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Commit 306d99e8 authored by Peter Eastman's avatar Peter Eastman
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Enhancements to CUDAStream to reduce the risk of bugs and make debugging easier

parent 968cb132
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Showing with 292 additions and 284 deletions
platforms/cuda/src/kernels/cudatypes.h
View file @ 306d99e8
...@@ -76,40 +76,42 @@ struct CUDAStream : public SoADeviceObject ...@@ -76,40 +76,42 @@ struct CUDAStream : public SoADeviceObject
T** _pDevStream; T** _pDevStream;
T* _pSysData; T* _pSysData;
T* _pDevData; T* _pDevData;
CUDAStream(int length, int subStreams = 1); std::string _name;
CUDAStream(unsigned int length, unsigned int subStreams = 1); CUDAStream(int length, int subStreams = 1, std::string name="");
CUDAStream(unsigned int length, int subStreams = 1); CUDAStream(unsigned int length, unsigned int subStreams = 1, std::string name="");
CUDAStream(int length, unsigned int subStreams = 1); CUDAStream(unsigned int length, int subStreams = 1, std::string name="");
CUDAStream(int length, unsigned int subStreams = 1, std::string name="");
virtual ~CUDAStream(); virtual ~CUDAStream();
void Allocate(); void Allocate();
void Deallocate(); void Deallocate();
void Upload(); void Upload();
void Download(); void Download();
void Collapse(unsigned int newstreams = 1, unsigned int interleave = 1); void Collapse(unsigned int newstreams = 1, unsigned int interleave = 1);
T& operator[](int index);
}; };
float CompareStreams(CUDAStream<float>& s1, CUDAStream<float>& s2, float tolerance, unsigned int maxindex = 0); float CompareStreams(CUDAStream<float>& s1, CUDAStream<float>& s2, float tolerance, unsigned int maxindex = 0);
template <typename T> template <typename T>
CUDAStream<T>::CUDAStream(int length, unsigned int subStreams) : _length(length), _subStreams(subStreams), _stride((length + 0xf) & 0xfffffff0) CUDAStream<T>::CUDAStream(int length, unsigned int subStreams, std::string name) : _length(length), _subStreams(subStreams), _stride((length + 0xf) & 0xfffffff0), _name(name)
{ {
Allocate(); Allocate();
} }
template <typename T> template <typename T>
CUDAStream<T>::CUDAStream(unsigned int length, int subStreams) : _length(length), _subStreams(subStreams), _stride((length + 0xf) & 0xfffffff0) CUDAStream<T>::CUDAStream(unsigned int length, int subStreams, std::string name) : _length(length), _subStreams(subStreams), _stride((length + 0xf) & 0xfffffff0), _name(name)
{ {
Allocate(); Allocate();
} }
template <typename T> template <typename T>
CUDAStream<T>::CUDAStream(unsigned int length, unsigned int subStreams) : _length(length), _subStreams(subStreams), _stride((length + 0xf) & 0xfffffff0) CUDAStream<T>::CUDAStream(unsigned int length, unsigned int subStreams, std::string name) : _length(length), _subStreams(subStreams), _stride((length + 0xf) & 0xfffffff0), _name(name)
{ {
Allocate(); Allocate();
} }
template <typename T> template <typename T>
CUDAStream<T>::CUDAStream(int length, int subStreams) : _length(length), _subStreams(subStreams), _stride((length + 0xf) & 0xfffffff0) CUDAStream<T>::CUDAStream(int length, int subStreams, std::string name) : _length(length), _subStreams(subStreams), _stride((length + 0xf) & 0xfffffff0), _name(name)
{ {
Allocate(); Allocate();
} }
...@@ -129,7 +131,7 @@ void CUDAStream<T>::Allocate() ...@@ -129,7 +131,7 @@ void CUDAStream<T>::Allocate()
_pSysData = new T[_subStreams * _stride]; _pSysData = new T[_subStreams * _stride];
status = cudaMalloc((void **) &_pDevData, _stride * _subStreams * sizeof(T)); status = cudaMalloc((void **) &_pDevData, _stride * _subStreams * sizeof(T));
RTERROR(status, "cudaMalloc CUDAStream::Allocate failed"); RTERROR(status, (_name+": cudaMalloc in CUDAStream::Allocate failed").c_str());
for (unsigned int i = 0; i < _subStreams; i++) for (unsigned int i = 0; i < _subStreams; i++)
{ {
...@@ -149,7 +151,7 @@ void CUDAStream<T>::Deallocate() ...@@ -149,7 +151,7 @@ void CUDAStream<T>::Deallocate()
