Patches for Google Protobuf 2.5.0 release designed to add support for architectures that used to work in 2.4.1, but broken in 2.5.0. The patch is courtesy of this developer (https://code.google.com/u/110106420545796050291/) who posted it on the Google Protobuf discussion group (https://code.google.com/p/protobuf/issues/detail?id=488) in May, 2013.

0001-Add-generic-gcc-header-to-Makefile.am.patch

From b53d00e42cdc4a4b57e31d58244cb46b3b05bd6a Mon Sep 17 00:00:00 2001
From: Stanislav Ochotnicky <sochotnicky@redhat.com>
Date: Thu, 16 May 2013 12:01:10 +0200
Subject: [PATCH] Add generic gcc header to Makefile.am

This way it will get included properly during installation and
distribution generation
---
 src/Makefile.am | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/Makefile.am b/src/Makefile.am
index 4069603..2458ceb 100644
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -42,6 +42,7 @@ nobase_include_HEADERS =                                        \
   google/protobuf/stubs/atomicops_internals_arm_gcc.h           \
   google/protobuf/stubs/atomicops_internals_arm_qnx.h           \
   google/protobuf/stubs/atomicops_internals_atomicword_compat.h \
+  google/protobuf/stubs/atomicops_internals_generic_gcc.h       \
   google/protobuf/stubs/atomicops_internals_macosx.h            \
   google/protobuf/stubs/atomicops_internals_mips_gcc.h          \
   google/protobuf/stubs/atomicops_internals_pnacl.h             \
-- 
1.8.1.4

0001-Add-generic-GCC-support-for-atomic-operations.patch

From d099ec11fc8c2eb97df2bf2fbb6996066eefca46 Mon Sep 17 00:00:00 2001
From: Stanislav Ochotnicky <sochotnicky@redhat.com>
Date: Thu, 2 May 2013 10:43:47 +0200
Subject: [PATCH] Add generic GCC support for atomic operations

This is useful for architectures where no specialized code has been
written.
---
 src/google/protobuf/stubs/atomicops.h              |   2 +-
 .../stubs/atomicops_internals_generic_gcc.h        | 139 +++++++++++++++++++++
 src/google/protobuf/stubs/platform_macros.h        |  14 ++-
 3 files changed, 153 insertions(+), 2 deletions(-)
 create mode 100644 src/google/protobuf/stubs/atomicops_internals_generic_gcc.h

diff --git a/src/google/protobuf/stubs/atomicops.h b/src/google/protobuf/stubs/atomicops.h
index b8581fa..883b125 100644
--- a/src/google/protobuf/stubs/atomicops.h
+++ b/src/google/protobuf/stubs/atomicops.h
@@ -185,7 +185,7 @@ GOOGLE_PROTOBUF_ATOMICOPS_ERROR
 #elif defined(__pnacl__)
 #include <google/protobuf/stubs/atomicops_internals_pnacl.h>
 #else
-GOOGLE_PROTOBUF_ATOMICOPS_ERROR
+#include <google/protobuf/stubs/atomicops_internals_generic_gcc.h>
 #endif
 
