Fix alignment issues with Jets.

1. Test that reproduces the failure on macos.
2. Move the alignment macros from manual_constructor.h
   to macros.h and rename them to prevent conflicts.
3. The inline array used by FixedArray is now aligned.
4. Jet has been modified to be eigen friendly.

Change-Id: I4563847a767a92156dabab1ab420f0cdddb8ba77

include/ceres/internal/fixed_array.h

diff --git a/include/ceres/internal/fixed_array.h b/include/ceres/internal/fixed_array.h
index 29ef157..02d3b71 100644
--- a/include/ceres/internal/fixed_array.h
+++ b/include/ceres/internal/fixed_array.h
@@ -34,6 +34,7 @@
 
 #include <cstddef>
 #include <glog/logging.h>
+#include "ceres/internal/macros.h"
 #include "ceres/internal/manual_constructor.h"
 
 namespace ceres {
@@ -149,7 +150,7 @@
 
   // Allocate some space, not an array of elements of type T, so that we can
   // skip calling the T constructors and destructors for space we never use.
-  ManualConstructor<InnerContainer> inline_space_[kInlineElements];
+  ManualConstructor<InnerContainer> inline_space_[kInlineElements] CERES_ALIGN_ATTRIBUTE(16);
 };
 
 // Implementation details follow

include/ceres/internal/macros.h

diff --git a/include/ceres/internal/macros.h b/include/ceres/internal/macros.h
index 7dd4e3e..0e84e9c 100644
--- a/include/ceres/internal/macros.h
+++ b/include/ceres/internal/macros.h
@@ -152,4 +152,19 @@
 #define MUST_USE_RESULT
 #endif
 
+// Platform independent macros to get aligned memory allocations.
+// For example
+//
+//   MyFoo my_foo CERES_ALIGN_ATTRIBUTE(16);
+//
+// Gives us an instance of MyFoo which is aligned at a 16 byte
+// boundary.
+#if defined(_MSC_VER)
+#define CERES_ALIGN_ATTRIBUTE(n) __declspec(align(n))
+#define CERES_ALIGN_OF(T) __alignof(T)
+#elif defined(__GNUC__)
+#define CERES_ALIGN_ATTRIBUTE(n) __attribute__((aligned(n)))
+#define CERES_ALIGN_OF(T) __alignof(T)
+#endif
+
 #endif  // CERES_PUBLIC_INTERNAL_MACROS_H_

include/ceres/internal/manual_constructor.h

diff --git a/include/ceres/internal/manual_constructor.h b/include/ceres/internal/manual_constructor.h
index a1d1f44..174d35e 100644
--- a/include/ceres/internal/manual_constructor.h
+++ b/include/ceres/internal/manual_constructor.h
@@ -45,60 +45,49 @@
 namespace ceres {
 namespace internal {
 
-// ------- Define ALIGNED_CHAR_ARRAY --------------------------------
+// ------- Define CERES_ALIGNED_CHAR_ARRAY --------------------------------
 
-#ifndef ALIGNED_CHAR_ARRAY
+#ifndef CERES_ALIGNED_CHAR_ARRAY
 
 // Because MSVC and older GCCs require that the argument to their alignment
 // construct to be a literal constant integer, we use a template instantiated
 // at all the possible powers of two.
 template<int alignment, int size> struct AlignType { };
 template<int size> struct AlignType<0, size> { typedef char result[size]; };
-#if defined(_MSC_VER)
-#define BASE_PORT_H_ALIGN_ATTRIBUTE(X) __declspec(align(X))
-#define BASE_PORT_H_ALIGN_OF(T) __alignof(T)
-#elif defined(__GNUC__)
-#define BASE_PORT_H_ALIGN_ATTRIBUTE(X) __attribute__((aligned(X)))
-#define BASE_PORT_H_ALIGN_OF(T) __alignof__(T)
-#endif
 
-#if defined(BASE_PORT_H_ALIGN_ATTRIBUTE)
+#if !defined(CERES_ALIGN_ATTRIBUTE)
+#define CERES_ALIGNED_CHAR_ARRAY you_must_define_CERES_ALIGNED_CHAR_ARRAY_for_your_compiler
+#else  // !defined(CERES_ALIGN_ATTRIBUTE)
 
-#define BASE_PORT_H_ALIGNTYPE_TEMPLATE(X) \
+#define CERES_ALIGN_TYPE_TEMPLATE(X) \
   template<int size> struct AlignType<X, size> { \
-    typedef BASE_PORT_H_ALIGN_ATTRIBUTE(X) char result[size]; \
+    typedef CERES_ALIGN_ATTRIBUTE(X) char result[size]; \
   }
 
