Merge pull request #567 from peastman/pnacl

Support Chrome portable native client

CMakeLists.txt

@@ -115,7 +115,7 @@ ELSE( CMAKE_SIZEOF_VOID_P EQUAL 8 )
   SET( LIB64  )
 ENDIF( CMAKE_SIZEOF_VOID_P EQUAL 8 )
 
-IF (APPLE)
+IF (APPLE AND (NOT PNACL))
     # Build universal binaries compatible with OS X 10.7
     IF (NOT CMAKE_OSX_DEPLOYMENT_TARGET)
         SET (CMAKE_OSX_DEPLOYMENT_TARGET "10.7" CACHE STRING "The minimum version of OS X to support" FORCE)
@@ -127,13 +127,13 @@ IF (APPLE)
     # Improve the linking behavior of Mac libraries
     SET (CMAKE_INSTALL_NAME_DIR "@rpath")
     SET(EXTRA_COMPILE_FLAGS "-msse2 -stdlib=libc++")
-ELSE (APPLE)
-    IF (MSVC OR ANDROID)
+ELSE (APPLE AND (NOT PNACL))
+    IF (MSVC OR ANDROID OR PNACL)
         SET(EXTRA_COMPILE_FLAGS)
-    ELSE (MSVC OR ANDROID)
+    ELSE (MSVC OR ANDROID OR PNACL)
         SET(EXTRA_COMPILE_FLAGS "-msse2")
-    ENDIF (MSVC OR ANDROID)
-ENDIF (APPLE)
+    ENDIF (MSVC OR ANDROID OR PNACL)
+ENDIF (APPLE AND (NOT PNACL))
 
 IF(UNIX AND NOT CMAKE_BUILD_TYPE)
     SET(CMAKE_BUILD_TYPE Release CACHE STRING "Debug or Release build" FORCE)
@@ -264,11 +264,11 @@ FOREACH(subdir ${OPENMM_SOURCE_SUBDIRS})
     ## OpenMM was previously installed there.
     INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/${subdir}/include)
 ENDFOREACH(subdir)
-IF (ANDROID)
+IF (ANDROID OR PNACL)
     SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/libraries/sfmt/src/SFMT.cpp PROPERTIES COMPILE_FLAGS "-UHAVE_SSE2")
-ELSE (ANDROID)
+ELSE (ANDROID OR PNACL)
     SET_SOURCE_FILES_PROPERTIES(${CMAKE_SOURCE_DIR}/libraries/sfmt/src/SFMT.cpp PROPERTIES COMPILE_FLAGS "-DHAVE_SSE2=1")
-ENDIF(ANDROID)
+ENDIF(ANDROID OR PNACL)
 
 # If API wrappers are being generated, and add them to the build.
 SET(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS ON CACHE BOOL "Build wrappers for C and Fortran")
@@ -280,11 +280,15 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
 
 INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 
-ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY")
-IF(WIN32)
+SET(OPENMM_BUILD_SHARED_LIB ON CACHE BOOL "Whether to build shared OpenMM libraries")
+
+IF(OPENMM_BUILD_SHARED_LIB)
+    ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY -DLEPTON_BUILDING_SHARED_LIBRARY -DOPENMM_VALIDATE_BUILDING_SHARED_LIBRARY")
+    IF(WIN32)
         ADD_DEPENDENCIES(${SHARED_TARGET} PthreadsLibraries)
-ENDIF(WIN32)
+    ENDIF(WIN32)
+ENDIF(OPENMM_BUILD_SHARED_LIB)
 
 SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
 IF(OPENMM_BUILD_STATIC_LIB)
@@ -303,17 +307,21 @@ ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
 # On Linux need to link to libdl
 FIND_LIBRARY(DL_LIBRARY dl)
 IF(DL_LIBRARY)
+    IF(OPENMM_BUILD_SHARED_LIB)
         TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${DL_LIBRARY} ${PTHREADS_LIB})
+    ENDIF(OPENMM_BUILD_SHARED_LIB)
     IF(OPENMM_BUILD_STATIC_LIB)
         TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${DL_LIBRARY} ${PTHREADS_LIB})
     ENDIF(OPENMM_BUILD_STATIC_LIB)
     MARK_AS_ADVANCED(DL_LIBRARY)
 ELSE(DL_LIBRARY)
+    IF(OPENMM_BUILD_SHARED_LIB)
         IF (ANDROID)
             TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${PTHREADS_LIB} cpufeatures)
         ELSE (ANDROID)
             TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${PTHREADS_LIB})
         ENDIF (ANDROID)
+    ENDIF(OPENMM_BUILD_SHARED_LIB)
 ENDIF(DL_LIBRARY)
 