 // Unknown.
diff --git a/src/google/protobuf/stubs/atomicops_internals_generic_gcc.h b/src/google/protobuf/stubs/atomicops_internals_generic_gcc.h
new file mode 100644
index 0000000..3fc2a9b
--- /dev/null
+++ b/src/google/protobuf/stubs/atomicops_internals_generic_gcc.h
@@ -0,0 +1,139 @@
+// Protocol Buffers - Google's data interchange format
+// Copyright 2013 Red Hat Inc.  All rights reserved.
+// http://code.google.com/p/protobuf/
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions are
+// met:
+//
+//     * Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//     * Redistributions in binary form must reproduce the above
+// copyright notice, this list of conditions and the following disclaimer
+// in the documentation and/or other materials provided with the
+// distribution.
+//     * Neither the name of Red Hat Inc. nor the names of its
+// contributors may be used to endorse or promote products derived from
+// this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+// This file is an internal atomic implementation, use atomicops.h instead.
+
+#ifndef GOOGLE_PROTOBUF_ATOMICOPS_INTERNALS_GENERIC_GCC_H_
+#define GOOGLE_PROTOBUF_ATOMICOPS_INTERNALS_GENERIC_GCC_H_
+
+namespace google {
+namespace protobuf {
+namespace internal {
+
+inline Atomic32 NoBarrier_CompareAndSwap(volatile Atomic32* ptr,
+                                         Atomic32 old_value,
+                                         Atomic32 new_value) {
+  __atomic_compare_exchange_n(ptr, &old_value, new_value, true,
+                              __ATOMIC_RELAXED, __ATOMIC_RELAXED);
+  return old_value;
+}
+
+inline Atomic32 NoBarrier_AtomicExchange(volatile Atomic32* ptr,
+                                         Atomic32 new_value) {
+  return __atomic_exchange_n(ptr, new_value, __ATOMIC_RELAXED);
+}
+
+inline Atomic32 NoBarrier_AtomicIncrement(volatile Atomic32* ptr,
+                                          Atomic32 increment) {
+  return __atomic_add_fetch(ptr, increment, __ATOMIC_RELAXED);
+}
+
+inline Atomic32 Barrier_AtomicIncrement(volatile Atomic32* ptr,
+                                        Atomic32 increment) {
+  return __atomic_add_fetch(ptr, increment, __ATOMIC_SEQ_CST);
+}
+
+inline Atomic32 Acquire_CompareAndSwap(volatile Atomic32* ptr,
+                                       Atomic32 old_value,
+                                       Atomic32 new_value) {
+  __atomic_compare_exchange(ptr, &old_value, &new_value, true,
+                            __ATOMIC_ACQUIRE, __ATOMIC_ACQUIRE);
+  return old_value;
+}
+
+inline Atomic32 Release_CompareAndSwap(volatile Atomic32* ptr,
+                                       Atomic32 old_value,
+                                       Atomic32 new_value) {
+  __atomic_compare_exchange_n(ptr, &old_value, new_value, true,
+                            __ATOMIC_RELEASE, __ATOMIC_ACQUIRE);
+  return old_value;
+}
+
+inline void NoBarrier_Store(volatile Atomic32* ptr, Atomic32 value) {
+  __atomic_store_n(ptr, value, __ATOMIC_RELAXED);
+}
+
+inline void MemoryBarrier() {
+  __sync_synchronize();
+}
+
+inline void Acquire_Store(volatile Atomic32* ptr, Atomic32 value) {
+  __atomic_store_n(ptr, value, __ATOMIC_ACQUIRE);
+}
+
+inline void Release_Store(volatile Atomic32* ptr, Atomic32 value) {
+  __atomic_store_n(ptr, value, __ATOMIC_RELEASE);
+}
+
+inline Atomic32 NoBarrier_Load(volatile const Atomic32* ptr) {
+  return __atomic_load_n(ptr, __ATOMIC_RELAXED);
+}
+
+inline Atomic32 Acquire_Load(volatile const Atomic32* ptr) {
+  return __atomic_load_n(ptr, __ATOMIC_ACQUIRE);
+}
+
+inline Atomic32 Release_Load(volatile const Atomic32* ptr) {
+  return __atomic_load_n(ptr, __ATOMIC_RELEASE);
+}
+
+#ifdef __LP64__
+
+inline void Release_Store(volatile Atomic64* ptr, Atomic64 value) {
+  __atomic_store_n(ptr, value, __ATOMIC_RELEASE);
+}
+
+inline Atomic64 Acquire_Load(volatile const Atomic64* ptr) {
+  return __atomic_load_n(ptr, __ATOMIC_ACQUIRE);
+}
+
+inline Atomic64 Acquire_CompareAndSwap(volatile Atomic64* ptr,
+                                       Atomic64 old_value,
+                                       Atomic64 new_value) {
+  __atomic_compare_exchange_n(ptr, &old_value, new_value, true,
+                              __ATOMIC_ACQUIRE, __ATOMIC_ACQUIRE);
+  return old_value;
+}
+
+inline Atomic64 NoBarrier_CompareAndSwap(volatile Atomic64* ptr,
+                                         Atomic64 old_value,
+                                         Atomic64 new_value) {
+  __atomic_compare_exchange_n(ptr, &old_value, new_value, true,
+                            __ATOMIC_RELAXED, __ATOMIC_RELAXED);
+  return old_value;
+}
+
+#endif // defined(__LP64__)
+
+}  // namespace internal
+}  // namespace protobuf
+}  // namespace google
+
+#endif  // GOOGLE_PROTOBUF_ATOMICOPS_INTERNALS_GENERIC_GCC_H_
diff --git a/src/google/protobuf/stubs/platform_macros.h b/src/google/protobuf/stubs/platform_macros.h
index b1df60e..db691d8 100644
--- a/src/google/protobuf/stubs/platform_macros.h
+++ b/src/google/protobuf/stubs/platform_macros.h
@@ -43,6 +43,9 @@
 #elif defined(_M_IX86) || defined(__i386__)
 #define GOOGLE_PROTOBUF_ARCH_IA32 1
 #define GOOGLE_PROTOBUF_ARCH_32_BIT 1
+#elif defined(__aarch64__)
+#define GOOGLE_PROTOBUF_ARCH_AARCH64 1
+#define GOOGLE_PROTOBUF_ARCH_64_BIT 1
 #elif defined(__QNX__)
 #define GOOGLE_PROTOBUF_ARCH_ARM_QNX 1
 #define GOOGLE_PROTOBUF_ARCH_32_BIT 1
@@ -54,9 +57,18 @@
 #define GOOGLE_PROTOBUF_ARCH_32_BIT 1
 #elif defined(__pnacl__)
 #define GOOGLE_PROTOBUF_ARCH_32_BIT 1
-#elif defined(__ppc__)
+#elif defined(__ppc64__) || defined(__PPC64__)
+#define GOOGLE_PROTOBUF_ARCH_PPC64 1
+#define GOOGLE_PROTOBUF_ARCH_64_BIT 1
+#elif defined(__ppc__) || defined(__PPC__)
 #define GOOGLE_PROTOBUF_ARCH_PPC 1
 #define GOOGLE_PROTOBUF_ARCH_32_BIT 1
+#elif defined(__s390x__)
+#define GOOGLE_PROTOBUF_ARCH_64_BIT 1
+#define GOOGLE_PROTOBUF_ARCH_S390X 1
+#elif defined(__s390__)
+#define GOOGLE_PROTOBUF_ARCH_32_BIT 1
+#define GOOGLE_PROTOBUF_ARCH_S390 1
 #else
 #error Host architecture was not detected as supported by protobuf
 #endif
-- 
1.8.1.4

Excellent work, Bennett. Verified as working when cross-compiling for armv8a. For others that arrive here after me, what I did was to download Bennett's patches and apply them with

git apply 0001-Add-generic-gcc-header-to-Makefile.am.patch
git apply 0001-Add-generic-GCC-support-for-atomic-operations.patch

And then ndk-build then passed just fine and all remaining compilation errors were gone. I'm using CrystaX's NDK, by the way, because I was also having problems trying to build Boost. You may want to check CrystaX if you're having problems with Boost as well.