Added pthreads library for Windows. Fixed other errors and warnings under Windows.

CMakeLists.txt

@@ -75,6 +75,19 @@ ENDIF(${CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT})
 # The source is organized into subdirectories, but we handle them all from
 # this CMakeLists file rather than letting CMake visit them as SUBDIRS.
 SET(OPENMM_SOURCE_SUBDIRS . openmmapi olla libraries/jama libraries/quern libraries/lepton libraries/sfmt libraries/lbfgs platforms/reference libraries/validate)
+IF(WIN32)
+    SET(OPENMM_SOURCE_SUBDIRS ${OPENMM_SOURCE_SUBDIRS} libraries/pthreads)
+    ADD_CUSTOM_TARGET(PthreadsLibraries ALL)
+    FILE(GLOB PTHREADS_LIBRARIES libraries/pthreads/lib/*)
+    FOREACH(lib ${PTHREADS_LIBRARIES})
+        ADD_CUSTOM_COMMAND(TARGET PthreadsLibraries COMMAND ${CMAKE_COMMAND} ARGS -E copy ${lib} "${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_CFG_INTDIR}")
+        INSTALL(FILES ${lib} DESTINATION "lib/")
+    ENDFOREACH(lib)
+    LINK_DIRECTORIES("${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_CFG_INTDIR}")
+    SET(PTHREADS_LIB pthreadVC2)
+ELSE(WIN32)
+    SET(PTHREADS_LIB pthread)
+ENDIF(WIN32)
 
 # The build system will set ARCH64 for 64 bit builds, which require
 # use of the lib64/ library directories rather than lib/.