 ADD_SUBDIRECTORY(platforms/reference/tests)
@@ -433,7 +441,9 @@ IF(OPENMM_BUILD_PME_PLUGIN)
    ADD_SUBDIRECTORY(plugins/cpupme)
 ENDIF(OPENMM_BUILD_PME_PLUGIN)
 
-INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_TARGET})
+IF(OPENMM_BUILD_SHARED_LIB)
+    INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${SHARED_TARGET})
+ENDIF(OPENMM_BUILD_SHARED_LIB)
 IF(OPENMM_BUILD_STATIC_LIB)
   INSTALL_TARGETS(/lib RUNTIME_DIRECTORY /lib ${STATIC_TARGET})
 ENDIF(OPENMM_BUILD_STATIC_LIB)

examples/CMakeLists.txt

@@ -21,14 +21,8 @@ SET(CPP_EXAMPLES HelloArgon HelloSodiumChloride HelloEthane HelloWaterBox)
 SET(C_EXAMPLES HelloArgonInC HelloSodiumChlorideInC)
 SET(F_EXAMPLES HelloArgonInFortran HelloSodiumChlorideInFortran)
 
-SET(BUILD_TESTING_SHARED 1)
-SET(BUILD_TESTING_STATIC OFF)
-IF(OPENMM_BUILD_STATIC_LIB)
-    SET(BUILD_TESTING_STATIC ON)
-ENDIF(OPENMM_BUILD_STATIC_LIB)
-
 FOREACH(EX_ROOT ${CPP_EXAMPLES})
-    IF (BUILD_TESTING_SHARED)
+    IF (OPENMM_BUILD_SHARED_LIB)
         # Link with shared library
         ADD_EXECUTABLE(${EX_ROOT} ${EX_ROOT}.cpp)
         SET_TARGET_PROPERTIES(${EX_ROOT}
@@ -37,9 +31,9 @@ FOREACH(EX_ROOT ${CPP_EXAMPLES})
             LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
             COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
         TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
-    ENDIF (BUILD_TESTING_SHARED)
+    ENDIF (OPENMM_BUILD_SHARED_LIB)
 
-    IF (BUILD_TESTING_STATIC)
+    IF (OPENMM_BUILD_STATIC_LIB)
         # Link with static library
         SET(EX_STATIC ${EX_ROOT}Static)
         ADD_EXECUTABLE(${EX_STATIC} ${EX_ROOT}.cpp)
@@ -49,7 +43,7 @@ FOREACH(EX_ROOT ${CPP_EXAMPLES})
             LINK_FLAGS "${EXTRA_COMPILE_FLAGS}"
             COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
         TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
-    ENDIF (BUILD_TESTING_STATIC)
+    ENDIF (OPENMM_BUILD_STATIC_LIB)
 
     INSTALL(FILES ${EX_ROOT}.cpp DESTINATION examples)
 
@@ -60,7 +54,7 @@ IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
     INCLUDE_DIRECTORIES(BEFORE ${PROJECT_BINARY_DIR}/wrappers)
 
     FOREACH(EX_ROOT ${C_EXAMPLES})
-        IF (BUILD_TESTING_SHARED)
+        IF (OPENMM_BUILD_SHARED_LIB)
             # Link with shared library
             # We need at least one .cpp here to get CMake to include
             # C++ libraries on the link line.
@@ -72,9 +66,9 @@ IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
                 COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
             TARGET_LINK_LIBRARIES(${EX_ROOT} ${SHARED_TARGET})
             ADD_DEPENDENCIES(${EX_ROOT} ApiWrappers)
-        ENDIF (BUILD_TESTING_SHARED)
+        ENDIF (OPENMM_BUILD_SHARED_LIB)
 
