Replace pthreads with C++ threads (#4833)

* Replace pthreads with C++ threads * Try to fix CI errors * Try including -pthread linker option

Replace pthreads with C++ threads (#4833)
* Replace pthreads with C++ threads * Try to fix CI errors * Try including -pthread linker option
68c97c5b · Peter Eastman · GitHub · 55b3c86d · 68c97c5b · 68c97c5b
Unverified Commit 68c97c5b authored Mar 10, 2025 by Peter Eastman Committed by GitHub Mar 10, 2025
10 changed files
--- a/plugins/amoeba/platforms/opencl/CMakeLists.txt
+++ b/plugins/amoeba/platforms/opencl/CMakeLists.txt
@@ -85,7 +85,7 @@ IF (OPENMM_BUILD_SHARED_LIB)
    ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
    ADD_DEPENDENCIES(${SHARED_TARGET} AmoebaCommonKernels)

-    TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
+    TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME})
    TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}OpenCL)
    TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_AMOEBA_TARGET})
    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")
@@ -98,7 +98,7 @@ ENDIF (OPENMM_BUILD_SHARED_LIB)
 IF(OPENMM_BUILD_STATIC_LIB)
    ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})

-    TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
+    TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME})
    TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}OpenCL)
    TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${STATIC_AMOEBA_TARGET})
    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_STATIC_LIBRARY")

--- a/plugins/cpupme/CMakeLists.txt
+++ b/plugins/cpupme/CMakeLists.txt
@@ -71,7 +71,7 @@ INCLUDE_DIRECTORIES("${CMAKE_SOURCE_DIR}/libraries/include/pocketfft")
 IF (OPENMM_BUILD_SHARED_LIB)
    ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES})

-    TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
+    TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME})
    SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_SHARED_LIBRARY")

    INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${SHARED_TARGET})
@@ -81,7 +81,7 @@ ENDIF (OPENMM_BUILD_SHARED_LIB)
 IF(OPENMM_BUILD_STATIC_LIB)
    ADD_LIBRARY(${STATIC_TARGET} STATIC ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_INCLUDE_FILES})

-    TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}_static ${PTHREADS_LIB})
+    TARGET_LINK_LIBRARIES(${STATIC_TARGET} ${OPENMM_LIBRARY_NAME}_static)
    SET_TARGET_PROPERTIES(${STATIC_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_PME_BUILDING_STATIC_LIBRARY")

    INSTALL_TARGETS(/lib/plugins RUNTIME_DIRECTORY /lib/plugins ${STATIC_TARGET})

--- a/plugins/cpupme/src/CpuPmeKernels.cpp
+++ b/plugins/cpupme/src/CpuPmeKernels.cpp
@@ -6,7 +6,7 @@
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
 *                                                                            *
- * Portions copyright (c) 2013-2022 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2025 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
@@ -460,17 +460,15 @@ void CpuCalcPmeReciprocalForceKernel::initialize(int xsize, int ysize, int zsize
    // Initialize threads.
    
    isFinished = false;
-    pthread_cond_init(&startCondition, NULL);
-    pthread_cond_init(&endCondition, NULL);
-    pthread_mutex_init(&lock, NULL);
-    pthread_create(&mainThread, NULL, threadBody, this);
+    mainThread = thread(threadBody, this);
    
    // Wait until the main thread is up and running.
    
-    pthread_mutex_lock(&lock);
+    {
+        unique_lock<mutex> ul(lock);
        while (!isFinished)
-        pthread_cond_wait(&endCondition, &lock);
-    pthread_mutex_unlock(&lock);
+            endCondition.wait(ul);
+    }
    
    // Initialize the FFT grids.