libraries/pthreads/include/sched.h

+/*
+ * Module: sched.h
+ *
+ * Purpose:
+ *      Provides an implementation of POSIX realtime extensions
+ *      as defined in 
+ *
+ *              POSIX 1003.1b-1993      (POSIX.1b)
+ *
+ * --------------------------------------------------------------------------
+ *
+ *      Pthreads-win32 - POSIX Threads Library for Win32
+ *      Copyright(C) 1998 John E. Bossom
+ *      Copyright(C) 1999,2005 Pthreads-win32 contributors
+ * 
+ *      Contact Email: rpj@callisto.canberra.edu.au
+ * 
+ *      The current list of contributors is contained
+ *      in the file CONTRIBUTORS included with the source
+ *      code distribution. The list can also be seen at the
+ *      following World Wide Web location:
+ *      http://sources.redhat.com/pthreads-win32/contributors.html
+ * 
+ *      This library is free software; you can redistribute it and/or
+ *      modify it under the terms of the GNU Lesser General Public
+ *      License as published by the Free Software Foundation; either
+ *      version 2 of the License, or (at your option) any later version.
+ * 
+ *      This library is distributed in the hope that it will be useful,
+ *      but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *      Lesser General Public License for more details.
+ * 
+ *      You should have received a copy of the GNU Lesser General Public
+ *      License along with this library in the file COPYING.LIB;
+ *      if not, write to the Free Software Foundation, Inc.,
+ *      59 Temple Place - Suite 330, Boston, MA 02111-1307, USA
+ */
+#ifndef _SCHED_H
+#define _SCHED_H
+
+#undef PTW32_LEVEL
+
+#if defined(_POSIX_SOURCE)
+#define PTW32_LEVEL 0
+/* Early POSIX */
+#endif
+
+#if defined(_POSIX_C_SOURCE) && _POSIX_C_SOURCE >= 199309
+#undef PTW32_LEVEL
+#define PTW32_LEVEL 1
+/* Include 1b, 1c and 1d */
+#endif
+
+#if defined(INCLUDE_NP)
+#undef PTW32_LEVEL
+#define PTW32_LEVEL 2
+/* Include Non-Portable extensions */
+#endif
+
+#define PTW32_LEVEL_MAX 3
+
+#if !defined(PTW32_LEVEL)
+#define PTW32_LEVEL PTW32_LEVEL_MAX
+/* Include everything */
+#endif
+
+
+#if __GNUC__ && ! defined (__declspec)
+# error Please upgrade your GNU compiler to one that supports __declspec.
+#endif
+
+/*
+ * When building the DLL code, you should define PTW32_BUILD so that
+ * the variables/functions are exported correctly. When using the DLL,
+ * do NOT define PTW32_BUILD, and then the variables/functions will
+ * be imported correctly.
+ */
+#ifndef PTW32_STATIC_LIB
+#  ifdef PTW32_BUILD
+#    define PTW32_DLLPORT __declspec (dllexport)
+#  else
+#    define PTW32_DLLPORT __declspec (dllimport)
+#  endif
+#else
+#  define PTW32_DLLPORT
+#endif
+
+/*
+ * This is a duplicate of what is in the autoconf config.h,
+ * which is only used when building the pthread-win32 libraries.
+ */
+
+#ifndef PTW32_CONFIG_H
+#  if defined(WINCE)
+#    define NEED_ERRNO
+#    define NEED_SEM
+#  endif
+#  if defined(_UWIN) || defined(__MINGW32__)
+#    define HAVE_MODE_T
+#  endif
+#endif
+
+/*
+ *
+ */
+
+#if PTW32_LEVEL >= PTW32_LEVEL_MAX
+#ifdef NEED_ERRNO
+#include "need_errno.h"
+#else
+#include <errno.h>
+#endif
+#endif /* PTW32_LEVEL >= PTW32_LEVEL_MAX */
+
+#if defined(__MINGW32__) || defined(_UWIN)
+#if PTW32_LEVEL >= PTW32_LEVEL_MAX
+/* For pid_t */
+#  include <sys/types.h>
+/* Required by Unix 98 */
+#  include <time.h>
+#endif /* PTW32_LEVEL >= PTW32_LEVEL_MAX */
+#else
+typedef int pid_t;
+#endif
+
+/* Thread scheduling policies */
+
+enum {
+  SCHED_OTHER = 0,
+  SCHED_FIFO,
+  SCHED_RR,
+  SCHED_MIN   = SCHED_OTHER,
+  SCHED_MAX   = SCHED_RR
+};
+
+struct sched_param {
+  int sched_priority;
+};
+
+#ifdef __cplusplus
+extern "C"
+{
+#endif                          /* __cplusplus */
+
+PTW32_DLLPORT int __cdecl sched_yield (void);
+
+PTW32_DLLPORT int __cdecl sched_get_priority_min (int policy);
+
+PTW32_DLLPORT int __cdecl sched_get_priority_max (int policy);
+
+PTW32_DLLPORT int __cdecl sched_setscheduler (pid_t pid, int policy);
+
+PTW32_DLLPORT int __cdecl sched_getscheduler (pid_t pid);
+
+/*
+ * Note that this macro returns ENOTSUP rather than
+ * ENOSYS as might be expected. However, returning ENOSYS
+ * should mean that sched_get_priority_{min,max} are
+ * not implemented as well as sched_rr_get_interval.
+ * This is not the case, since we just don't support
+ * round-robin scheduling. Therefore I have chosen to
+ * return the same value as sched_setscheduler when
+ * SCHED_RR is passed to it.
+ */
+#define sched_rr_get_interval(_pid, _interval) \
+  ( errno = ENOTSUP, (int) -1 )
+
+
+#ifdef __cplusplus
+}                               /* End of extern "C" */
+#endif                          /* __cplusplus */
+
+#undef PTW32_LEVEL
+#undef PTW32_LEVEL_MAX
+
+#endif                          /* !_SCHED_H */
+