-        IF (BUILD_TESTING_STATIC)
+        IF (OPENMM_BUILD_STATIC_LIB)
             # Link with static library
             SET(EX_STATIC ${EX_ROOT}Static)
             # We need at least one .cpp here to get CMake to include
@@ -87,7 +81,7 @@ IF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
                 COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_USE_STATIC_LIBRARIES")
             TARGET_LINK_LIBRARIES(${EX_STATIC} ${STATIC_TARGET})
             ADD_DEPENDENCIES(${EX_STATIC} ApiWrappers)
-        ENDIF (BUILD_TESTING_STATIC)
+        ENDIF (OPENMM_BUILD_STATIC_LIB)
   ENDFOREACH(EX_ROOT ${C_EXAMPLES})
 ENDIF(OPENMM_BUILD_C_AND_FORTRAN_WRAPPERS)
 

libraries/csha1/include/SHA1.h

@@ -116,7 +116,6 @@
 #endif
 #endif
 
-#include <memory.h>
 #include <limits.h>
 
 #ifdef SHA1_UTILITY_FUNCTIONS

libraries/lbfgs/src/arithmetic_ansi.h

@@ -26,7 +26,7 @@
 /* $Id: arithmetic_ansi.h 65 2010-01-29 12:19:16Z naoaki $ */
 
 #include <stdlib.h>
-#include <memory.h>
+#include <string.h>
 
 #if     LBFGS_FLOAT == 32 && LBFGS_IEEE_FLOAT
 #define fsigndiff(x, y) (((*(uint32_t*)(x)) ^ (*(uint32_t*)(y))) & 0x80000000U)

olla/src/Platform.cpp

@@ -38,7 +38,9 @@
 #include <windows.h>
 #include <sstream>
 #else
-#include <dlfcn.h>
+#ifndef __PNACL__
+    #include <dlfcn.h>
+#endif
 #include <dirent.h>
 #include <cstdlib>
 #endif
@@ -187,13 +189,18 @@ static void initializePlugins(vector<HMODULE>& plugins) {
 }
 #else
 static void* loadOneLibrary(const string& file) {
+#ifdef __PNACL__
+    throw OpenMMException("Loading dynamic libraries is not supported on PNaCl");
+#else    
     void *handle = dlopen(file.c_str(), RTLD_LAZY | RTLD_GLOBAL);
     if (handle == NULL)
         throw OpenMMException("Error loading library "+file+": "+dlerror());
     return handle;
+#endif
 }
 
 static void initializePlugins(vector<void*>& plugins) {
+#ifndef __PNACL__
     for (int i = 0; i < (int) plugins.size(); i++) {
         void (*init)();
         *(void **)(&init) = dlsym(plugins[i], "registerPlatforms");
@@ -206,6 +213,7 @@ static void initializePlugins(vector<void*>& plugins) {
         if (init != NULL)
             (*init)();
     }
+#endif
 }
 #endif
 

openmmapi/include/openmm/internal/hardware.h

@@ -50,7 +50,6 @@
       #ifdef __ANDROID__
         #include <cpu-features.h>
       #else
-        #include <dlfcn.h>
         #include <unistd.h>
       #endif
    #endif
@@ -93,7 +92,7 @@ static int getNumProcessors() {
 #ifdef _WIN32
 #define cpuid __cpuid
 #else
-#ifndef __ANDROID__
+#if !defined(__ANDROID__) && !defined(__PNACL__)
     static void cpuid(int cpuInfo[4], int infoType){
     #ifdef __LP64__
         __asm__ __volatile__ (

openmmapi/include/openmm/internal/vectorize.h

@@ -35,7 +35,11 @@
 #if defined(__ANDROID__)
     #include "vectorize_neon.h"
 #else
+    #if defined(__PNACL__)
+        #include "vectorize_pnacl.h"
+    #else
         #include "vectorize_sse.h"
+    #endif
 #endif
 
 #endif /*OPENMM_VECTORIZE_H_*/

openmmapi/include/openmm/internal/vectorize_neon.h

@@ -40,6 +40,14 @@ typedef int int32_t;
 
 // This file defines classes and functions to simplify vectorizing code with NEON.
 
