Merge pull request #567 from peastman/pnacl

Support Chrome portable native client

plugins/cpupme/src/CpuPmeKernels.cpp

@@ -569,20 +569,7 @@ double CpuCalcPmeReciprocalForceKernel::finishComputation(IO& io) {
 }
 
 bool CpuCalcPmeReciprocalForceKernel::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();
 }
 
 int CpuCalcPmeReciprocalForceKernel::findFFTDimension(int minimum) {

plugins/cpupme/tests/CMakeLists.txt

@@ -3,19 +3,16 @@
 #
 ENABLE_TESTING()
 
-SET(SHARED_OPENMM_PME_TARGET OpenMMPME)
-
-#LINK_DIRECTORIES
-
 # Automatically create tests using files named "Test*.cpp"
 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} ${TEST_PROG})
-    TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${SHARED_OPENMM_TARGET} ${SHARED_OPENMM_PME_TARGET})
+    IF (OPENMM_BUILD_SHARED_LIB)
+        TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET} ${OPENMM_LIBRARY_NAME})
+    ELSE (OPENMM_BUILD_SHARED_LIB)
+        TARGET_LINK_LIBRARIES(${TEST_ROOT} ${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}_static)
+    ENDIF (OPENMM_BUILD_SHARED_LIB)
     SET_TARGET_PROPERTIES(${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})

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} ${TEST_PROG})
+    IF (OPENMM_BUILD_SHARED_LIB)
         TARGET_LINK_LIBRARIES(${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

@@ -8,10 +8,17 @@ 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} ${TEST_PROG})
+    IF (OPENMM_BUILD_SHARED_LIB)
         TARGET_LINK_LIBRARIES(${TEST_ROOT} ${SHARED_TARGET})
-    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_COMPILE_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    ELSE (OPENMM_BUILD_SHARED_LIB)
+        TARGET_LINK_LIBRARIES(${TEST_ROOT} ${STATIC_TARGET})
+    ENDIF (OPENMM_BUILD_SHARED_LIB)
+    SET(EXTRA_TEST_FLAGS "${EXTRA_COMPILE_FLAGS}")
+    IF ((${TEST_ROOT} MATCHES TestVectorize) AND NOT (MSVC OR ANDROID OR PNACL))
+        SET(EXTRA_TEST_FLAGS "${EXTRA_COMPILE_FLAGS} -msse4.1")
+    ENDIF ((${TEST_ROOT} MATCHES TestVectorize) AND NOT (MSVC OR ANDROID OR PNACL))
+    SET_TARGET_PROPERTIES(${TEST_ROOT} PROPERTIES LINK_FLAGS "${EXTRA_TEST_FLAGS}" COMPILE_FLAGS "${EXTRA_TEST_FLAGS}")
     ADD_TEST(${TEST_ROOT} ${EXECUTABLE_OUTPUT_PATH}/${TEST_ROOT})
 ENDFOREACH(TEST_PROG ${TEST_PROGS})
 

