Preliminary support for Chrome portable native client

CMakeLists.txt

@@ -128,11 +128,11 @@ IF (APPLE)
     SET (CMAKE_INSTALL_NAME_DIR "@rpath")
     SET(EXTRA_COMPILE_FLAGS "-msse2 -stdlib=libc++")
 ELSE (APPLE)
-    IF (MSVC OR ANDROID)
+    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 (MSVC OR ANDROID OR PNACL)
 ENDIF (APPLE)
 
 IF(UNIX AND NOT CMAKE_BUILD_TYPE)
@@ -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)
-    ADD_DEPENDENCIES(${SHARED_TARGET} PthreadsLibraries)
-ENDIF(WIN32)
+SET(OPENMM_BUILD_SHARED_LIB ON CACHE BOOL "Whether to build shared OpenMM libraries")
+
+IF(OPENMM_BUILD_SHARED_LIB)
+    ADD_LIBRARY(${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(OPENMM_BUILD_SHARED_LIB)
 
 SET(OPENMM_BUILD_STATIC_LIB OFF CACHE BOOL "Whether to build static OpenMM libraries")
 IF(OPENMM_BUILD_STATIC_LIB)
@@ -309,11 +313,13 @@ IF(DL_LIBRARY)
     ENDIF(OPENMM_BUILD_STATIC_LIB)
     MARK_AS_ADVANCED(DL_LIBRARY)
 ELSE(DL_LIBRARY)
-    IF (ANDROID)
-        TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${PTHREADS_LIB} cpufeatures)
-    ELSE (ANDROID)
-        TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${PTHREADS_LIB})
-    ENDIF (ANDROID)
+    IF(OPENMM_BUILD_SHARED_LIB)
+        IF (ANDROID)
+            TARGET_LINK_LIBRARIES(${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)
@@ -434,7 +440,9 @@ 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__ (

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} ${TEST_PROG})
-    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
+    IF (OPENMM_BUILD_SHARED_LIB)
+        TARGET_LINK_LIBRARIES(${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);

serialization/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} ${TEST_PROG})
-    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
+    IF (OPENMM_BUILD_SHARED_LIB)
+        TARGET_LINK_LIBRARIES(${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})
 

serialization/tests/TestSerializeCustomTorsionForce.cpp

@@ -84,7 +84,7 @@ void testSerialization() {
         ASSERT_EQUAL(c2, c2);
         ASSERT_EQUAL(d2, d2);
         ASSERT_EQUAL(params1.size(), params2.size());
-        for (int j = 0; j < params1.size(); j++)
+        for (int j = 0; j < (int) params1.size(); j++)
             ASSERT_EQUAL(params1[j], params2[j]);
     }
 }

serialization/tests/TestSerializeIntegrator.cpp

@@ -151,16 +151,16 @@ void testSerializeCustomIntegrator() {
     XmlSerializer::serialize<Integrator>(intg, "CustomIntegrator", ss);
     CustomIntegrator *intg2 = dynamic_cast<CustomIntegrator*>(XmlSerializer::deserialize<Integrator>(ss));
     ASSERT_EQUAL(intg->getNumGlobalVariables(), intg->getNumGlobalVariables());
-    for(int i=0; i < intg->getNumGlobalVariables(); i++) {
+    for (int i = 0; i < intg->getNumGlobalVariables(); i++) {
         ASSERT_EQUAL(intg->getGlobalVariable(i), intg2->getGlobalVariable(i));
         ASSERT_EQUAL(intg->getGlobalVariableName(i), intg2->getGlobalVariableName(i));
     }
     ASSERT_EQUAL(intg->getNumPerDofVariables(), intg2->getNumPerDofVariables());
-    for(int i=0; i<intg->getNumPerDofVariables(); i++) {
+    for(int i = 0; i < intg->getNumPerDofVariables(); i++) {
         vector<Vec3> vars1; intg->getPerDofVariable(i, vars1);
         vector<Vec3> vars2; intg2->getPerDofVariable(i, vars2);
         ASSERT_EQUAL(vars1.size(),vars2.size());
-        for(int j=0; j<vars1.size(); j++) {
+        for (int j = 0; j < (int) vars1.size(); j++) {
             ASSERT_EQUAL(vars1[j][0], vars2[j][0]);
             ASSERT_EQUAL(vars1[j][1], vars2[j][1]);
             ASSERT_EQUAL(vars1[j][2], vars2[j][2]);

serialization/tests/TestSerializeState.cpp

@@ -71,11 +71,11 @@ void testSerialization() {
 	
 	// Set positions, velocities, forces
 	vector<Vec3> positions;
-	for(int i=0;i<numParticles;i++) {
+	for (int i = 0; i < numParticles; i++) {
 		positions.push_back(Vec3( ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2));
 	}
 	vector<Vec3> velocities;
-	for(int i=0;i<numParticles;i++) {
+	for (int i = 0; i < numParticles; i++) {
 		velocities.push_back(Vec3( ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2, ((float) rand()/(float) RAND_MAX)*6.2));
 	}
 
@@ -95,19 +95,19 @@ void testSerialization() {
 	vector<Vec3> pos2 = s2.getPositions();
 	ASSERT_EQUAL(pos1.size(), pos2.size());
 	ASSERT_EQUAL(pos1.size(), positions.size());
-	for(int i=0; i<pos1.size(); i++) {
+	for (int i = 0; i < (int) pos1.size(); i++) {
 		ASSERT_EQUAL_VEC(pos1[i],pos2[i],0);
 	}
 	vector<Vec3> vel1 = s1.getVelocities();
 	vector<Vec3> vel2 = s2.getVelocities();
 	ASSERT_EQUAL(vel1.size(), vel2.size());
-	for(int i=0; i<pos1.size(); i++) {
+	for (int i = 0; i < (int) pos1.size(); i++) {
 		ASSERT_EQUAL_VEC(vel1[i],vel2[i],0);
 	}
 	vector<Vec3> forces1 = s1.getForces();
 	vector<Vec3> forces2 = s2.getForces();
 	ASSERT_EQUAL(forces1.size(), forces2.size());
-	for(int i=0; i<pos1.size(); i++) {
+	for (int i = 0; i < (int) pos1.size(); i++) {
 		ASSERT_EQUAL_VEC(forces1[i],forces2[i],0);
 	}
 	Vec3 a1,a2,a3,b1,b2,b3;
@@ -128,7 +128,7 @@ void testSerialization() {
 	map<string, double>::const_iterator it1=p1.begin();
 	map<string, double>::const_iterator it2=p2.begin();
 	//maps are ordered, so iterators should be in the same order. 
-	for(it1=p1.begin(); it1!=p1.end(); it1++, it2++) {
+	for (it1 = p1.begin(); it1 != p1.end(); it1++, it2++) {
 		assert((it1->first).compare(it2->first) == 0);
 		ASSERT_EQUAL(it1->second, it2->second);
 	}

tests/CMakeLists.txt

@@ -8,9 +8,12 @@ ENABLE_TESTING()
 FILE(GLOB TEST_PROGS "*Test*.cpp")
 FOREACH(TEST_PROG ${TEST_PROGS})
     GET_FILENAME_COMPONENT(TEST_ROOT ${TEST_PROG} NAME_WE)
-    # All tests use shared library only
     ADD_EXECUTABLE(${TEST_ROOT} ${TEST_PROG})
-    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
+    IF (OPENMM_BUILD_SHARED_LIB)
+        TARGET_LINK_LIBRARIES(${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})
 ENDFOREACH(TEST_PROG ${TEST_PROGS})