+/**
+ * Determine whether ivec4 and fvec4 are supported on this processor.
+ */
+static bool isVec4Supported() {
+    uint64_t features = android_getCpuFeatures();
+    return (features & ANDROID_CPU_ARM_FEATURE_NEON) != 0;
+}
+
 class ivec4;
 
 /**

openmmapi/include/openmm/internal/vectorize_pnacl.h

+#ifndef OPENMM_VECTORIZE_PNACL_H_
+#define OPENMM_VECTORIZE_PNACL_H_
+
+/* -------------------------------------------------------------------------- *
+ *                                   OpenMM                                   *
+ * -------------------------------------------------------------------------- *
+ * This is part of the OpenMM molecular simulation toolkit originating from   *
+ * Simbios, the NIH National Center for Physics-Based Simulation of           *
+ * Biological Structures at Stanford, funded under the NIH Roadmap for        *
+ * Medical Research, grant U54 GM072970. See https://simtk.org.               *
+ *                                                                            *
+ * Portions copyright (c) 2013-2014 Stanford University and the Authors.      *
+ * Authors: Peter Eastman                                                     *
+ * Contributors:                                                              *
+ *                                                                            *
+ * Permission is hereby granted, free of charge, to any person obtaining a    *
+ * copy of this software and associated documentation files (the "Software"), *
+ * to deal in the Software without restriction, including without limitation  *
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *
+ * and/or sell copies of the Software, and to permit persons to whom the      *
+ * Software is furnished to do so, subject to the following conditions:       *
+ *                                                                            *
+ * The above copyright notice and this permission notice shall be included in *
+ * all copies or substantial portions of the Software.                        *
+ *                                                                            *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *
+ * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *
+ * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *
+ * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *
+ * -------------------------------------------------------------------------- */
+
+#include <cmath>
+#include <cstdlib>
+
+// This file defines classes and functions to simplify vectorizing code with portable SIMD vectors.
+
+/**
+ * Determine whether ivec4 and fvec4 are supported on this processor.
+ */
+static bool isVec4Supported() {
+    return true;
+}
+
+typedef float __m128 __attribute__((vector_size(16), aligned(4)));
+typedef int __m128i __attribute__((vector_size(16), aligned(4)));
+
+class ivec4;
+
+/**
+ * A four element vector of floats.
+ */
+class fvec4 {
+public:
+    __m128 val;
+    
+    fvec4() {}
+    fvec4(float v) {
+        val = {v, v, v, v};
+    }
+    fvec4(float v1, float v2, float v3, float v4) {
+        val = {v1, v2, v3, v4};
+    }
+    fvec4(__m128 v) : val(v) {}
+    fvec4(const float* v) {
+        val = *((__m128*) v);
+    }
+    operator __m128() const {
+        return val;
+    }
+    float operator[](int i) const {
+        return val[i];
+    }
+    void store(float* v) const {
+        *((__m128*) v) = val;
+    }
+    fvec4 operator+(const fvec4& other) const {
+        return val+other;
+    }
+    fvec4 operator-(const fvec4& other) const {
+        return val-other;
+    }
+    fvec4 operator*(const fvec4& other) const {
+        return val*other;
+    }
+    fvec4 operator/(const fvec4& other) const {
+        return val/other;
+    }
+    void operator+=(const fvec4& other) {
+        val = val+other;
+    }
+    void operator-=(const fvec4& other) {
+        val = val-other;
+    }
+    void operator*=(const fvec4& other) {
+        val = val*other;
+    }
+    void operator/=(const fvec4& other) {
+        val = val/other;
+    }
+    fvec4 operator-() const {
+        return -val;
+    }
+    fvec4 operator&(const fvec4& other) const {
+        return (fvec4) (((__m128i)val)&((__m128i)other.val));
+    }
+    fvec4 operator|(const fvec4& other) const {
+        return (fvec4) (((__m128i)val)|((__m128i)other.val));
+    }
+    fvec4 operator==(const fvec4& other) const {
+        return (val==other.val);
+    }
+    fvec4 operator!=(const fvec4& other) const {
+        return (val!=other.val);
+    }
+    fvec4 operator>(const fvec4& other) const {
+        return (val>other.val);
+    }
+    fvec4 operator<(const fvec4& other) const {
+        return (val<other.val);
+    }
+    fvec4 operator>=(const fvec4& other) const {
+        return (val>=other.val);
+    }
+    fvec4 operator<=(const fvec4& other) const {
+        return (val<=other.val);
+    }
+    operator ivec4() const;
+};
+
+/**
+ * A four element vector of ints.
+ */
+class ivec4 {
+public:
+    __m128i val;
+    
+    ivec4() {}
+    ivec4(int v) {
+        val = {v, v, v, v};
+    }
