Installing caffe (digits version) on OS X

0Readme.md

• Virtualenv

Create a new virtualenv with conda. Install digits' requirements:

conda create -n digits --file requirements.txt -c https://conda.binstar.org/slobodan -c https://conda.binstar.org/dougal -c https://conda.binstar.org/pyetras

• Dependencies

First apply brew-boost.patch to brew repository (patches boost to version 1.5.5)

brew install --fresh snappy leveldb gflags glog szip lmdb opencv3 openblas
brew install --build-from-source --with-python --fresh protobuf
brew install --build-from-source --fresh boost boost-python

touch .../anaconda/envs/digits/lib/python2.7/site-packages/opencv3.pth
echo /usr/local/opt/opencv3/lib/python2.7/site-packages >> .../anaconda/envs/digits/lib/python2.7/site-packages/opencv3.pth
touch .../anaconda/envs/digits/lib/python2.7/site-packages/homebrew.pth
echo 'import site; site.addsitedir("/usr/local/lib/python2.7/site-packages")' >> .../anaconda/envs/digits/lib/python2.7/site-packages/homebrew.pth

Install CUDA-7.0.

• Building caffe

git clone --branch caffe-0.12 https://github.com/NVIDIA/caffe.git

Apply Makefile.patch. Copy Makefile.config and replace ANACONDA_HOME with correct path to your virtualenv. Compile with

DYLD_FALLBACK_LIBRARY_PATH="/usr/local/lib:/Developer/NVIDIA/CUDA-7.0/lib:.../anaconda/envs/digits/lib/" LD_LIBRARY_PATH= CMAKE_CPLUS_INCLUDE_PATH="$CPLUS_INCLUDE_PATH;.../anaconda/envs/digits/include/python2.7" make all

substituting ... with correct anaconda path. Also run

make test
make runtest
make py
make distribute

with the same env. Now the $DYLD_FALLBACK_LIBRARY_PATH as above adding caffe-path/build/lib as well has to be included in your .bashrc or equivalent, as make doesn't link with absolute paths (probably due to OS X not being supported in Nvidia's caffe port).

brew-boost.patch

From db0014657a52a44d5eef8ac983694483e7d3b990 Mon Sep 17 00:00:00 2001
From: Pietras <p@pyetras.com>
Date: Tue, 11 Aug 2015 15:06:29 +0200
Subject: [PATCH 1/2] oldbp

---
 Library/Formula/boost-python.rb | 59 ++++++++++++++++++++++++-----------------
 1 file changed, 34 insertions(+), 25 deletions(-)

diff --git a/Library/Formula/boost-python.rb b/Library/Formula/boost-python.rb
index d3610e6..b95ddc0 100644
--- a/Library/Formula/boost-python.rb
+++ b/Library/Formula/boost-python.rb
@@ -1,31 +1,40 @@
+class UniversalPython < Requirement
+  satisfy(:build_env => false) { archs_for_command("python").universal? }
+
+  def message; <<-EOS.undent
+    A universal build was requested, but Python is not a universal build
+
+    Boost compiles against the Python it finds in the path; if this Python
+    is not a universal build then linking will likely fail.
+    EOS
+  end
+end
+
+class UniversalPython3 < Requirement
+  satisfy(:build_env => false) { archs_for_command("python3").universal? }
+
+  def message; <<-EOS.undent
+    A universal build was requested, but Python 3 is not a universal build
+
+    Boost compiles against the Python 3 it finds in the path; if this Python
+    is not a universal build then linking will likely fail.
+    EOS
+  end
+end
+
 class BoostPython < Formula
-  desc "C++ library for C++/Python interoperability"
   homepage "http://www.boost.org"
-  url "https://downloads.sourceforge.net/project/boost/boost/1.58.0/boost_1_58_0.tar.bz2"
-  sha256 "fdfc204fc33ec79c99b9a74944c3e54bd78be4f7f15e260c0e2700a36dc7d3e5"
+  url "https://downloads.sourceforge.net/project/boost/boost/1.57.0/boost_1_57_0.tar.bz2"
+  sha1 "e151557ae47afd1b43dc3fac46f8b04a8fe51c12"
   head "https://github.com/boostorg/boost.git"
 
