anaconda" in sys.version or
-             "Continuum" in sys.version) and
-                "linux" in sys.platform):
-            lib_path = os.path.join(sys.prefix, 'lib')
-            ret.append('-Wl,-rpath,' + lib_path)
-            res = try_blas_flag(ret)
-            if res:
-                return res
-
-    except KeyError:
-        pass
-
-    # Even if we could not detect what was used for numpy, or if these
-    # libraries are not found, most Linux systems have a libblas.so
-    # readily available. We try to see if that's the case, rather
-    # than disable blas. To test it correctly, we must load a program.
-    # Otherwise, there could be problem in the LD_LIBRARY_PATH.
-    return try_blas_flag(['-lblas'])
-
-
-def try_blas_flag(flags):
-    test_code = textwrap.dedent("""\
-        extern "C" double ddot_(int*, double*, int*, double*, int*);
-        int main(int argc, char** argv)
-        {
-            int Nx = 5;
-            int Sx = 1;
-            double x[5] = {0, 1, 2, 3, 4};
-            double r = ddot_(&Nx, x, &Sx, x, &Sx);
-
-            if ((r - 30.) > 1e-6 || (r - 30.) < -1e-6)
-            {
-                return -1;
-            }
-            return 0;
-        }
-        """)
-    cflags = flags + ['-L' + d for d in theano.gof.cmodule.std_lib_dirs()]
-    res = GCC_compiler.try_compile_tmp(
-        test_code, tmp_prefix='try_blas_',
-        flags=cflags, try_run=True)
-    # res[0]: shows successful compilation
-    # res[1]: shows successful execution
-    if res and res[0] and res[1]:
-        return ' '.join(flags)
-    else:
-        return ""
-
-
-AddConfigVar('blas.ldflags',
-             "lib[s] to include for [Fortran] level-3 blas implementation",
-             StrParam(default_blas_ldflags))
-
-
 try:
     import scipy.linalg.blas
     have_fblas = True