@@ -535,26 +533,23 @@ void CpuCalcPmeReciprocalForceKernel::initialize(int xsize, int ysize, int zsize

 CpuCalcPmeReciprocalForceKernel::~CpuCalcPmeReciprocalForceKernel() {
    isDeleted = true;
-    pthread_mutex_lock(&lock);
-    pthread_cond_broadcast(&startCondition);
-    pthread_mutex_unlock(&lock);
-    pthread_join(mainThread, NULL);
-    pthread_mutex_destroy(&lock);
-    pthread_cond_destroy(&startCondition);
-    pthread_cond_destroy(&endCondition);
+    lock.lock();
+    startCondition.notify_all();
+    lock.unlock();
+    mainThread.join();
 }

 void CpuCalcPmeReciprocalForceKernel::runMainThread() {
    // This is the main thread that coordinates all the other ones.

-    pthread_mutex_lock(&lock);
+    unique_lock<mutex> ul(lock);
    isFinished = true;
-    pthread_cond_signal(&endCondition);
+    endCondition.notify_one();
    ThreadPool threads(numThreads);
    while (true) {
        // Wait for the signal to start.

-        pthread_cond_wait(&startCondition, &lock);
+        startCondition.wait(ul);
        if (isDeleted)
            break;
        posq = io->getPosq();
@@ -584,9 +579,8 @@ void CpuCalcPmeReciprocalForceKernel::runMainThread() {
        lastBoxVectors[0] = periodicBoxVectors[0];
        lastBoxVectors[1] = periodicBoxVectors[1];
        lastBoxVectors[2] = periodicBoxVectors[2];
-        pthread_cond_signal(&endCondition);
+        endCondition.notify_one();
    }
-    pthread_mutex_unlock(&lock);
 }

 void CpuCalcPmeReciprocalForceKernel::runWorkerThread(ThreadPool& threads, int index) {
@@ -640,18 +634,18 @@ void CpuCalcPmeReciprocalForceKernel::beginComputation(IO& io, const Vec3* perio

    // Do the calculation.

-    pthread_mutex_lock(&lock);
+    unique_lock<mutex> ul(lock);
    isFinished = false;
-    pthread_cond_signal(&startCondition);
-    pthread_mutex_unlock(&lock);
+    startCondition.notify_one();
 }

 double CpuCalcPmeReciprocalForceKernel::finishComputation(IO& io) {
-    pthread_mutex_lock(&lock);
+    {
+        unique_lock<mutex> ul(lock);
        while (!isFinished) {
-        pthread_cond_wait(&endCondition, &lock);
+            endCondition.wait(ul);
+        }
    }
-    pthread_mutex_unlock(&lock);
    io.setForce(&force[0]);
    return energy;
 }
@@ -742,18 +736,15 @@ void CpuCalcDispersionPmeReciprocalForceKernel::initialize(int xsize, int ysize,
    // Initialize threads.
    
    isFinished = false;
-    pthread_cond_init(&startCondition, NULL);
-    pthread_cond_init(&endCondition, NULL);
-    pthread_mutex_init(&lock, NULL);
-    pthread_create(&mainThread, NULL, dispersionThreadBody, this);
+    mainThread = thread(dispersionThreadBody, this);
    
    // Wait until the main thread is up and running.
    
-    pthread_mutex_lock(&lock);
+    {
+        unique_lock<mutex> ul(lock);
        while (!isFinished)
-        pthread_cond_wait(&endCondition, &lock);
-    pthread_mutex_unlock(&lock);
-    
+            endCondition.wait(ul);
+    }

    // Initialize the FFT grids.

@@ -818,26 +809,23 @@ void CpuCalcDispersionPmeReciprocalForceKernel::initialize(int xsize, int ysize,

 CpuCalcDispersionPmeReciprocalForceKernel::~CpuCalcDispersionPmeReciprocalForceKernel() {
    isDeleted = true;
-    pthread_mutex_lock(&lock);
-    pthread_cond_broadcast(&startCondition);
-    pthread_mutex_unlock(&lock);
-    pthread_join(mainThread, NULL);
-    pthread_mutex_destroy(&lock);
-    pthread_cond_destroy(&startCondition);
-    pthread_cond_destroy(&endCondition);
+    lock.lock();
+    startCondition.notify_all();
+    lock.unlock();
+    mainThread.join();
 }

 void CpuCalcDispersionPmeReciprocalForceKernel::runMainThread() {
    // This is the main thread that coordinates all the other ones.