-  stable do
-    # don't explicitly link a Python framework
-    # https://github.com/boostorg/build/pull/78
-    patch do
-      url "https://gist.githubusercontent.com/tdsmith/9026da299ac1bfd3f419/raw/b73a919c38af08941487ca37d46e711864104c4d/boost-python.diff"
-      sha256 "9f374761ada11eecd082e7f9d5b80efeb387039d3a290f45b61f0730bce3801a"
-    end
-  end
-
-  bottle do
-    cellar :any
-    sha256 "7f627fb1887ecaaea4b6b363d300a21c5274a1607c7dc64f2114d3794b5fec11" => :yosemite
-    sha256 "6239719b00615abb9ce2bd40c680b14182325c2e1844c1bea410c002b42ce1db" => :mavericks
-    sha256 "24acf2ddde1edfabe04239856dec6ce85e8652f3c0d5d8cf357b219c2bf3272a" => :mountain_lion
-  end
-
   option :universal
   option :cxx11
 
-  option "without-python", "Build without python 2 support"
+  depends_on :python => :recommended
   depends_on :python3 => :optional
+  depends_on UniversalPython if build.universal? and build.with? "python"
+  depends_on UniversalPython3 if build.universal? and build.with? "python3"
 
   if build.cxx11?
     depends_on "boost" => "c++11"
@@ -105,12 +114,12 @@ class BoostPython < Formula
         boost::python::def("greet", greet);
       }
     EOS
-    Language::Python.each_python(build) do |python, _|
-      pyflags = (`#{python}-config --includes`.strip +
-                 `#{python}-config --ldflags`.strip).split(" ")
-      system ENV.cxx, "-shared", "hello.cpp", "-lboost_#{python}", "-o", "hello.so", *pyflags
+    Language::Python.each_python(build) do |python, version|
+      pycflags = `#{python}-config --includes`.strip
+      pyldflags = `#{python}-config --ldflags`.strip
+      system "#{ENV.cxx} -shared hello.cpp #{pycflags} #{pyldflags} -lboost_#{python} -o hello.so"
       output = `#{python} -c "from __future__ import print_function; import hello; print(hello.greet())"`
-      assert_match "Hello, world!", output
+      assert output.include?("Hello, world!")
     end
   end
 end
-- 
2.1.0


From e91af7212a3330b34ae33b4367385d8c10cd42b3 Mon Sep 17 00:00:00 2001
From: Pietras <p@pyetras.com>
Date: Tue, 11 Aug 2015 18:00:44 +0200
Subject: [PATCH 2/2] asdf

---
 Library/Formula/boost-python.rb |   5 +-
 Library/Formula/boost.rb        | 197 +++++++++++++++++++++++++++-------------
 2 files changed, 137 insertions(+), 65 deletions(-)

diff --git a/Library/Formula/boost-python.rb b/Library/Formula/boost-python.rb
index b95ddc0..76941c4 100644
--- a/Library/Formula/boost-python.rb
+++ b/Library/Formula/boost-python.rb
@@ -24,8 +24,9 @@ end
 
 class BoostPython < Formula
   homepage "http://www.boost.org"
-  url "https://downloads.sourceforge.net/project/boost/boost/1.57.0/boost_1_57_0.tar.bz2"
-  sha1 "e151557ae47afd1b43dc3fac46f8b04a8fe51c12"
+  url "https://downloads.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.bz2"
+  sha1 "cef9a0cc7084b1d639e06cd3bc34e4251524c840"
+  revision 2
   head "https://github.com/boostorg/boost.git"
 
   option :universal
diff --git a/Library/Formula/boost.rb b/Library/Formula/boost.rb
index 83ff291..8f48924 100644
--- a/Library/Formula/boost.rb
+++ b/Library/Formula/boost.rb
@@ -1,35 +1,108 @@
+require 'formula'
+
+class UniversalPython < Requirement
+  satisfy(:build_env => false) { archs_for_command("python").universal? }
+
+  def message; <<-EOS.undent
+    A universal build was requested, but Python is not a universal build
+
+    Boost compiles against the Python it finds in the path; if this Python
+    is not a universal build then linking will likely fail.
+    EOS
+  end
+end
+
+class UniversalPython3 < Requirement
+  satisfy(:build_env => false) { archs_for_command("python3").universal? }
+
+  def message; <<-EOS.undent
+    A universal build was requested, but Python 3 is not a universal build
+
+    Boost compiles against the Python 3 it finds in the path; if this Python
+    is not a universal build then linking will likely fail.
+    EOS
+  end
+end
+
 class Boost < Formula
-  desc "Collection of portable C++ source libraries"
-  homepage "http://www.boost.org"
-  url "https://downloads.sourceforge.net/project/boost/boost/1.58.0/boost_1_58_0.tar.bz2"
-  sha256 "fdfc204fc33ec79c99b9a74944c3e54bd78be4f7f15e260c0e2700a36dc7d3e5"
+  homepage 'http://www.boost.org'
+  url 'https://downloads.sourceforge.net/project/boost/boost/1.55.0/boost_1_55_0.tar.bz2'
+  sha1 'cef9a0cc7084b1d639e06cd3bc34e4251524c840'
+  revision 2
 
