diff --git a/src/Angle.h b/src/Angle.h
index 4333de667c46639f3a97d500467c541297699053..a4e9542c0878b6b195092bfef5b3ea8a4633f1df 100644
--- a/src/Angle.h
+++ b/src/Angle.h
@@ -24,15 +24,15 @@ public:
ind1(ind1), ind2(ind2), ind3(ind3), fileName(fileName), tabFileIndex(-1) { }
int ind1, ind2, ind3;
+ String fileName;
// tabFileIndex will be assigned after ComputeForce loads the
// TabulatedAnglePotentials. The tabefileIndex is used by ComputeForce to
// discern which TabulatedAnglePotential this Angle uses.
int tabFileIndex;
- String fileName;
inline Angle(const Angle& a) : ind1(a.ind1), ind2(a.ind2), ind3(a.ind3),
- tabFileIndex(a.tabFileIndex),
- fileName(a.fileName) { }
+ fileName(a.fileName),
+ tabFileIndex(a.tabFileIndex) { }
HOST DEVICE inline float calcAngle(Vector3* pos, BaseGrid* sys) {
const Vector3& posa = pos[ind1];
diff --git a/src/ComputeForce.cu b/src/ComputeForce.cu
index dd4ed64f31a7ecbc1a84de0acf8aec1f923afae8..580a73496e52be0476e250f0c097ec318a2bc3e6 100644
--- a/src/ComputeForce.cu
+++ b/src/ComputeForce.cu
@@ -71,6 +71,8 @@ ComputeForce::ComputeForce(int num, const BrownianParticleType part[],
// Create the bond table
tableBond = new TabulatedPotential*[numTabBondFiles];
tableBond_addr = new TabulatedPotential*[numTabBondFiles];
+ bondList_d = NULL;
+ tableBond_d = NULL;
for (int i = 0; i < numTabBondFiles; i++) {
tableBond_addr[i] = NULL;
tableBond[i] = NULL;
@@ -80,6 +82,8 @@ ComputeForce::ComputeForce(int num, const BrownianParticleType part[],
// Create the angle table
tableAngle = new TabulatedAnglePotential*[numTabAngleFiles];
tableAngle_addr = new TabulatedAnglePotential*[numTabAngleFiles];
+ angleList_d = NULL;
+ tableAngle_d = NULL;
for (int i = 0; i < numTabAngleFiles; i++) {
tableAngle_addr[i] = NULL;
tableAngle[i] = NULL;
@@ -89,6 +93,8 @@ ComputeForce::ComputeForce(int num, const BrownianParticleType part[],
// Create the dihedral table
tableDihedral = new TabulatedDihedralPotential*[numTabDihedralFiles];
tableDihedral_addr = new TabulatedDihedralPotential*[numTabDihedralFiles];
+ dihedralList_d = NULL;
+ tableDihedral_d = NULL;
for (int i = 0; i < numTabDihedralFiles; i++) {
tableDihedral_addr[i] = NULL;
tableDihedral[i] = NULL;
@@ -149,13 +155,24 @@ ComputeForce::~ComputeForce() {
gpuErrchk( cudaFree(pos_d) );
gpuErrchk( cudaFree(forceInternal_d) );
gpuErrchk( cudaFree(type_d) );
- gpuErrchk( cudaFree(bonds_d) );
- gpuErrchk( cudaFree(bondMap_d) );
- gpuErrchk( cudaFree(excludes_d) );
- gpuErrchk( cudaFree(excludeMap_d) );
- gpuErrchk( cudaFree(angles_d) );
- gpuErrchk( cudaFree(dihedrals_d) );
- gpuErrchk( cudaFree(bondList_d) );
+ if (numBonds > 0) {
+ gpuErrchk( cudaFree(bonds_d) );
+ gpuErrchk( cudaFree(bondMap_d) );
+ gpuErrchk( cudaFree(bondList_d) );
+ }
+ if (numAngles > 0) {
+ gpuErrchk( cudaFree(angles_d) );
+ gpuErrchk( cudaFree(angleList_d) );
+ }
+ if (numDihedrals > 0) {
+ gpuErrchk( cudaFree(dihedrals_d) );
+ gpuErrchk( cudaFree(dihedralList_d) );
+ gpuErrchk( cudaFree(dihedralPotList_d) );
+ }
+ if (numExcludes > 0) {
+ gpuErrchk( cudaFree(excludes_d) );
+ gpuErrchk( cudaFree(excludeMap_d) );
+ }
}
gpuErrchk(cudaFree(numPairs_d));
diff --git a/src/DcdWriter.h b/src/DcdWriter.h
index d5ab57d2933eab11315383df196c82edbb094865..50904e021fb9074000070f042fbb17f8f618e4ac 100644
--- a/src/DcdWriter.h
+++ b/src/DcdWriter.h
@@ -287,7 +287,8 @@ public:
/* Unit cell */
if (cell) {
- out_integer = 48;
+ // out_integer = 48;
+ out_integer = 6*4; // this seems correct for float
NAMD_write(fd, (char *) &out_integer, sizeof(int));
NAMD_write(fd, (char *) cell, out_integer);
NAMD_write(fd, (char *) &out_integer, sizeof(int));
diff --git a/src/GrandBrownTown.cu b/src/GrandBrownTown.cu
index 5cc934bee06c78cd7b38b5fe11834928d985fec4..bc776402cf64b11ef27e70250614e1e508df3d3e 100644
--- a/src/GrandBrownTown.cu
+++ b/src/GrandBrownTown.cu
@@ -302,9 +302,17 @@ GrandBrownTown::~GrandBrownTown() {
