Merge pull request #4464 from nouiz/small

doc/install.txt

@@ -815,21 +815,6 @@ try the following.
       [gcc]
       cxxflags = -L/opt/local/lib
 
-- An obscure ``Bus error`` can sometimes be caused when linking
-  Theano-generated object files against the ``framework`` library in Leopard.
-  For this reason, we have disabled linking with ``-framework Python``, since on
-  most configurations this solves the ``Bus error`` problem. If this default
-  configuration causes problems with your Python/Theano installation and you think
-  that linking with ``-framework Python`` might help, then either set
-  the :envvar:`THEANO_FLAGS` environment variable with
-  ``THEANO_FLAGS=cmodule.mac_framework_link`` or edit your ``~/.theanorc`` to
-  contain
-
-    .. code-block:: cfg
-
-      [cmodule]
-      mac_framework_link=True
-
 - More generally, to investigate libraries issues, you can use the ``otool -L``
   command on ``.so`` files found under your ``~/.theano`` directory. This will
   list shared libraries dependencies, and may help identify incompatibilities.

doc/install_ubuntu.txt

@@ -12,6 +12,31 @@ For NVIDIA Jetson TX1 embedded platform:
     sudo apt-get install python-numpy python-scipy python-dev python-pip python-nose g++ libblas-dev git
     pip install --upgrade --no-deps git+git://github.com/Theano/Theano.git --user  # Need Theano 0.8(not yet released) or more recent
 
+For Ubuntu 16.04 with cuda 7.5
+
+.. code-block:: bash
+
+    sudo apt-get install python-numpy python-scipy python-dev python-pip python-nose g++ libopenblas-dev git
+    sudo pip install Theano
+
+    # cuda 7.5 don't support the default g++ version. Install an supported version and make it the default.
+    sudo apt-get install g++-4.9
+
+    sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 20
+    sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 10
+
+    sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 20
+    sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-5 10
+
+    sudo update-alternatives --install /usr/bin/cc cc /usr/bin/gcc 30
+    sudo update-alternatives --set cc /usr/bin/gcc
+
+    sudo update-alternatives --install /usr/bin/c++ c++ /usr/bin/g++ 30
+    sudo update-alternatives --set c++ /usr/bin/g++
+
+    # Work around a glibc bug
+    echo -e "\n[nvcc]\nflags=-D_FORCE_INLINES\n" >> ~/.theanorc
+
 For Ubuntu 11.10 through 14.04:
 
 .. code-block:: bash

doc/library/config.txt

@@ -940,13 +940,6 @@ import theano and print the config variable, as in:
     code that can't be cached because there is no c_code_cache_version()
     function associated to at least one of those Ops.
 
-.. attribute:: config.cmodule.mac_framework_link
-
-    Bool value, default: False
-
-    If set to True, breaks certain MacOS installations with the infamous
-    Bus Error.
-
 .. attribute:: config.cmodule.remove_gxx_opt
 
     Bool value, default: False

doc/tutorial/conditions.txt

@@ -75,3 +75,12 @@ is not currently set by default to ``cvm``, it will be in the near future.
 There is no automatic optimization replacing a ``switch`` with a
 broadcasted scalar to an ``ifelse``, as this is not always faster. See
 this `ticket <http://www.assembla.com/spaces/theano/tickets/764>`_.
+
+.. note::
+
+   If you use :ref:`test values <test_values>`, then all branches of
+   the IfElse will be computed. This is normal, as using test_value
+   means everything will be computed when we build it, due to Python's
+   greedy evaluation and the semantic of test value. As we build both
+   branches, they will be executed for test values. This doesn't cause
+   any changes during the execution of the compiled Theano function.

doc/tutorial/debug_faq.txt

@@ -84,6 +84,8 @@ We can here see that the error can be traced back to the line ``z = z + y``.
 For this example, using ``optimizer=fast_compile`` worked. If it did not,
 you could set ``optimizer=None`` or use test values.
 
+.. _test_values:
+
 Using Test Values
 -----------------
 

theano/configdefaults.py

@@ -42,6 +42,8 @@ AddConfigVar('floatX',
              "Note: float16 support is experimental, use at your own risk.",
              EnumStr('float64', 'float32', 'float16',
                      convert=floatX_convert,),
+             # TODO: see gh-4466 for how to remove it.
+             in_c_key=True
              )
 
 AddConfigVar('warn_float64',
@@ -343,11 +345,15 @@ def default_dnn_path(suffix):
 
 AddConfigVar('dnn.include_path',
              "Location of the cudnn header (defaults to the cuda root)",
-             StrParam(default_dnn_path('include')))
+             StrParam(default_dnn_path('include')),
+             # Added elsewhere in the c key only when needed.
+             in_c_key=False)
 
 AddConfigVar('dnn.library_path',
              "Location of the cudnn header (defaults to the cuda root)",
-             StrParam(default_dnn_path('lib' if sys.platform == 'darwin' else 'lib64')))
+             StrParam(default_dnn_path('lib' if sys.platform == 'darwin' else 'lib64')),
+             # Added elsewhere in the c key only when needed.
+             in_c_key=False)
 