-  head "https://github.com/boostorg/boost.git"
+  head 'https://github.com/boostorg/boost.git'
 
   bottle do
     cellar :any
-    sha256 "9a3929bec0e9e9db36e005f57193433ac6b5ff9ff86b2ed3262b975d58488c19" => :yosemite
-    sha256 "c5ad1f8591ed91c551658fd198ce31cf9f6a8026fcbfd5970a39cb479e64faa2" => :mavericks
-    sha256 "7b154bf42d72bbb90c3017bb94b24fdd2e0605ceab8717283f5c9f456ac5c03d" => :mountain_lion
+    revision 4
+    sha1 "81b8843487a6f0017fac77b4bf58bdc20f3298fa" => :mavericks
+    sha1 "40089f76eddb25ac418032fa0055b6f0b6d76847" => :mountain_lion
+    sha1 "da4fb2a221fd83f50741f757eefe4bc38b5e910c" => :lion
   end
 
   env :userpaths
 
   option :universal
-  option "with-icu4c", "Build regexp engine with icu support"
-  option "without-single", "Disable building single-threading variant"
-  option "without-static", "Disable building static library variant"
-  option "with-mpi", "Build with MPI support"
+  option 'with-icu', 'Build regexp engine with icu support'
+  option 'without-single', 'Disable building single-threading variant'
+  option 'without-static', 'Disable building static library variant'
+  option 'with-mpi', 'Build with MPI support'
   option :cxx11
 
-  deprecated_option "with-icu" => "with-icu4c"
-
-  if build.cxx11?
-    depends_on "icu4c" => [:optional, "c++11"]
-    depends_on "open-mpi" => "c++11" if build.with? "mpi"
-  else
-    depends_on "icu4c" => :optional
-    depends_on :mpi => [:cc, :cxx, :optional]
+  depends_on :python => :optional
+  depends_on :python3 => :optional
+  depends_on UniversalPython if build.universal? and build.with? "python"
+  depends_on UniversalPython3 if build.universal? and build.with? "python3"
+
+  if build.with?("python3") && build.with?("python")
+    odie "boost: --with-python3 cannot be specified when using --with-python"
+  end
+
+  if build.with? 'icu'
+    if build.cxx11?
+      depends_on 'icu4c' => 'c++11'
+    else
+      depends_on 'icu4c'
+    end
+  end
+
+  if build.with? 'mpi'
+    if build.cxx11?
+      depends_on 'open-mpi' => 'c++11'
+    else
+      depends_on :mpi => [:cc, :cxx, :optional]
+    end
+  end
+
+  stable do
+    # Patches boost::atomic for LLVM 3.4 as it is used on OS X 10.9 with Xcode 5.1
+    # https://github.com/Homebrew/homebrew/issues/27396
+    # https://github.com/Homebrew/homebrew/pull/27436
+    patch :p2 do
+      url "https://github.com/boostorg/atomic/commit/6bb71fdd.diff"
+      sha1 "ca8679011d5293a7fd02cb3b97dde3515b8b2b03"
+    end
+
+    patch :p2 do
+      url "https://github.com/boostorg/atomic/commit/e4bde20f.diff"
+      sha1 "b68f5536474c9f543879698299bd4975538a89eb"
+    end
+
+    # Patch fixes upstream issue reported here (https://svn.boost.org/trac/boost/ticket/9698).
+    # Will be fixed in Boost 1.56 and can be removed once that release is available.
+    # See this issue (https://github.com/Homebrew/homebrew/issues/30592) for more details.
+
+    patch :p2 do
+      url "https://github.com/boostorg/chrono/commit/143260d.diff"
+      sha1 "2600214608e7706116831d6ffc302d099ba09950"
+    end
+
+    # Patch boost::serialization for Clang
+    # https://svn.boost.org/trac/boost/ticket/8757
+    patch :p1 do
+      url "https://gist.githubusercontent.com/philacs/375303205d5f8918e700/raw/d6ded52c3a927b6558984d22efe0a5cf9e59cd8c/0005-Boost.S11n-include-missing-algorithm.patch"
+      sha1 "a37552d48e5c1c0507ee9d48fb82a3fa5e3bc9fa"
+    end
   end
 
   fails_with :llvm do
@@ -37,38 +110,59 @@ class Boost < Formula
     cause "Dropped arguments to functions when linking with boost"
   end
 