-    pthread_mutex_lock(&lock);
+    unique_lock<mutex> ul(lock);
    isFinished = true;
-    pthread_cond_signal(&endCondition);
+    endCondition.notify_one();
    ThreadPool threads(numThreads);
    while (true) {
        // Wait for the signal to start.

-        pthread_cond_wait(&startCondition, &lock);
+        startCondition.wait(ul);
        if (isDeleted)
            break;
        posq = io->getPosq();
@@ -868,9 +856,8 @@ void CpuCalcDispersionPmeReciprocalForceKernel::runMainThread() {
        lastBoxVectors[0] = periodicBoxVectors[0];
        lastBoxVectors[1] = periodicBoxVectors[1];
        lastBoxVectors[2] = periodicBoxVectors[2];
-        pthread_cond_signal(&endCondition);
+        endCondition.notify_one();
    }
-    pthread_mutex_unlock(&lock);
 }

 void CpuCalcDispersionPmeReciprocalForceKernel::runWorkerThread(ThreadPool& threads, int index) {
@@ -926,18 +913,18 @@ void CpuCalcDispersionPmeReciprocalForceKernel::beginComputation(CalcPmeReciproc

    // Do the calculation.

-    pthread_mutex_lock(&lock);
+    unique_lock<mutex> ul(lock);
    isFinished = false;
-    pthread_cond_signal(&startCondition);
-    pthread_mutex_unlock(&lock);
+    startCondition.notify_one();
 }

 double CpuCalcDispersionPmeReciprocalForceKernel::finishComputation(CalcPmeReciprocalForceKernel::IO& io) {
-    pthread_mutex_lock(&lock);
+    {
+        unique_lock<mutex> ul(lock);
        while (!isFinished) {
-        pthread_cond_wait(&endCondition, &lock);
+            endCondition.wait(ul);
+        }
    }
-    pthread_mutex_unlock(&lock);
    io.setForce(&force[0]);
    return energy;
 }

--- a/plugins/cpupme/src/CpuPmeKernels.h
+++ b/plugins/cpupme/src/CpuPmeKernels.h
@@ -9,7 +9,7 @@
 * Biological Structures at Stanford, funded under the NIH Roadmap for        *
 * Medical Research, grant U54 GM072970. See https://simtk.org.               *
 *                                                                            *
- * Portions copyright (c) 2013-2022 Stanford University and the Authors.      *
+ * Portions copyright (c) 2013-2025 Stanford University and the Authors.      *
 * Authors: Peter Eastman                                                     *
 * Contributors:                                                              *
 *                                                                            *
@@ -39,7 +39,9 @@
 #include "openmm/internal/ThreadPool.h"
 #include <atomic>
 #include <complex>
-#include <pthread.h>
+#include <condition_variable>
+#include <mutex>
+#include <thread>
 #include <vector>

 namespace OpenMM {
@@ -123,9 +125,9 @@ private:
    std::vector<std::size_t> gridShape, fftAxes;
    std::vector<std::ptrdiff_t> realGridStride, complexGridStride;
    int waitCount;
-    pthread_cond_t startCondition, endCondition;
-    pthread_mutex_t lock;
-    pthread_t mainThread;
+    std::condition_variable startCondition, endCondition;
+    std::mutex lock;
+    std::thread mainThread;
    // The following variables are used to store information about the calculation currently being performed.
    IO* io;
    float energy;
@@ -217,9 +219,9 @@ private:
    std::vector<std::size_t> gridShape, fftAxes;
    std::vector<std::ptrdiff_t> realGridStride, complexGridStride;
    int waitCount;
-    pthread_cond_t startCondition, endCondition;
-    pthread_mutex_t lock;
-    pthread_t mainThread;
+    std::condition_variable startCondition, endCondition;
+    std::mutex lock;
+    std::thread mainThread;
    // The following variables are used to store information about the calculation currently being performed.
    CalcPmeReciprocalForceKernel::IO* io;
    float energy;