+    ivec4(int v1, int v2, int v3, int v4) {
+        val = {v1, v2, v3, v4};
+    }
+    ivec4(__m128i v) : val(v) {}
+    ivec4(const int* v) {
+        val = *((__m128*) v);
+    }
+    operator __m128i() const {
+        return val;
+    }
+    int operator[](int i) const {
+        return val[i];
+    }
+    void store(int* v) const {
+        *((__m128*) v) = val;
+    }
+    ivec4 operator+(const ivec4& other) const {
+        return val+other;
+    }
+    ivec4 operator-(const ivec4& other) const {
+        return val-other;
+    }
+    ivec4 operator*(const ivec4& other) const {
+        return val*other;
+    }
+    void operator+=(const ivec4& other) {
+        val = val+other;
+    }
+    void operator-=(const ivec4& other) {
+        val = val-other;
+    }
+    void operator*=(const ivec4& other) {
+        val = val*other;
+    }
+    ivec4 operator-() const {
+        return -val;
+    }
+    ivec4 operator&(const ivec4& other) const {
+        return val&other.val;
+    }
+    ivec4 operator|(const ivec4& other) const {
+        return val|other.val;
+    }
+    ivec4 operator==(const ivec4& other) const {
+        return (val==other.val);
+    }
+    ivec4 operator!=(const ivec4& other) const {
+        return (val!=other.val);
+    }
+    ivec4 operator>(const ivec4& other) const {
+        return (val>other.val);
+    }
+    ivec4 operator<(const ivec4& other) const {
+        return (val<other.val);
+    }
+    ivec4 operator>=(const ivec4& other) const {
+        return (val>=other.val);
+    }
+    ivec4 operator<=(const ivec4& other) const {
+        return (val<=other.val);
+    }
+    operator fvec4() const;
+};
+
+// Conversion operators.
+
+inline fvec4::operator ivec4() const {
+    return __builtin_convertvector(val, __m128i);
+}
+
+inline ivec4::operator fvec4() const {
+    return __builtin_convertvector(val, __m128);
+}
+
+// Functions that operate on fvec4s.
+
+static inline fvec4 floor(const fvec4& v) {
+    return fvec4(std::floor(v[0]), std::floor(v[1]), std::floor(v[2]), std::floor(v[3]));
+}
+
+static inline fvec4 ceil(const fvec4& v) {
+    return fvec4(std::ceil(v[0]), std::ceil(v[1]), std::ceil(v[2]), std::ceil(v[3]));
+}
+
+static inline fvec4 round(const fvec4& v) {
+    return fvec4(std::round(v[0]), std::round(v[1]), std::round(v[2]), std::round(v[3]));
+}
+
+static inline fvec4 min(const fvec4& v1, const fvec4& v2) {
+    return fvec4(std::min(v1[0], v2[0]), std::min(v1[1], v2[1]), std::min(v1[2], v2[2]), std::min(v1[3], v2[3]));
+}
+
+static inline fvec4 max(const fvec4& v1, const fvec4& v2) {
+    return fvec4(std::max(v1[0], v2[0]), std::max(v1[1], v2[1]), std::max(v1[2], v2[2]), std::max(v1[3], v2[3]));
+}
+
+static inline fvec4 abs(const fvec4& v) {
+    return fvec4(std::abs(v[0]), std::abs(v[1]), std::abs(v[2]), std::abs(v[3]));
+}
+
+static inline fvec4 sqrt(const fvec4& v) {
+    return fvec4(std::sqrt(v[0]), std::sqrt(v[1]), std::sqrt(v[2]), std::sqrt(v[3]));
+}
+
+static inline float dot3(const fvec4& v1, const fvec4& v2) {
+    fvec4 r = v1*v2;
+    return r[0]+r[1]+r[2];
+}
+
+static inline float dot4(const fvec4& v1, const fvec4& v2) {
+    fvec4 r = v1*v2;
+    return r[0]+r[1]+r[2]+r[3];
+}
+
+static inline void transpose(fvec4& v1, fvec4& v2, fvec4& v3, fvec4& v4) {
+    __m128 a1 = __builtin_shufflevector(v1.val, v2.val, 0, 4, 2, 6);
+    __m128 a2 = __builtin_shufflevector(v1.val, v2.val, 1, 5, 3, 7);
+    __m128 a3 = __builtin_shufflevector(v3.val, v4.val, 0, 4, 2, 6);
+    __m128 a4 = __builtin_shufflevector(v3.val, v4.val, 1, 5, 3, 7);
+    v1 = __builtin_shufflevector(a1, a3, 0, 1, 4, 5);
+    v2 = __builtin_shufflevector(a2, a4, 0, 1, 4, 5);
+    v3 = __builtin_shufflevector(a1, a3, 2, 3, 6, 7);
+    v4 = __builtin_shufflevector(a2, a4, 2, 3, 6, 7);
+}
+
+// Functions that operate on ivec4s.
+
+static inline ivec4 min(const ivec4& v1, const ivec4& v2) {
+    return ivec4(std::min(v1[0], v2[0]), std::min(v1[1], v2[1]), std::min(v1[2], v2[2]), std::min(v1[3], v2[3]));
+}
+
+static inline ivec4 max(const ivec4& v1, const ivec4& v2) {
+    return ivec4(std::max(v1[0], v2[0]), std::max(v1[1], v2[1]), std::max(v1[2], v2[2]), std::max(v1[3], v2[3]));
+}
+
+static inline ivec4 abs(const ivec4& v) {
+    return ivec4(abs(v[0]), abs(v[1]), abs(v[2]), abs(v[3]));
+}
+
+static inline bool any(const __m128i& v) {
+    return (v[0] || v[1] || v[2] || v[3]);
+}
+
+// Mathematical operators involving a scalar and a vector.
+
+static inline fvec4 operator+(float v1, const fvec4& v2) {
+    return fvec4(v1)+v2;
+}
+
+static inline fvec4 operator-(float v1, const fvec4& v2) {
+    return fvec4(v1)-v2;
+}
+
+static inline fvec4 operator*(float v1, const fvec4& v2) {
+    return fvec4(v1)*v2;
+}
+
+static inline fvec4 operator/(float v1, const fvec4& v2) {
+    return fvec4(v1)/v2;
+}
+
+// Operations for blending fvec4s based on an ivec4.
+
+static inline fvec4 blend(const fvec4& v1, const fvec4& v2, const __m128i& mask) {
+    return fvec4(mask[0] ? v2[0] : v1[0], mask[1] ? v2[1] : v1[1], mask[2] ? v2[2] : v1[2], mask[3] ? v2[3] : v1[3]);
+}
+
+#endif /*OPENMM_VECTORIZE_PNACL_H_*/
+