-  needs :cxx11 if build.cxx11?
-
   def install
     # https://svn.boost.org/trac/boost/ticket/8841
-    if build.with?("mpi") && build.with?("single")
+    if build.with? 'mpi' and build.with? 'single'
       raise <<-EOS.undent
         Building MPI support for both single and multi-threaded flavors
-        is not supported.  Please use "--with-mpi" together with
-        "--without-single".
+        is not supported.  Please use '--with-mpi' together with
+        '--without-single'.
+      EOS
+    end
+
+    if build.cxx11? and build.with? 'mpi' and (build.with? 'python' \
+                                               or build.with? 'python3')
+      raise <<-EOS.undent
+        Building MPI support for Python using C++11 mode results in
+        failure and hence disabled.  Please don't use this combination
+        of options.
       EOS
     end
 
     ENV.universal_binary if build.universal?
 
-    # Force boost to compile with the desired compiler
+    # Force boost to compile using the appropriate GCC version.
     open("user-config.jam", "a") do |file|
       file.write "using darwin : : #{ENV.cxx} ;\n"
-      file.write "using mpi ;\n" if build.with? "mpi"
+      file.write "using mpi ;\n" if build.with? 'mpi'
+
+      # Link against correct version of Python if python3 build was requested
+      if build.with? 'python3'
+        py3executable = `which python3`.strip
+        py3version = `python3 -c "import sys; print(sys.version[:3])"`.strip
+        py3prefix = `python3 -c "import sys; print(sys.prefix)"`.strip
+
+        file.write <<-EOS.undent
+          using python : #{py3version}
+                       : #{py3executable}
+                       : #{py3prefix}/include/python#{py3version}m
+                       : #{py3prefix}/lib ;
+        EOS
+      end
     end
 
-    # libdir should be set by --prefix but isn't
-    bootstrap_args = ["--prefix=#{prefix}", "--libdir=#{lib}"]
+    # we specify libdir too because the script is apparently broken
+    bargs = ["--prefix=#{prefix}", "--libdir=#{lib}"]
 
-    if build.with? "icu4c"
-      icu4c_prefix = Formula["icu4c"].opt_prefix
-      bootstrap_args << "--with-icu=#{icu4c_prefix}"
+    if build.with? 'icu'
+      icu4c_prefix = Formula['icu4c'].opt_prefix
+      bargs << "--with-icu=#{icu4c_prefix}"
     else
-      bootstrap_args << "--without-icu"
+      bargs << '--without-icu'
     end
 
     # Handle libraries that will not be built.
-    without_libraries = ["python"]
+    without_libraries = []
 
     # The context library is implemented as x86_64 ASM, so it
     # won't build on PPC or 32-bit builds
@@ -82,11 +176,12 @@ class Boost < Formula
     # Boost.Log cannot be built using Apple GCC at the moment. Disabled
     # on such systems.
     without_libraries << "log" if ENV.compiler == :gcc || ENV.compiler == :llvm
-    without_libraries << "mpi" if build.without? "mpi"
+    without_libraries << "python" if (build.without? 'python' \
+                                      and build.without? 'python3')
+    without_libraries << "mpi" if build.without? 'mpi'
 
-    bootstrap_args << "--without-libraries=#{without_libraries.join(",")}"
+    bargs << "--without-libraries=#{without_libraries.join(',')}"
 
-    # layout should be synchronized with boost-python
     args = ["--prefix=#{prefix}",
             "--libdir=#{lib}",
             "-d2",
@@ -118,12 +213,12 @@ class Boost < Formula
       end
     end
 
-    system "./bootstrap.sh", *bootstrap_args
+    system "./bootstrap.sh", *bargs
     system "./b2", *args
   end
 
   def caveats
-    s = ""
+    s = ''
     # ENV.compiler doesn't exist in caveats. Check library availability
     # instead.
     if Dir["#{lib}/libboost_log*"].empty?
@@ -143,28 +238,4 @@ class Boost < Formula
 
     s
   end
-
-  test do
-    (testpath/"test.cpp").write <<-EOS.undent
-      #include <boost/algorithm/string.hpp>
-      #include <string>
-      #include <vector>
-      #include <assert.h>
-      using namespace boost::algorithm;
-      using namespace std;
-
-      int main()
-      {
-        string str("a,b");
-        vector<string> strVec;
-        split(strVec, str, is_any_of(","));
-        assert(strVec.size()==2);
-        assert(strVec[0]=="a");
-        assert(strVec[1]=="b");
-        return 0;
-      }
-    EOS
-    system ENV.cxx, "test.cpp", "-std=c++1y", "-lboost_system", "-o", "test"
-    system "./test"
-  end
 end
-- 
2.1.0

Makefile.config

## Refer to http://caffe.berkeleyvision.org/installation.html
# Contributions simplifying and improving our build system are welcome!