--- a/plugins/drude/platforms/cuda/CMakeLists.txt
+++ b/plugins/drude/platforms/cuda/CMakeLists.txt
@@ -79,7 +79,7 @@ SET_SOURCE_FILES_PROPERTIES(${COMMON_KERNELS_CPP} PROPERTIES GENERATED TRUE)
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 ADD_DEPENDENCIES(${SHARED_TARGET} DrudeCommonKernels)

-TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}CUDA)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_DRUDE_TARGET})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")

--- a/plugins/drude/platforms/hip/CMakeLists.txt
+++ b/plugins/drude/platforms/hip/CMakeLists.txt
@@ -77,7 +77,7 @@ SET_SOURCE_FILES_PROPERTIES(${COMMON_KERNELS_CPP} PROPERTIES GENERATED TRUE)
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 ADD_DEPENDENCIES(${SHARED_TARGET} DrudeCommonKernels)

-TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}HIP)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_DRUDE_TARGET})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")

--- a/plugins/drude/platforms/opencl/CMakeLists.txt
+++ b/plugins/drude/platforms/opencl/CMakeLists.txt
@@ -79,7 +79,7 @@ SET_SOURCE_FILES_PROPERTIES(${COMMON_KERNELS_CPP} PROPERTIES GENERATED TRUE)
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 ADD_DEPENDENCIES(${SHARED_TARGET} DrudeCommonKernels)

-TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}  ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${OPENCL_LIBRARIES})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}OpenCL)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_DRUDE_TARGET})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")

--- a/plugins/rpmd/platforms/cuda/CMakeLists.txt
+++ b/plugins/rpmd/platforms/cuda/CMakeLists.txt
@@ -79,7 +79,7 @@ SET_SOURCE_FILES_PROPERTIES(${COMMON_KERNELS_CPP} PROPERTIES GENERATED TRUE)
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 ADD_DEPENDENCIES(${SHARED_TARGET} RpmdCommonKernels)

-TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}CUDA)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_RPMD_TARGET})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")

--- a/plugins/rpmd/platforms/hip/CMakeLists.txt
+++ b/plugins/rpmd/platforms/hip/CMakeLists.txt
@@ -77,7 +77,7 @@ SET_SOURCE_FILES_PROPERTIES(${COMMON_KERNELS_CPP} PROPERTIES GENERATED TRUE)
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 ADD_DEPENDENCIES(${SHARED_TARGET} RpmdCommonKernels)

-TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${PTHREADS_LIB})
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}HIP)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_RPMD_TARGET})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")

--- a/plugins/rpmd/platforms/opencl/CMakeLists.txt
+++ b/plugins/rpmd/platforms/opencl/CMakeLists.txt
@@ -79,7 +79,7 @@ SET_SOURCE_FILES_PROPERTIES(${COMMON_KERNELS_CPP} PROPERTIES GENERATED TRUE)
 ADD_LIBRARY(${SHARED_TARGET} SHARED ${SOURCE_FILES} ${SOURCE_INCLUDE_FILES} ${API_ABS_INCLUDE_FILES})
 ADD_DEPENDENCIES(${SHARED_TARGET} RpmdCommonKernels)

-TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}  ${OPENCL_LIBRARIES} ${PTHREADS_LIB})
+TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME} ${OPENCL_LIBRARIES})
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${OPENMM_LIBRARY_NAME}OpenCL)
 TARGET_LINK_LIBRARIES(${SHARED_TARGET} ${SHARED_RPMD_TARGET})
 SET_TARGET_PROPERTIES(${SHARED_TARGET} PROPERTIES LINK_FLAGS "${EXTRA_LINK_FLAGS}" COMPILE_FLAGS "${EXTRA_COMPILE_FLAGS} -DOPENMM_BUILDING_SHARED_LIBRARY")