libraries/pthreads/include/semaphore.h

+/*
+ * Module: semaphore.h
+ *
+ * Purpose:
+ *	Semaphores aren't actually part of the PThreads standard.
+ *	They are defined by the POSIX Standard:
+ *
+ *		POSIX 1003.1b-1993	(POSIX.1b)
+ *
+ * --------------------------------------------------------------------------
+ *
+ *      Pthreads-win32 - POSIX Threads Library for Win32
+ *      Copyright(C) 1998 John E. Bossom
+ *      Copyright(C) 1999,2005 Pthreads-win32 contributors
+ * 
+ *      Contact Email: rpj@callisto.canberra.edu.au
+ * 
+ *      The current list of contributors is contained
+ *      in the file CONTRIBUTORS included with the source
+ *      code distribution. The list can also be seen at the
+ *      following World Wide Web location:
+ *      http://sources.redhat.com/pthreads-win32/contributors.html
+ * 
+ *      This library is free software; you can redistribute it and/or
+ *      modify it under the terms of the GNU Lesser General Public
+ *      License as published by the Free Software Foundation; either
+ *      version 2 of the License, or (at your option) any later version.
+ * 
+ *      This library is distributed in the hope that it will be useful,
+ *      but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *      MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+ *      Lesser General Public License for more details.
+ * 
+ *      You should have received a copy of the GNU Lesser General Public
+ *      License along with this library in the file COPYING.LIB;
+ *      if not, write to the Free Software Foundation, Inc.,
+ *      59 Temple Place - Suite 330, Boston, MA 02111-1307, USA
+ */
+#if !defined( SEMAPHORE_H )
+#define SEMAPHORE_H
+
+#undef PTW32_LEVEL
+
+#if defined(_POSIX_SOURCE)
+#define PTW32_LEVEL 0
+/* Early POSIX */
+#endif
+
+#if defined(_POSIX_C_SOURCE) && _POSIX_C_SOURCE >= 199309
+#undef PTW32_LEVEL
+#define PTW32_LEVEL 1
+/* Include 1b, 1c and 1d */
+#endif
+
+#if defined(INCLUDE_NP)
+#undef PTW32_LEVEL
+#define PTW32_LEVEL 2
+/* Include Non-Portable extensions */
+#endif
+
+#define PTW32_LEVEL_MAX 3
+
+#if !defined(PTW32_LEVEL)
+#define PTW32_LEVEL PTW32_LEVEL_MAX
+/* Include everything */
+#endif
+
+#if __GNUC__ && ! defined (__declspec)
+# error Please upgrade your GNU compiler to one that supports __declspec.
+#endif
+
+/*
+ * When building the DLL code, you should define PTW32_BUILD so that
+ * the variables/functions are exported correctly. When using the DLL,
+ * do NOT define PTW32_BUILD, and then the variables/functions will
+ * be imported correctly.
+ */
+#ifndef PTW32_STATIC_LIB
+#  ifdef PTW32_BUILD
+#    define PTW32_DLLPORT __declspec (dllexport)
+#  else
+#    define PTW32_DLLPORT __declspec (dllimport)
+#  endif
+#else
+#  define PTW32_DLLPORT
+#endif
+
+/*
+ * This is a duplicate of what is in the autoconf config.h,
+ * which is only used when building the pthread-win32 libraries.
+ */
+
+#ifndef PTW32_CONFIG_H
+#  if defined(WINCE)
+#    define NEED_ERRNO
+#    define NEED_SEM
+#  endif
+#  if defined(_UWIN) || defined(__MINGW32__)
+#    define HAVE_MODE_T
+#  endif
+#endif
+
+/*
+ *
+ */
+
+#if PTW32_LEVEL >= PTW32_LEVEL_MAX
+#ifdef NEED_ERRNO
+#include "need_errno.h"
+#else
+#include <errno.h>
+#endif
+#endif /* PTW32_LEVEL >= PTW32_LEVEL_MAX */
+
+#define _POSIX_SEMAPHORES
+
+#ifdef __cplusplus
+extern "C"
+{
+#endif				/* __cplusplus */
+
+#ifndef HAVE_MODE_T
+typedef unsigned int mode_t;
+#endif
+
+
+typedef struct sem_t_ * sem_t;
+
+PTW32_DLLPORT int __cdecl sem_init (sem_t * sem,
+			    int pshared,
+			    unsigned int value);
+
+PTW32_DLLPORT int __cdecl sem_destroy (sem_t * sem);
+
+PTW32_DLLPORT int __cdecl sem_trywait (sem_t * sem);
+
+PTW32_DLLPORT int __cdecl sem_wait (sem_t * sem);
+
+PTW32_DLLPORT int __cdecl sem_timedwait (sem_t * sem,
+				 const struct timespec * abstime);
+
+PTW32_DLLPORT int __cdecl sem_post (sem_t * sem);
+
+PTW32_DLLPORT int __cdecl sem_post_multiple (sem_t * sem,
+				     int count);
+
+PTW32_DLLPORT int __cdecl sem_open (const char * name,
+			    int oflag,
+			    mode_t mode,
+			    unsigned int value);
+
+PTW32_DLLPORT int __cdecl sem_close (sem_t * sem);
+
+PTW32_DLLPORT int __cdecl sem_unlink (const char * name);
+
+PTW32_DLLPORT int __cdecl sem_getvalue (sem_t * sem,
+				int * sval);
+
+#ifdef __cplusplus
+}				/* End of extern "C" */
+#endif				/* __cplusplus */
+
+#undef PTW32_LEVEL
+#undef PTW32_LEVEL_MAX
+
+#endif				/* !SEMAPHORE_H */

