Integrate GROMACS GPU implementation into master branch

Signed-off-by: Rafael Ravedutti <rafaelravedutti@gmail.com>

common/device.c

@@ -0,0 +1,68 @@
+/*
+ * Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
+ * All rights reserved. This file is part of MD-Bench.
+ * Use of this source code is governed by a LGPL-3.0
+ * license that can be found in the LICENSE file.
+ */
+#include <stdio.h>
+#include <stdlib.h>
+//---
+#include <device.h>
+
+#ifdef CUDA_TARGET
+#include <cuda_runtime.h>
+
+void cuda_assert(const char *label, cudaError_t err) {
+    if (err != cudaSuccess) {
+        printf("[CUDA Error]: %s: %s\r\n", label, cudaGetErrorString(err));
+        exit(-1);
+    }
+}
+
+void *allocateGPU(size_t bytesize) {
+    void *ptr;
+    #ifdef CUDA_HOST_MEMORY
+    cuda_assert("allocateGPU", cudaMallocHost((void **) &ptr, bytesize));
+    #else
+    cuda_assert("allocateGPU", cudaMalloc((void **) &ptr, bytesize));
+    #endif
+    return ptr;
+}
+
+// Data is not preserved
+void *reallocateGPU(void *ptr, size_t new_bytesize) {
+    if(ptr != NULL) {
+        #ifdef CUDA_HOST_MEMORY
+        cudaFreeHost(ptr);
+        #else
+        cudaFree(ptr);
+        #endif
+    }
+
+    return allocateGPU(new_bytesize);
+}
+
+void memcpyToGPU(void *d_ptr, void *h_ptr, size_t bytesize) {
+    #ifndef CUDA_HOST_MEMORY
+    cuda_assert("memcpyToGPU", cudaMemcpy(d_ptr, h_ptr, bytesize, cudaMemcpyHostToDevice));
+    #endif
+}
+
+void memcpyFromGPU(void *h_ptr, void *d_ptr, size_t bytesize) {
+    #ifndef CUDA_HOST_MEMORY
+    cuda_assert("memcpyFromGPU", cudaMemcpy(h_ptr, d_ptr, bytesize, cudaMemcpyDeviceToHost));
+    #endif
+}
+
+void memsetGPU(void *d_ptr, int value, size_t bytesize) {
+    cuda_assert("memsetGPU", cudaMemset(d_ptr, value, bytesize));
+}
+
+#else
+void initDevice(Atom *atom, Neighbor *neighbor) {}
+void *allocateGPU(size_t bytesize) { return NULL; }
+void *reallocateGPU(void *ptr, size_t new_bytesize) { return NULL; }
+void memcpyToGPU(void *d_ptr, void *h_ptr, size_t bytesize) {}
+void memcpyFromGPU(void *h_ptr, void *d_ptr, size_t bytesize) {}
+void memsetGPU(void *d_ptr, int value, size_t bytesize) {}
+#endif

common/includes/device.h

@@ -0,0 +1,26 @@
+/*
+ * Copyright (C) 2022 NHR@FAU, University Erlangen-Nuremberg.
+ * All rights reserved. This file is part of MD-Bench.
+ * Use of this source code is governed by a LGPL-3.0
+ * license that can be found in the LICENSE file.
+ */
+#include <stddef.h>
+//---
+#include <atom.h>
+#include <neighbor.h>
+
+#ifndef __DEVICE_H_
+#define __DEVICE_H_
+
+#ifdef CUDA_TARGET
+#include <cuda_runtime.h>
+extern void cuda_assert(const char *msg, cudaError_t err);
+#endif
+
+extern void initDevice(Atom*, Neighbor*);
+extern void *allocateGPU(size_t bytesize);
+extern void *reallocateGPU(void *ptr, size_t new_bytesize);
+extern void memcpyToGPU(void *d_ptr, void *h_ptr, size_t bytesize);
+extern void memcpyFromGPU(void *h_ptr, void *d_ptr, size_t bytesize);
+extern void memsetGPU(void *d_ptr, int value, size_t bytesize);
+#endif