# cuDNN acceleration switch (comment to build without cuDNN).
USE_CUDNN := 0

# CPU-only switch (uncomment to build without GPU support).
# CPU_ONLY := 1

# To customize your choice of compiler, uncomment and set the following.
# N.B. the default for Linux is g++ and the default for OSX is clang++
# CUSTOM_CXX := g++

# CUDA directory contains bin/ and lib/ directories that we need.
CUDA_DIR := /Developer/NVIDIA/CUDA-7.0
# On Ubuntu 14.04, if cuda tools are installed via
# "sudo apt-get install nvidia-cuda-toolkit" then use this instead:
# CUDA_DIR := /usr

# CUDA architecture setting: going with all of them.
# For CUDA < 6.0, comment the *_50 lines for compatibility.
CUDA_ARCH := -gencode arch=compute_20,code=sm_20 \
		-gencode arch=compute_20,code=sm_21 \
		-gencode arch=compute_30,code=sm_30 \
		-gencode arch=compute_35,code=sm_35 \
		-gencode arch=compute_50,code=sm_50 \
		-gencode arch=compute_50,code=compute_50

# BLAS choice:
# atlas for ATLAS (default)
# mkl for MKL
# open for OpenBlas
BLAS := open
# Custom (MKL/ATLAS/OpenBLAS) include and lib directories.
# Leave commented to accept the defaults for your choice of BLAS
# (which should work)!
BLAS_INCLUDE := /usr/local/opt/openblas/include
BLAS_LIB := /usr/local/opt/openblas/lib

# This is required only if you will compile the matlab interface.
# MATLAB directory should contain the mex binary in /bin.
# MATLAB_DIR := /usr/local
# MATLAB_DIR := /Applications/MATLAB_R2012b.app

# NOTE: this is required only if you will compile the python interface.
# We need to be able to find Python.h and numpy/arrayobject.h.
# Anaconda Python distribution is quite popular. Include path:
# Verify anaconda location, sometimes it's in root.
ANACONDA_HOME := $(HOME)/.env/anaconda/envs/digits
PYTHON_INCLUDE := $(ANACONDA_HOME)/include \
		$(ANACONDA_HOME)/include/python2.7 \
		$(ANACONDA_HOME)/lib/python2.7/site-packages/numpy/core/include \

# We need to be able to find libpythonX.X.so or .dylib.
# PYTHON_LIB := /usr/lib
PYTHON_LIB := $(ANACONDA_HOME)/lib

# Uncomment to support layers written in Python (will link against Python libs)
WITH_PYTHON_LAYER := 1

# Whatever else you find you need goes here.
INCLUDE_DIRS := $(PYTHON_INCLUDE) /usr/local/include /usr/local/opt/opencv3/include
LIBRARY_DIRS := $(PYTHON_LIB) /usr/local/lib /usr/lib /usr/local/opt/opencv3/lib

# Uncomment to use `pkg-config` to specify OpenCV library paths.
# (Usually not necessary -- OpenCV libraries are normally installed in one of the above $LIBRARY_DIRS.)
# USE_PKG_CONFIG := 1

BUILD_DIR := build
DISTRIBUTE_DIR := distribute

# Uncomment for debugging. Does not work on OSX due to https://github.com/BVLC/caffe/issues/171
# DEBUG := 1

# The ID of the GPU that 'make runtest' will use to run unit tests.
TEST_GPUID := 0

# enable pretty build (comment to see full commands)
Q ?= @

# Adds timing info in logs
# BENCHMARK_DATA := 1
# BENCHMARK_SOLVER := 1

# shared object suffix name to differentiate branches
LIBRARY_NAME_SUFFIX := -nv

Makefile.patch

From 7cf273b7cea65058f1a05e314224105e4cbca582 Mon Sep 17 00:00:00 2001
From: Pietras <p@pyetras.com>
Date: Tue, 11 Aug 2015 19:33:13 +0200
Subject: [PATCH] makefile

---
 Makefile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Makefile b/Makefile
index 3946b03..54c602c 100644
--- a/Makefile
+++ b/Makefile
@@ -178,7 +178,7 @@ ifneq ($(CPU_ONLY), 1)
 endif
 LIBRARIES += glog gflags protobuf leveldb snappy \
 	lmdb boost_system hdf5_hl hdf5 m \
-	opencv_core opencv_highgui opencv_imgproc
+	opencv_core opencv_highgui opencv_imgproc opencv_imgcodecs
 PYTHON_LIBRARIES := boost_python python2.7
 WARNINGS := -Wall -Wno-sign-compare
 
-- 
2.1.0