platforms/opencl/sharedTarget/CMakeLists.txt

@@ -18,7 +18,7 @@ IF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
 ELSE (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
     SET(MAIN_OPENMM_LIB ${OPENMM_LIBRARY_NAME})
 ENDIF (UNIX AND CMAKE_BUILD_TYPE MATCHES Debug)
-TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB}  ${OPENCL_LIBRARIES})
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${MAIN_OPENMM_LIB}  ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "-DOPENMM_BUILDING_SHARED_LIBRARY")
 
 INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})

platforms/opencl/src/OpenCLContext.cpp

@@ -126,10 +126,10 @@ OpenCLContext::OpenCLContext(int numParticles, int deviceIndex, OpenCLPlatform::
 
     cl::Kernel accuracyKernel(utilities, "determineNativeAccuracy");
     OpenCLArray<mm_float8> values(*this, 20, "values", true);
-    float nextValue = 1e-4;
+    float nextValue = 1e-4f;
     for (int i = 0; i < values.getSize(); ++i) {
         values[i].s0 = nextValue;
-        nextValue *= M_PI;
+        nextValue *= (float) M_PI;
     }
     values.upload();
     accuracyKernel.setArg<cl::Buffer>(0, values.getDeviceBuffer());

platforms/opencl/src/OpenCLIntegrationUtilities.cpp

@@ -466,7 +466,7 @@ OpenCLIntegrationUtilities::OpenCLIntegrationUtilities(OpenCLContext& context, c
             int c = ccmaConstraints[index];
             atomsVec[i].x = atom1[c];
             atomsVec[i].y = atom2[c];
-            distanceVec[i].w = distance[c];
+            distanceVec[i].w = (float) distance[c];
             reducedMassVec[i] = (float) (0.5/(1.0/system.getParticleMass(atom1[c])+1.0/system.getParticleMass(atom2[c])));
             for (unsigned int j = 0; j < matrix[index].size(); j++) {
                 constraintMatrixColumnVec[i+j*numCCMA] = matrix[index][j].first;