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(1);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(2);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(4);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(8);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(16);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(32);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(64);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(128);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(256);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(512);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(1024);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(2048);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(4096);
-BASE_PORT_H_ALIGNTYPE_TEMPLATE(8192);
+CERES_ALIGN_TYPE_TEMPLATE(1);
+CERES_ALIGN_TYPE_TEMPLATE(2);
+CERES_ALIGN_TYPE_TEMPLATE(4);
+CERES_ALIGN_TYPE_TEMPLATE(8);
+CERES_ALIGN_TYPE_TEMPLATE(16);
+CERES_ALIGN_TYPE_TEMPLATE(32);
+CERES_ALIGN_TYPE_TEMPLATE(64);
+CERES_ALIGN_TYPE_TEMPLATE(128);
+CERES_ALIGN_TYPE_TEMPLATE(256);
+CERES_ALIGN_TYPE_TEMPLATE(512);
+CERES_ALIGN_TYPE_TEMPLATE(1024);
+CERES_ALIGN_TYPE_TEMPLATE(2048);
+CERES_ALIGN_TYPE_TEMPLATE(4096);
+CERES_ALIGN_TYPE_TEMPLATE(8192);
 // Any larger and MSVC++ will complain.
 
-#define ALIGNED_CHAR_ARRAY(T, Size) \
-  typename AlignType<BASE_PORT_H_ALIGN_OF(T), sizeof(T) * Size>::result
+#undef CERES_ALIGN_TYPE_TEMPLATE
 
-#undef BASE_PORT_H_ALIGNTYPE_TEMPLATE
-#undef BASE_PORT_H_ALIGN_ATTRIBUTE
+#define CERES_ALIGNED_CHAR_ARRAY(T, Size) \
+  typename AlignType<CERES_ALIGN_OF(T), sizeof(T) * Size>::result
 
-#else  // defined(BASE_PORT_H_ALIGN_ATTRIBUTE)
-#define ALIGNED_CHAR_ARRAY you_must_define_ALIGNED_CHAR_ARRAY_for_your_compiler
-#endif // defined(BASE_PORT_H_ALIGN_ATTRIBUTE)
+#endif  // !defined(CERES_ALIGN_ATTRIBUTE)
 
-#undef BASE_PORT_H_ALIGNTYPE_TEMPLATE
-#undef BASE_PORT_H_ALIGN_ATTRIBUTE
-
-#endif  // ALIGNED_CHAR_ARRAY
+#endif  // CERES_ALIGNED_CHAR_ARRAY
 
 template <typename Type>
 class ManualConstructor {
@@ -203,10 +192,10 @@
   }
 
  private:
-  ALIGNED_CHAR_ARRAY(Type, 1) space_;
+  CERES_ALIGNED_CHAR_ARRAY(Type, 1) space_;
 };
 
-#undef ALIGNED_CHAR_ARRAY
+#undef CERES_ALIGNED_CHAR_ARRAY
 
 }  // namespace internal
 }  // namespace ceres

include/ceres/jet.h

diff --git a/include/ceres/jet.h b/include/ceres/jet.h
index e42abb5..50b5555 100644
--- a/include/ceres/jet.h
+++ b/include/ceres/jet.h
@@ -210,8 +210,20 @@
     return *this;
   }
 
-  T a;  // The scalar part.
+  // The infinitesimal part comes before the scalar part to ensure
+  // alignment. Jets get allocated as an array of type FixedArray
+  // which can allocate memory on the stack or on the heap depending
+  // upon the size of the array. We force the memory allocated on the
+  // stack to be 16 byte boundary aligned, but we also need to ensure
+  // that the elements of the struct are themselves aligned.
   Eigen::Matrix<T, N, 1> v;  // The infinitesimal part.
+  T a;  // The scalar part.
+
+  // Needed to make sure that new instances of Jets are properly
+  // aligned. For more details see
+  //
+  // http://eigen.tuxfamily.org/dox/TopicStructHavingEigenMembers.html
+  EIGEN_MAKE_ALIGNED_OPERATOR_NEW
 };
 
 // Unary +

internal/ceres/autodiff_test.cc

diff --git a/internal/ceres/autodiff_test.cc b/internal/ceres/autodiff_test.cc
index a9fb833..d0bf97a 100644
--- a/internal/ceres/autodiff_test.cc
+++ b/internal/ceres/autodiff_test.cc
@@ -377,5 +377,30 @@
   }
 }
 
+// This is fragile test that triggers the alignment bug on
+// i686-apple-darwin10-llvm-g++-4.2 (GCC) 4.2.1. It is quite possible,
+// that other combinations of operating system + compiler will
+// re-arrange the operations in this test.
+//
+// But this is the best (and only) way we know of to trigger this
+// problem for now. A more robust solution that guarantees the
+// alignment of Eigen types used for automatic differentiation would
+// be nice.
+TEST(AutoDiff, AlignedAllocationTest) {
+  // This int is needed to allocate 16 bits on the stack, so that the
+  // next allocation is not aligned by default.
+  char y = 0;
+
+  // This is needed to prevent the compiler from optimizing y out of
+  // this function.
+  y += 1;
+
+  typedef Jet<double, 2> JetT;
+  FixedArray<JetT, (256 * 7) / sizeof(JetT)> x(3);
+
+  // Need this to makes sure that x does not get optimized out.
+  x[0] = x[0] + JetT(1.0);
+}
+
 }  // namespace internal
 }  // namespace ceres