 AddConfigVar('dnn.enabled',
              "'auto', use cuDNN if available, but silently fall back"
@@ -543,7 +549,9 @@ AddConfigVar(
 AddConfigVar(
     'lib.amdlibm',
     "Use amd's amdlibm numerical library",
-    BoolParam(False))
+    BoolParam(False),
+    # Added elsewhere in the c key only when needed.
+    in_c_key=False)
 
 AddConfigVar(
     'gpuelemwise.sync',
@@ -564,10 +572,6 @@ AddConfigVar(
     IntParam(8),
     in_c_key=False)
 
-AddConfigVar('experimental.mrg',
-             "Another random number generator that work on the gpu",
-             BoolParam(False))
-
 AddConfigVar('experimental.unpickle_gpu_on_cpu',
              "Allow unpickling of pickled CudaNdarrays as numpy.ndarrays."
              "This is useful, if you want to open a CudaNdarray without "
@@ -854,7 +858,8 @@ AddConfigVar(
     "It can be used to speed up compilation, reduce overhead "
     "(particularly for scalars) and reduce the number of generated C "
     "files.",
-    BoolParam(True))
+    BoolParam(True),
+    in_c_key=True)
 
 AddConfigVar(
     'cache_optimizations',
@@ -863,7 +868,8 @@ AddConfigVar(
     "any optimized graph and its optimization. Actually slow downs a lot "
     "the first optimization, and could possibly still contains some bugs. "
     "Use at your own risks.",
-    BoolParam(False))
+    BoolParam(False),
+    in_c_key=False)
 
 
 def good_seed_param(seed):
@@ -1072,13 +1078,9 @@ AddConfigVar('optdb.max_use_ratio',
 
 AddConfigVar('gcc.cxxflags',
              "Extra compiler flags for gcc",
-             StrParam(""))
-
-AddConfigVar(
-    'cmodule.mac_framework_link',
-    "If set to True, breaks certain MacOS installations with the infamous "
-    "Bus Error",
-    BoolParam(False))
+             StrParam(""),
+             # Added elsewhere in the c key only when needed.
+             in_c_key=False)
 
 AddConfigVar('cmodule.warn_no_version',
              "If True, will print a warning when compiling one or more Op "
@@ -1092,11 +1094,15 @@ AddConfigVar('cmodule.remove_gxx_opt',
              "If True, will remove the -O* parameter passed to g++."
              "This is useful to debug in gdb modules compiled by Theano."
              "The parameter -g is passed by default to g++",
-             BoolParam(False))
+             BoolParam(False),
+             # TODO: change so that this isn't needed.
+             # This can be done by handing this in compile_args()
+             in_c_key=True)
 
 AddConfigVar('cmodule.compilation_warning',
              "If True, will print compilation warnings.",
-             BoolParam(False))
+             BoolParam(False),
+             in_c_key=False)
 
 
 AddConfigVar('cmodule.preload_cache',
@@ -1315,7 +1321,9 @@ def try_blas_flag(flags):
 
 AddConfigVar('blas.ldflags',
              "lib[s] to include for [Fortran] level-3 blas implementation",
-             StrParam(default_blas_ldflags))
+             StrParam(default_blas_ldflags),
+             # Added elsewhere in the c key only when needed.
+             in_c_key=False)
 
 AddConfigVar(
     'metaopt.verbose',
@@ -1399,12 +1407,14 @@ AddConfigVar(
 
 AddConfigVar('scan.allow_gc',
              "Allow/disallow gc inside of Scan (default: False)",
-             BoolParam(False))
+             BoolParam(False),
+             in_c_key=False)
 
 AddConfigVar('scan.allow_output_prealloc',
              "Allow/disallow memory preallocation for outputs inside of scan "
              "(default: True)",
-             BoolParam(True))
+             BoolParam(True),
+             in_c_key=False)
 
 AddConfigVar('pycuda.init',
              """If True, always initialize PyCUDA when Theano want to
@@ -1419,7 +1429,9 @@ AddConfigVar('pycuda.init',
 
 AddConfigVar('cublas.lib',
              """Name of the cuda blas library for the linker.""",
-             StrParam('cublas'))
+             StrParam('cublas'),
+             # Added elsewhere in the c key only when needed.
+             in_c_key=False)
 
 AddConfigVar('lib.cnmem',
              """Do we enable CNMeM or not (a faster CUDA memory allocator).

theano/gof/cc.py

@@ -1229,10 +1229,6 @@ class CLinker(link.Linker):
         It is followed by elements for every node in the topological ordering
         of `self.fgraph`.
 