tests/TestVectorize.cpp

+/* -------------------------------------------------------------------------- *
+ *                                   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) 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.                                     *
+ * -------------------------------------------------------------------------- */
+
+/**
+ * This tests vectorized operations.
+ */
+
+#include "openmm/internal/AssertionUtilities.h"
+#include "openmm/internal/vectorize.h"
+#include <iostream>
+
+using namespace OpenMM;
+using namespace std;
+
+#define ASSERT_VEC4_EQUAL(found, expected0, expected1, expected2, expected3) {if (std::abs((found)[0]-(expected0))>1e-6 || std::abs((found)[1]-(expected1))>1e-6 || std::abs((found)[2]-(expected2))>1e-6 || std::abs((found)[3]-(expected3))>1e-6) {std::stringstream details; details << " Expected ("<<(expected0)<<","<<(expected1)<<","<<(expected2)<<","<<(expected3)<<"), found ("<<(found)[0]<<","<<(found)[1]<<","<<(found)[2]<<","<<(found)[3]<<")"; throwException(__FILE__, __LINE__, details.str());}};
+
+void testLoadStore() {
+    fvec4 f1(2.0);
+    ivec4 i1(3);
+    ASSERT_VEC4_EQUAL(f1, 2.0, 2.0, 2.0, 2.0);
+    ASSERT_VEC4_EQUAL(i1, 3, 3, 3, 3);
+    fvec4 f2(2.5, 3.0, 3.5, 4.0);
+    ivec4 i2(2, 3, 4, 5);
+    ASSERT_VEC4_EQUAL(f2, 2.5, 3.0, 3.5, 4.0);
+    ASSERT_VEC4_EQUAL(i2, 2, 3, 4, 5);
+    float farray[4];
+    int iarray[4];
+    f2.store(farray);
+    i2.store(iarray);
+    fvec4 f3(farray);
+    ivec4 i3(iarray);
+    ASSERT_VEC4_EQUAL(f3, 2.5, 3.0, 3.5, 4.0);
+    ASSERT_VEC4_EQUAL(i3, 2, 3, 4, 5);
+    ASSERT_EQUAL(f3[0], 2.5);
+    ASSERT_EQUAL(f3[1], 3.0);
+    ASSERT_EQUAL(f3[2], 3.5);
+    ASSERT_EQUAL(f3[3], 4.0);
+    ASSERT_EQUAL(i3[0], 2);
+    ASSERT_EQUAL(i3[1], 3);
+    ASSERT_EQUAL(i3[2], 4);
+    ASSERT_EQUAL(i3[3], 5);
+}
+
+void testArithmetic() {
+    fvec4 f1(0.5, 1.0, 1.5, 2.0);
+    ASSERT_VEC4_EQUAL(f1+fvec4(1, 2, 3, 4), 1.5, 3, 4.5, 6);
+    ASSERT_VEC4_EQUAL(f1-fvec4(1, 2, 3, 4), -0.5, -1.0, -1.5, -2.0);
+    ASSERT_VEC4_EQUAL(f1*fvec4(1, 2, 3, 4), 0.5, 2.0, 4.5, 8.0);
+    ASSERT_VEC4_EQUAL(f1/fvec4(1, 2, 3, 4), 0.5, 0.5, 0.5, 0.5);
+    ivec4 i1(1, 2, 3, 4);
+    ASSERT_VEC4_EQUAL(i1+ivec4(5, 2, 1, 3), 6, 4, 4, 7);
+    ASSERT_VEC4_EQUAL(i1-ivec4(5, 2, 1, 3), -4, 0, 2, 1);
+    ASSERT_VEC4_EQUAL(i1*ivec4(5, 2, 1, 3), 5, 4, 3, 12);
+    f1 = fvec4(0.5, 1.0, 1.5, 2.0);
+    f1 += fvec4(1, 2, 3, 4);
+    ASSERT_VEC4_EQUAL(f1, 1.5, 3, 4.5, 6);
+    f1 = fvec4(0.5, 1.0, 1.5, 2.0);
+    f1 -= fvec4(1, 2, 3, 4);
+    ASSERT_VEC4_EQUAL(f1, -0.5, -1.0, -1.5, -2.0);
+    f1 = fvec4(0.5, 1.0, 1.5, 2.0);
+    f1 *= fvec4(1, 2, 3, 4);
+    ASSERT_VEC4_EQUAL(f1, 0.5, 2.0, 4.5, 8.0);
+    f1 = fvec4(0.5, 1.0, 1.5, 2.0);
+    f1 /= fvec4(1, 2, 3, 4);
+    ASSERT_VEC4_EQUAL(f1, 0.5, 0.5, 0.5, 0.5);
+    i1 = ivec4(1, 2, 3, 4);
+    i1 += ivec4(5, 2, 1, 3);
+    ASSERT_VEC4_EQUAL(i1, 6, 4, 4, 7);
+    i1 = ivec4(1, 2, 3, 4);
+    i1 -= ivec4(5, 2, 1, 3);
+    ASSERT_VEC4_EQUAL(i1, -4, 0, 2, 1);
+    i1 = ivec4(1, 2, 3, 4);
+    i1 *= ivec4(5, 2, 1, 3);
+    ASSERT_VEC4_EQUAL(i1, 5, 4, 3, 12);
+}
+
+void testLogic() {
+    int allBits = -1;
+    float allBitsf = *((float*) &allBits);
+    ivec4 mask(0, allBits, allBits, 0);
+    fvec4 fmask(0, allBitsf, allBitsf, 0);;
+    fvec4 f1(0.5, 1.0, 1.5, 2.0);
+    ivec4 i1(1, 2, 3, 4);
+    ASSERT_VEC4_EQUAL(f1&fmask, 0, 1.0, 1.5, 0);