delete[] pos;
delete[] type;
delete[] serial;
- delete[] bondList;
delete randoGen;
+ if (numBonds > 0)
+ delete[] bondList;
+ if (numAngles > 0)
+ delete[] angleList;
+ if (numDihedrals > 0) {
+ delete[] dihedralList;
+ delete[] dihedralPotList;
+ }
+
// Auxillary objects
delete internal;
for (int i = 0; i < numReplicas; ++i)
@@ -1041,9 +1049,9 @@ void GrandBrownTown::copyToCUDA() {
cudaMemcpyHostToDevice));*/
gpuErrchk(cudaMalloc(&randoGen_d, sizeof(Random)));
- gpuErrchk(cudaMemcpyAsync(randoGen_d, randoGen, sizeof(Random),
+ gpuErrchk(cudaMemcpy(randoGen_d, randoGen, sizeof(Random),
cudaMemcpyHostToDevice));
- gpuErrchk(cudaDeviceSynchronize());
+ // gpuErrchk(cudaDeviceSynchronize());
}
/*void GrandBrownTown::createBondList()
diff --git a/src/Makefile b/src/Makefile
index f359fd0962d8ba25d45f90877c3ea21a3f07c510..b58905be1702555a4e8dacb1080f8abc32c594ae 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -3,15 +3,14 @@ include ./findcudalib.mk
INCLUDE = $(CUDA_PATH)/include
ifeq ($(dbg),1)
- CC_FLAGS += -g -O0
NV_FLAGS += -g -G
- EX_FLAGS = -O0 -m$(OS_SIZE)
+ EX_FLAGS = -g -O0 -m$(OS_SIZE)
else
EX_FLAGS = -O3 -m$(OS_SIZE)
endif
CC_FLAGS += -I$(CUDA_PATH)/include
-# CC_FLAGS += -Wall -Wno-write-strings -std=c++0x -pedantic
+CC_FLAGS += -Wall -Wno-write-strings -std=c++0x -pedantic # TODO: test on Mac OSX
NV_FLAGS += -lineinfo
ifneq ($(DARWIN),)
diff --git a/src/arbd.cpp b/src/arbd.cpp
index 32bcccda9a257765acd9933fda17b33774b783fd..78ae60cb43105678eaabed93309bd7c4e011959b 100644
--- a/src/arbd.cpp
+++ b/src/arbd.cpp
@@ -31,13 +31,12 @@ int main(int argc, char* argv[]) {
return 0;
} else if (argc == 2 && (strcmp(argv[1], "--version") == 0)) {
// --version
- printf("%s 0.1a\n", argv[0]);
- printf("Written by Jeff Comer, Justin Dufresne, and Terrance Howard.\n");
+ printf("%s Nov 2016 (alpha)\n", argv[0]);
return 0;
} else if (argc == 2 && (strcmp(argv[1], "--info") == 0)) {
// --info
GPUManager::load_info();
- size_t n_gpus = max(GPUManager::gpus.size(), 1lu);
+ // size_t n_gpus = max(GPUManager::gpus.size(), 1lu);
return 0;
} else if (argc < 3) {
printf("%s: missing arguments\n", argv[0]);
@@ -50,7 +49,7 @@ int main(int argc, char* argv[]) {
bool debug = false, safe = true;
int replicas = 1;
- unsigned int imd_port;
+ unsigned int imd_port = 0;
bool imd_on = false;
int num_flags = 0;
for (int pos = 1; pos < argc; pos++) {
@@ -66,7 +65,7 @@ int main(int argc, char* argv[]) {
num_flags++;
} else if (strcmp(arg, "-g") == 0 || strcmp(arg, "--gpu") == 0) {
- int arg_val = atoi(argv[pos + 1]);
+ unsigned int arg_val = atoi(argv[pos + 1]);
gpuID = arg_val;
num_flags += 2;
if (arg_val < 0 || arg_val > n_gpus) {
diff --git a/src/findcudalib.mk b/src/findcudalib.mk
index 4694c946b5466539734bf91bfd21628b12079b26..7f4c10c89b10f502c17e95ebc9f5205820e76109 100644
--- a/src/findcudalib.mk
+++ b/src/findcudalib.mk
@@ -36,7 +36,7 @@
## Find Location of most recent CUDA Toolkit
ifeq (,$(CUDA_PATH))
- CUDA_PATH := $(shell echo $(wildcard /usr/local/cuda*) | tail -n1)
+ CUDA_PATH := $(shell echo $(wildcard /usr/local/cuda*) | tr ' ' '\n' | tail -n1)
ifeq (,$(CUDA_PATH))
$(error Could not CUDA_PATH. Please pass as follows: $(MAKE) CUDA_PATH=/path/to/cuda)
endif
diff --git a/src/useful.h b/src/useful.h
index 1618b9a463b4132658ea1a2a5fffc49591e63daf..25d2951e7e296b1e33a12b91f11e5a5cd9bdca97 100644
--- a/src/useful.h
+++ b/src/useful.h
@@ -267,9 +267,9 @@ public:
HOST DEVICE inline Matrix3() {}
HOST DEVICE Matrix3(float s);
HOST DEVICE Matrix3(float xx, float xy, float xz, float yx, float yy, float yz, float zx, float zy, float zz);
- Matrix3(float x, float y, float z);
- Matrix3(const Vector3& ex, const Vector3& ey, const Vector3& ez);
- Matrix3(const float* d);
+ HOST DEVICE Matrix3(float x, float y, float z);
+ HOST DEVICE Matrix3(const Vector3& ex, const Vector3& ey, const Vector3& ez);
+ HOST DEVICE Matrix3(const float* d);
// Operators