-        If the Op of any Apply in the FunctionGraph does not have
-        c_code_cache_ok()==True, then this function raises a KeyError
-        exception.
-
         Input Signature
         ---------------
 

theano/misc/do_nightly_build

@@ -53,6 +53,7 @@ FLAGS=${FLAGS},device=cpu,floatX=float64
 
 if [ "$RELEASE" ]; then
     echo "Executing tests with default mode and compute_test_value"
+    date
     THEANO_FLAGS=${FLAGS},compute_test_value=ignore ${NOSETESTS} ${ARGS}
     echo "Number of elements in the compiledir:"
     ls ${COMPILEDIR}|wc -l
@@ -60,6 +61,7 @@ if [ "$RELEASE" ]; then
 
     echo "Executing tests with linker=vm,floatX=float32"
     echo "THEANO_FLAGS=${FLAGS},linker=vm,floatX=float32 ${NOSETESTS} ${ARGS}"
+    date
     THEANO_FLAGS=${FLAGS},linker=vm,floatX=float32 ${NOSETESTS} ${ARGS}
     echo "Number of elements in the compiledir:"
     ls ${COMPILEDIR}|wc -l
@@ -67,6 +69,7 @@ if [ "$RELEASE" ]; then
 
     echo "Executing tests with cxx="
     echo "THEANO_FLAGS=${FLAGS},cxx= ${NOSETESTS} ${ARGS}"
+    date
     THEANO_FLAGS=${FLAGS},cxx= ${NOSETESTS} ${ARGS}
     echo "Number of elements in the compiledir:"
     ls ${COMPILEDIR}|wc -l
@@ -76,6 +79,7 @@ fi
 
 echo "Executing tests with mode=FAST_RUN"
 echo "THEANO_FLAGS=cmodule.warn_no_version=True,${FLAGS},mode=FAST_RUN ${NOSETESTS} ${PROFILING} ${ARGS}"
+date
 THEANO_FLAGS=cmodule.warn_no_version=True,${FLAGS},mode=FAST_RUN ${NOSETESTS} ${PROFILING} ${ARGS}
 echo "Number of elements in the compiledir:"
 ls ${COMPILEDIR}|wc -l
@@ -83,6 +87,7 @@ echo
 
 echo "Executing tests with mode=FAST_RUN,floatX=float32"
 echo "THEANO_FLAGS=${FLAGS},mode=FAST_RUN,floatX=float32 ${NOSETESTS} ${ARGS}"
+date
 THEANO_FLAGS=${FLAGS},mode=FAST_RUN,floatX=float32 ${NOSETESTS} ${ARGS}
 echo "Number of elements in the compiledir:"
 ls ${COMPILEDIR}|wc -l
@@ -90,6 +95,7 @@ echo
 
 echo "Executing tests with linker=vm,vm.lazy=True,floatX=float32"
 echo "THEANO_FLAGS=${FLAGS},linker=vm,vm.lazy=True,floatX=float32 ${NOSETESTS} ${ARGS}"
+date
 THEANO_FLAGS=${FLAGS},linker=vm,vm.lazy=True,floatX=float32 ${NOSETESTS} ${ARGS}
 echo "Number of elements in the compiledir:"
 ls ${COMPILEDIR}|wc -l
@@ -99,6 +105,7 @@ echo
 seed=$RANDOM
 echo "Executing tests with mode=DEBUG_MODE with seed of the day $seed"
 echo "THEANO_FLAGS=${FLAGS},unittests.rseed=$seed,mode=DEBUG_MODE,DebugMode.check_strides=0,DebugMode.patience=3,DebugMode.check_preallocated_output= ${NOSETESTS} ${ARGS}"
+date
 THEANO_FLAGS=${FLAGS},unittests.rseed=$seed,mode=DEBUG_MODE,DebugMode.check_strides=0,DebugMode.patience=3,DebugMode.check_preallocated_output= ${NOSETESTS} ${ARGS}
 
 echo "Number of elements in the compiledir:"
@@ -110,6 +117,7 @@ echo
 # with --batch=1000" # The buildbot freeze sometimes when collecting the tests to run
 echo "Executing tests with mode=FAST_COMPILE"
 echo "THEANO_FLAGS=${FLAGS},mode=FAST_COMPILE ${NOSETESTS} ${ARGS}"
+date
 THEANO_FLAGS=${FLAGS},mode=FAST_COMPILE ${NOSETESTS} ${ARGS}
 
 echo "Number of elements in the compiledir:"

theano/scan_module/scan.py

@@ -316,6 +316,21 @@ def scan(fn,
         Set the value of allow gc for the internal graph of scan.  If
         set to None, this will use the value of config.scan.allow_gc.
 
+        The full scan behavior related to allocation is determined by
+        this value and the Theano flag allow_gc. If the flag allow_gc
+        is True (default) and this scan parameter allow_gc is False
+        (default), then we let scan allocate all intermediate memory
+        on the first iteration, those are not garbage collected them
+        during that first iteration (this is determined by the scan
+        allow_gc). This speed up allocation of the following
+        iteration. But we free all those temp allocation at the end of
+        all iterations (this is what the Theano flag allow_gc mean).
+
+        If you use cnmem and this scan is on GPU, the speed up from
+        the scan allow_gc is small. If you are missing memory, disable
+        the scan allow_gc could help you run graph that request much
+        memory.
+
     strict
         If true, all the shared variables used in ``fn`` must be provided as a
         part of ``non_sequences`` or ``sequences``.