platforms/opencl/src/OpenCLKernels.cpp

@@ -888,10 +888,10 @@ void OpenCLCalcCMAPTorsionForceKernel::initialize(const System& system, const CM
         mapPositionsVec[i] = mm_int2(currentPosition, size);
         currentPosition += 4*size*size;
         for (int j = 0; j < size*size; j++) {
-            coeffVec.push_back(mm_float4(c[j][0], c[j][1], c[j][2], c[j][3]));
-            coeffVec.push_back(mm_float4(c[j][4], c[j][5], c[j][6], c[j][7]));
-            coeffVec.push_back(mm_float4(c[j][8], c[j][9], c[j][10], c[j][11]));
-            coeffVec.push_back(mm_float4(c[j][12], c[j][13], c[j][14], c[j][15]));
+            coeffVec.push_back(mm_float4((float) c[j][0], (float) c[j][1], (float) c[j][2], (float) c[j][3]));
+            coeffVec.push_back(mm_float4((float) c[j][4], (float) c[j][5], (float) c[j][6], (float) c[j][7]));
+            coeffVec.push_back(mm_float4((float) c[j][8], (float) c[j][9], (float) c[j][10], (float) c[j][11]));
+            coeffVec.push_back(mm_float4((float) c[j][12], (float) c[j][13], (float) c[j][14], (float) c[j][15]));
         }
     }
     vector<int> forceBufferCounter(system.getNumParticles(), 0);
@@ -1452,7 +1452,7 @@ double OpenCLCalcNonbondedForceKernel::execute(ContextImpl& context, bool includ
     if (cosSinSums != NULL && cl.getContextIndex() == 0) {
         mm_float4 boxSize = cl.getPeriodicBoxSize();
         mm_float4 recipBoxSize = mm_float4((float) (2*M_PI/boxSize.x), (float) (2*M_PI/boxSize.y), (float) (2*M_PI/boxSize.z), 0);
-        float recipCoefficient = ONE_4PI_EPS0*4*M_PI/(boxSize.x*boxSize.y*boxSize.z);
+        float recipCoefficient = (float) (ONE_4PI_EPS0*4*M_PI/(boxSize.x*boxSize.y*boxSize.z));
         ewaldSumsKernel.setArg<mm_float4>(3, recipBoxSize);
         ewaldSumsKernel.setArg<cl_float>(4, recipCoefficient);
         cl.executeKernel(ewaldSumsKernel, cosSinSums->getSize());
@@ -1581,7 +1581,7 @@ void OpenCLCalcCustomNonbondedForceKernel::initialize(const System& system, cons
         string arrayName = prefix+"table"+intToString(i);
         functionDefinitions.push_back(make_pair(name, arrayName));
         functions[name] = &fp;
-        tabulatedFunctionParamsVec[i] = mm_float4((float) min, (float) max, (float) ((values.size()-1)/(max-min)), values.size()-2);
+        tabulatedFunctionParamsVec[i] = mm_float4((float) min, (float) max, (float) ((values.size()-1)/(max-min)), (float) values.size()-2);
         vector<mm_float4> f = OpenCLExpressionUtilities::computeFunctionCoefficients(values, min, max);
         tabulatedFunctions.push_back(new OpenCLArray<mm_float4>(cl, values.size()-1, "TabulatedFunction"));
         tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
@@ -1932,7 +1932,7 @@ void OpenCLCalcCustomGBForceKernel::initialize(const System& system, const Custo
         string arrayName = prefix+"table"+intToString(i);
         functionDefinitions.push_back(make_pair(name, arrayName));
         functions[name] = &fp;
-        tabulatedFunctionParamsVec[i] = mm_float4((float) min, (float) max, (float) ((values.size()-1)/(max-min)), values.size()-2);
+        tabulatedFunctionParamsVec[i] = mm_float4((float) min, (float) max, (float) ((values.size()-1)/(max-min)), (float) values.size()-2);
         vector<mm_float4> f = OpenCLExpressionUtilities::computeFunctionCoefficients(values, min, max);
         tabulatedFunctions.push_back(new OpenCLArray<mm_float4>(cl, values.size()-1, "TabulatedFunction"));
         tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
@@ -3003,7 +3003,7 @@ void OpenCLCalcCustomHbondForceKernel::initialize(const System& system, const Cu
         string arrayName = "table"+intToString(i);
         functionDefinitions.push_back(make_pair(name, arrayName));
         functions[name] = &fp;
-        tabulatedFunctionParamsVec[i] = mm_float4((float) min, (float) max, (float) ((values.size()-1)/(max-min)), values.size()-2);
+        tabulatedFunctionParamsVec[i] = mm_float4((float) min, (float) max, (float) ((values.size()-1)/(max-min)), (float) values.size()-2);
         vector<mm_float4> f = OpenCLExpressionUtilities::computeFunctionCoefficients(values, min, max);
         tabulatedFunctions.push_back(new OpenCLArray<mm_float4>(cl, values.size()-1, "TabulatedFunction"));
         tabulatedFunctions[tabulatedFunctions.size()-1]->upload(f);
@@ -3387,7 +3387,7 @@ void OpenCLIntegrateLangevinStepKernel::execute(ContextImpl& context, const Lang
         p[1] = (cl_float) fscale;
         p[2] = (cl_float) noisescale;
         params->upload(p);
-        integration.getStepSize()[0].y = stepSize;
+        integration.getStepSize()[0].y = (cl_float) stepSize;
         integration.getStepSize().upload();
         prevTemp = temperature;
         prevFriction = friction;