+    fvec4 temp = f1|fmask;
+    ASSERT_EQUAL(0.5, temp[0]);
+    ASSERT(temp[1] != temp[1]); // All bits set, which is nan
+    ASSERT(temp[2] != temp[2]); // All bits set, which is nan
+    ASSERT_EQUAL(2.0, temp[3]);
+    ASSERT_VEC4_EQUAL(i1&mask, 0, 2, 3, 0);
+    ASSERT_VEC4_EQUAL(i1|mask, 1, allBits, allBits, 4);
+}
+
+void testComparisons() {
+    fvec4 v1(0.0, 0.0, 0.0, 0.0);
+    fvec4 v2(1.5, 1.5, 1.5, 1.5);
+    ASSERT_VEC4_EQUAL(blend(v1, v2, fvec4(1.0, 1.5, 3.0, 2.2)==fvec4(1.1, 1.5, 3.0, 2.1)), 0.0, 1.5, 1.5, 0.0);
+    ASSERT_VEC4_EQUAL(blend(v1, v2, fvec4(1.0, 1.5, 3.0, 2.2)!=fvec4(1.1, 1.5, 3.0, 2.1)), 1.5, 0.0, 0.0, 1.5);
+    ASSERT_VEC4_EQUAL(blend(v1, v2, fvec4(1.0, 1.5, 3.0, 2.2)<fvec4(1.1, 1.5, 3.0, 2.1)), 1.5, 0.0, 0.0, 0.0);
+    ASSERT_VEC4_EQUAL(blend(v1, v2, fvec4(1.0, 1.5, 3.0, 2.2)>fvec4(1.1, 1.5, 3.0, 2.1)), 0.0, 0.0, 0.0, 1.5);
+    ASSERT_VEC4_EQUAL(blend(v1, v2, fvec4(1.0, 1.5, 3.0, 2.2)<=fvec4(1.1, 1.5, 3.0, 2.1)), 1.5, 1.5, 1.5, 0.0);
+    ASSERT_VEC4_EQUAL(blend(v1, v2, fvec4(1.0, 1.5, 3.0, 2.2)>=fvec4(1.1, 1.5, 3.0, 2.1)), 0.0, 1.5, 1.5, 1.5);
+    fvec4 imask(3, 3, 3, 3);
+    ASSERT_VEC4_EQUAL((ivec4(1, 3, 7, 5)==ivec4(2, 3, 7, 4))&imask, 0, 3, 3, 0);
+    ASSERT_VEC4_EQUAL((ivec4(1, 3, 7, 5)!=ivec4(2, 3, 7, 4))&imask, 3, 0, 0, 3);
+    ASSERT_VEC4_EQUAL((ivec4(1, 3, 7, 5)<ivec4(2, 3, 7, 4))&imask, 3, 0, 0, 0);
+    ASSERT_VEC4_EQUAL((ivec4(1, 3, 7, 5)>ivec4(2, 3, 7, 4))&imask, 0, 0, 0, 3);
+    ASSERT_VEC4_EQUAL((ivec4(1, 3, 7, 5)<=ivec4(2, 3, 7, 4))&imask, 3, 3, 3, 0);
+    ASSERT_VEC4_EQUAL((ivec4(1, 3, 7, 5)>=ivec4(2, 3, 7, 4))&imask, 0, 3, 3, 3);
+}
+
+void testMathFunctions() {
+    fvec4 f1(0.4, 1.9, -1.2, -3.8);
+    fvec4 f2(1.1, 1.2, 1.3, -5.0);
+    ASSERT_VEC4_EQUAL(floor(f1), 0.0, 1.0, -2.0, -4.0);
+    ASSERT_VEC4_EQUAL(ceil(f1), 1.0, 2.0, -1.0, -3.0);
+    ASSERT_VEC4_EQUAL(round(f1), 0.0, 2.0, -1.0, -4.0);
+    ASSERT_VEC4_EQUAL(abs(f1), 0.4, 1.9, 1.2, 3.8);
+    ASSERT_VEC4_EQUAL(min(f1, f2), 0.4, 1.2, -1.2, -5.0);
+    ASSERT_VEC4_EQUAL(max(f1, f2), 1.1, 1.9, 1.3, -3.8);
+    ASSERT_VEC4_EQUAL(sqrt(fvec4(1.5, 3.1, 4.0, 15.0)), sqrt(1.5), sqrt(3.1), sqrt(4.0), sqrt(15.0));
+    ASSERT_EQUAL_TOL(f1[0]*f2[0]+f1[1]*f2[1]+f1[2]*f2[2], dot3(f1, f2), 1e-6);
+    ASSERT_EQUAL_TOL(f1[0]*f2[0]+f1[1]*f2[1]+f1[2]*f2[2]+f1[3]*f2[3], dot4(f1, f2), 1e-6);
+    ASSERT(any(f1 > 0.5));
+    ASSERT(!any(f1 > 2.0));
+    ASSERT_VEC4_EQUAL(blend(f1, f2, ivec4(-1, 0, -1, 0)), 1.1, 1.9, 1.3, -3.8);
+}
+
+void testTranspose() {
+    fvec4 f1(1.0, 2.0, 3.0, 4.0);
+    fvec4 f2(5.0, 6.0, 7.0, 8.0);
+    fvec4 f3(9.0, 10.0, 11.0, 12.0);
+    fvec4 f4(13.0, 14.0, 15.0, 16.0);
+    transpose(f1, f2, f3, f4);
+    ASSERT_VEC4_EQUAL(f1, 1.0, 5.0, 9.0, 13.0);
+    ASSERT_VEC4_EQUAL(f2, 2.0, 6.0, 10.0, 14.0);
+    ASSERT_VEC4_EQUAL(f3, 3.0, 7.0, 11.0, 15.0);
+    ASSERT_VEC4_EQUAL(f4, 4.0, 8.0, 12.0, 16.0);
+}
+
+int main(int argc, char* argv[]) {
+    try {
+        if (!isVec4Supported()) {
+            cout << "CPU is not supported.  Exiting." << endl;
+            return 0;
+        }
+        testLoadStore();
+        testArithmetic();
+        testLogic();
+        testComparisons();
+        testMathFunctions();
+        testTranspose();
+    }
+    catch(const exception& e) {
+        cout << "exception: " << e.what() << endl;
+        return 1;
+    }
+    cout << "Done" << endl;
+    return 0;
+}