openmmapi/include/openmm/internal/vectorize_sse.h

@@ -33,10 +33,23 @@
  * -------------------------------------------------------------------------- */
 
 #include <smmintrin.h>
-
+#include "hardware.h"
 
 // This file defines classes and functions to simplify vectorizing code with SSE.
 
+/**
+ * Determine whether ivec4 and fvec4 are supported on this processor.
+ */
+static bool isVec4Supported() {
+    int cpuInfo[4];
+    cpuid(cpuInfo, 0);
+    if (cpuInfo[0] >= 1) {
+        cpuid(cpuInfo, 1);
+        return ((cpuInfo[2] & ((int) 1 << 19)) != 0);
+    }
+    return false;
+}
+
 class ivec4;
 
 /**
@@ -146,7 +159,7 @@ public:
         return _mm_sub_epi32(val, other);
     }
     ivec4 operator*(const ivec4& other) const {
-        return _mm_mul_epi32(val, other);
+        return _mm_mullo_epi32(val, other);
     }
     void operator+=(const ivec4& other) {
         val = _mm_add_epi32(val, other);
@@ -155,7 +168,7 @@ public:
         val = _mm_sub_epi32(val, other);
     }
     void operator*=(const ivec4& other) {
-        val = _mm_mul_epi32(val, other);
+        val = _mm_mullo_epi32(val, other);
     }
     ivec4 operator-() const {
         return _mm_sub_epi32(_mm_set1_epi32(0), val);

platforms/cpu/CMakeLists.txt

@@ -76,7 +76,9 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 FILE(GLOB CORE_HEADERS include/*.h)
 INSTALL_FILES(/include/openmm/cpu FILES ${CORE_HEADERS})
 