platforms/opencl/src/OpenCLNonbondedUtilities.cpp

@@ -313,7 +313,7 @@ void OpenCLNonbondedUtilities::updateNeighborListSize() {
     if (!useCutoff)
         return;
     interactionCount->download();
-    if (interactionCount->get(0) <= interactingTiles->getSize())
+    if (interactionCount->get(0) <= (unsigned int) interactingTiles->getSize())
         return;
 
     // The most recent timestep had too many interactions to fit in the arrays.  Make the arrays bigger to prevent

platforms/opencl/src/OpenCLParallelKernels.cpp

@@ -34,17 +34,17 @@ using namespace std;
  */
 #ifdef _MSC_VER
     #include <Windows.h>
-    static long getTime() {
+    static long long getTime() {
         FILETIME ft;
         GetSystemTimeAsFileTime(&ft);	 // 100-nanoseconds since 1-1-1601
         ULARGE_INTEGER result;
         result.LowPart = ft.dwLowDateTime;
         result.HighPart = ft.dwHighDateTime;
-        return result/10;
+        return result.QuadPart/10;
     }
 #else
     #include <sys/time.h> 
-    static long getTime() {
+    static long long getTime() {
         struct timeval tod;
         gettimeofday(&tod, 0);
         return 1000000*tod.tv_sec+tod.tv_usec;
@@ -74,7 +74,7 @@ private:
 class OpenCLParallelCalcForcesAndEnergyKernel::FinishComputationTask : public OpenCLContext::WorkTask {
 public:
     FinishComputationTask(ContextImpl& context, OpenCLContext& cl, OpenCLCalcForcesAndEnergyKernel& kernel,
-            bool includeForce, bool includeEnergy, double& energy, long& completionTime) : context(context), cl(cl), kernel(kernel),
+            bool includeForce, bool includeEnergy, double& energy, long long& completionTime) : context(context), cl(cl), kernel(kernel),
             includeForce(includeForce), includeEnergy(includeEnergy), energy(energy), completionTime(completionTime) {
     }
     void execute() {
@@ -91,7 +91,7 @@ private:
     OpenCLCalcForcesAndEnergyKernel& kernel;
     bool includeForce, includeEnergy;
     double& energy;
-    long& completionTime;
+    long long& completionTime;
 };
 
 OpenCLParallelCalcForcesAndEnergyKernel::OpenCLParallelCalcForcesAndEnergyKernel(string name, const Platform& platform, OpenCLPlatform::PlatformData& data) :

platforms/opencl/src/OpenCLParallelKernels.h

@@ -76,7 +76,7 @@ private:
     class FinishComputationTask;
     OpenCLPlatform::PlatformData& data;
     std::vector<Kernel> kernels;
-    std::vector<long> completionTimes;
+    std::vector<long long> completionTimes;
     std::vector<int> contextTiles;
 };
 

platforms/opencl/src/OpenCLSort.h

@@ -87,7 +87,7 @@ public:
         sortKernelSize = rangeKernelSize/2;
         if (rangeKernelSize > length)
             rangeKernelSize = length;
-        int maxLocalBuffer = (context.getDevice().getInfo<CL_DEVICE_LOCAL_MEM_SIZE>()/sizeof(TYPE))/2;
+        int maxLocalBuffer = (int) ((context.getDevice().getInfo<CL_DEVICE_LOCAL_MEM_SIZE>()/sizeof(TYPE))/2);
         if (sortKernelSize > maxLocalBuffer)
             sortKernelSize = maxLocalBuffer;
         int targetBucketSize = sortKernelSize/2;