-SUBDIRS (sharedTarget)
+IF(OPENMM_BUILD_SHARED_LIB)
+    SUBDIRS (sharedTarget)
+ENDIF(OPENMM_BUILD_SHARED_LIB)
 IF(OPENMM_BUILD_STATIC_LIB)
     SUBDIRS (staticTarget)
 ENDIF(OPENMM_BUILD_STATIC_LIB)

platforms/cpu/include/CpuGBSAOBCForce.h

@@ -98,9 +98,9 @@ private:
     float periodicBoxSize[3];
     float cutoffDistance, soluteDielectric, solventDielectric;
     std::vector<std::pair<float, float> > particleParams;        
-    std::vector<float> bornRadii;
-    std::vector<std::vector<float> > threadBornForces;
-    std::vector<float> obcChain;
+    AlignedArray<float> bornRadii;
+    std::vector<AlignedArray<float> > threadBornForces;
+    AlignedArray<float> obcChain;
     std::vector<double> threadEnergy;
     std::vector<float> logTable;
     float logDX, logDXInv;

platforms/cpu/src/CpuGBSAOBCForce.cpp

@@ -213,7 +213,7 @@ void CpuGBSAOBCForce::threadComputeForce(ThreadPool& threads, int threadIndex) {
     const float probeRadius = 0.14f;
     const float surfaceAreaFactor = 28.3919551;
     double energy = 0.0;
-    vector<float>& bornForces = threadBornForces[threadIndex];
+    AlignedArray<float>& bornForces = threadBornForces[threadIndex];
     for (int i = 0; i < numParticles; i++)
         bornForces[i] = 0.0f;
     while (true) {

platforms/cpu/src/CpuPlatform.cpp

@@ -35,6 +35,7 @@
 #include "CpuSETTLE.h"
 #include "ReferenceConstraints.h"
 #include "openmm/internal/hardware.h"
+#include "openmm/internal/vectorize.h"
 #include <sstream>
 #include <stdlib.h>
 
@@ -94,20 +95,7 @@ bool CpuPlatform::supportsDoublePrecision() const {
 }
 
 bool CpuPlatform::isProcessorSupported() {
-    // Make sure the CPU supports SSE 4.1 or NEON.
-        
-    #ifdef __ANDROID__
-        uint64_t features = android_getCpuFeatures();
-        return (features & ANDROID_CPU_ARM_FEATURE_NEON) != 0;
-    #else
-        int cpuInfo[4];
-        cpuid(cpuInfo, 0);
-        if (cpuInfo[0] >= 1) {
-            cpuid(cpuInfo, 1);
-            return ((cpuInfo[2] & ((int) 1 << 19)) != 0);
-        }
-        return false;
-    #endif
+    return isVec4Supported();
 }
 
 void CpuPlatform::contextCreated(ContextImpl& context, const map<string, string>& properties) const {

platforms/cpu/src/CpuRandom.cpp

@@ -33,7 +33,7 @@ CpuRandom::CpuRandom() : hasInitialized(false) {
 }
 
 CpuRandom::~CpuRandom() {
-    for (int i = 0; i < threadRandom.size(); i++)
+    for (int i = 0; i < (int) threadRandom.size(); i++)
         delete threadRandom[i];
 }
 

platforms/cpu/staticTarget/CMakeLists.txt

@@ -2,18 +2,20 @@ FOREACH(file ${SOURCE_FILES})
     IF (file MATCHES ".*Vec8.*")
 		IF (MSVC)
             SET_SOURCE_FILES_PROPERTIES(${file} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} /arch:AVX /D__AVX__")
+        ELSEIF (PNACL)
+            SET_SOURCE_FILES_PROPERTIES(${file} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
 		ELSE (MSVC)
             SET_SOURCE_FILES_PROPERTIES(${file} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -msse4.1 -mavx")
 		ENDIF (MSVC)
     ELSE (file MATCHES ".*Vec8.*")
-		IF (NOT MSVC)
+		IF (NOT (MSVC OR ANDROID OR PNACL))
             SET_SOURCE_FILES_PROPERTIES(${file} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -msse4.1")
-		ENDIF (NOT MSVC)
+		ENDIF (NOT (MSVC OR ANDROID OR PNACL))
     ENDIF (file MATCHES ".*Vec8.*")
 ENDFOREACH(file)
 ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 
-TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB_STATIC})
+TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}_static ${PTHREADS_LIB_STATIC})
 #-DPTW32_STATIC_LIB only works for the windows pthreads.
 SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_CPU_BUILDING_STATIC_LIBRARY -DPTW32_STATIC_LIB")
 

platforms/cpu/tests/CMakeLists.txt

@@ -17,9 +17,12 @@ FILE(GLOB TEST_PROGS "*Test*.cpp")
 FOREACH(TEST_PROG ${TEST_PROGS})
     GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
 
-    # Link with shared library
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
+    IF (OPENMM_BUILD_SHARED_LIB)
         TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
+    ELSE (OPENMM_BUILD_SHARED_LIB)
+        TARGET_LINK_LIBRARIES(${TEST_ROOT} ${STATIC_TARGET})
+    ENDIF (OPENMM_BUILD_SHARED_LIB)
     SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT} single)
 

platforms/reference/tests/CMakeLists.txt

@@ -9,9 +9,12 @@ FILE(GLOB TEST_PROGS "*Test*.cpp")
 FOREACH(TEST_PROG ${TEST_PROGS})
     GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
 
-    # All tests use shared libraries
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
+    IF (OPENMM_BUILD_SHARED_LIB)
         TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
+    ELSE (OPENMM_BUILD_SHARED_LIB)
+        TARGET_LINK_LIBRARIES(${TEST_ROOT} ${STATIC_TARGET})
+    ENDIF (OPENMM_BUILD_SHARED_LIB)
     SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 

platforms/reference/tests/TestReferenceVirtualSites.cpp

@@ -79,8 +79,8 @@ void testMasslessParticle() {
     for (int i = 0; i < 1000; ++i) {
         State state = context.getState(State::Positions | State::Velocities | State::Forces);
         double time = state.getTime();
-        ASSERT_EQUAL_VEC(Vec3(), state.getPositions()[0], 0.0);
-        ASSERT_EQUAL_VEC(Vec3(), state.getVelocities()[0], 0.0);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getPositions()[0], 0.0);
+        ASSERT_EQUAL_VEC(Vec3(0, 0, 0), state.getVelocities()[0], 0.0);
         ASSERT_EQUAL_VEC(Vec3(cos(time), sin(time), 0), state.getPositions()[1], 0.01);
         ASSERT_EQUAL_VEC(Vec3(-sin(time), cos(time), 0), state.getVelocities()[1], 0.01);
         integrator.step(1);

plugins/cpupme/CMakeLists.txt

@@ -57,32 +57,34 @@ ENDFOREACH(subdir)
 
 INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_SOURCE_DIR}/src)
 IF (NOT MSVC)
-    IF (ANDROID)
+    IF (ANDROID OR PNACL)
         SET_SOURCE_FILES_PROPERTIES(${SOURCE_FILES} PROPERTIES COMPILE_FLAGS "")
-    ELSE (ANDROID)
+    ELSE (ANDROID OR PNACL)
         SET_SOURCE_FILES_PROPERTIES(${SOURCE_FILES} PROPERTIES COMPILE_FLAGS "-msse4.1")
-    ENDIF (ANDROID)
+    ENDIF (ANDROID OR PNACL)
 ENDIF (NOT MSVC)
 
 # Include FFTW related files.
 INCLUDE_DIRECTORIES(${FFTW_INCLUDES})
 
 # Build the shared plugin library.
-ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES})
+IF (OPENMM_BUILD_SHARED_LIB)
+    ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES})
 
-TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB} ${FFTW_LIBRARY})
-IF (FFTW_THREADS_LIBRARY)
+    TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB} ${FFTW_LIBRARY})
+    IF (FFTW_THREADS_LIBRARY)
         TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${FFTW_THREADS_LIBRARY})
-ENDIF (FFTW_THREADS_LIBRARY)
-SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_SHARED_LIBRARY")
+    ENDIF (FFTW_THREADS_LIBRARY)
+    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_SHARED_LIBRARY")
 
-INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
+    INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
+ENDIF (OPENMM_BUILD_SHARED_LIB)
 
 # Build the static plugin library.
 IF(OPENMM_BUILD_STATIC_LIB)
     ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES})
 
-    TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB} ${FFTW_LIBRARY})
+    TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}_static ${PTHREADS_LIB} ${FFTW_LIBRARY})
     IF (FFTW_THREADS_LIBRARY)
         TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${FFTW_THREADS_LIBRARY})
     ENDIF (FFTW_THREADS_LIBRARY)