delete[] _pSysData; delete[] _pSysData;
_pSysData = NULL; _pSysData = NULL;
status = cudaFree(_pDevData); status = cudaFree(_pDevData);
RTERROR(status, "cudaFree CUDAStream::Deallocate failed"); RTERROR(status, (_name+": cudaFree in CUDAStream::Deallocate failed").c_str());
} }
template <typename T> template <typename T>
...@@ -157,7 +159,7 @@ void CUDAStream<T>::Upload() ...@@ -157,7 +159,7 @@ void CUDAStream<T>::Upload()
{ {
cudaError_t status; cudaError_t status;
status = cudaMemcpy(_pDevData, _pSysData, _stride * _subStreams * sizeof(T), cudaMemcpyHostToDevice); status = cudaMemcpy(_pDevData, _pSysData, _stride * _subStreams * sizeof(T), cudaMemcpyHostToDevice);
RTERROR(status, "cudaMemcpy CUDAStream::Upload failed"); RTERROR(status, (_name+": cudaMemcpy in CUDAStream::Upload failed").c_str());
} }
template <typename T> template <typename T>
...@@ -165,7 +167,7 @@ void CUDAStream<T>::Download() ...@@ -165,7 +167,7 @@ void CUDAStream<T>::Download()
{ {
cudaError_t status; cudaError_t status;
status = cudaMemcpy(_pSysData, _pDevData, _stride * _subStreams * sizeof(T), cudaMemcpyDeviceToHost); status = cudaMemcpy(_pSysData, _pDevData, _stride * _subStreams * sizeof(T), cudaMemcpyDeviceToHost);
RTERROR(status, "cudaMemcpy CUDAStream::Download failed"); RTERROR(status, (_name+": cudaMemcpy in CUDAStream::Download failed").c_str());
} }
template <typename T> template <typename T>
...@@ -210,6 +212,12 @@ void CUDAStream<T>::Collapse(unsigned int newstreams, unsigned int interleave) ...@@ -210,6 +212,12 @@ void CUDAStream<T>::Collapse(unsigned int newstreams, unsigned int interleave)
delete[] pTemp; delete[] pTemp;
} }
template <typename T>
T& CUDAStream<T>::operator[](int index)
{
return _pSysData[index];
}
static const unsigned int GRID = 32; static const unsigned int GRID = 32;
static const unsigned int GRIDBITS = 5; static const unsigned int GRIDBITS = 5;
static const int G8X_NONBOND_THREADS_PER_BLOCK = 256; static const int G8X_NONBOND_THREADS_PER_BLOCK = 256;
......
platforms/cuda/src/kernels/gpu.cpp
View file @ 306d99e8
...@@ -128,29 +128,29 @@ void gpuSetBondParameters(gpuContext gpu, const vector<int>& atom1, const vector ...@@ -128,29 +128,29 @@ void gpuSetBondParameters(gpuContext gpu, const vector<int>& atom1, const vector
{ {
int bonds = atom1.size(); int bonds = atom1.size();
gpu->sim.bonds = bonds; gpu->sim.bonds = bonds;
CUDAStream<int4>* psBondID = new CUDAStream<int4>(bonds, 1); CUDAStream<int4>* psBondID = new CUDAStream<int4>(bonds, 1, "BondID");
gpu->psBondID = psBondID; gpu->psBondID = psBondID;
gpu->sim.pBondID = psBondID->_pDevStream[0]; gpu->sim.pBondID = psBondID->_pDevStream[0];
CUDAStream<float2>* psBondParameter = new CUDAStream<float2>(bonds, 1); CUDAStream<float2>* psBondParameter = new CUDAStream<float2>(bonds, 1, "BondParameter");
gpu->psBondParameter = psBondParameter; gpu->psBondParameter = psBondParameter;
gpu->sim.pBondParameter = psBondParameter->_pDevStream[0]; gpu->sim.pBondParameter = psBondParameter->_pDevStream[0];
for (int i = 0; i < bonds; i++) for (int i = 0; i < bonds; i++)
{ {
psBondID->_pSysStream[0][i].x = atom1[i]; (*psBondID)[i].x = atom1[i];
psBondID->_pSysStream[0][i].y = atom2[i]; (*psBondID)[i].y = atom2[i];
psBondParameter->_pSysStream[0][i].x = length[i]; (*psBondParameter)[i].x = length[i];
psBondParameter->_pSysStream[0][i].y = k[i]; (*psBondParameter)[i].y = k[i];
psBondID->_pSysStream[0][i].z = gpu->pOutputBufferCounter[psBondID->_pSysStream[0][i].x]++; psBondID->_pSysData[i].z = gpu->pOutputBufferCounter[psBondID->_pSysData[i].x]++;
psBondID->_pSysStream[0][i].w = gpu->pOutputBufferCounter[psBondID->_pSysStream[0][i].y]++; psBondID->_pSysData[i].w = gpu->pOutputBufferCounter[psBondID->_pSysData[i].y]++;
#if (DUMP_PARAMETERS == 1) #if (DUMP_PARAMETERS == 1)
cout << cout <<
i << " " << i << " " <<
psBondID->_pSysStream[0][i].x << " " << (*psBondID)[i].x << " " <<
psBondID->_pSysStream[0][i].y << " " << (*psBondID)[i].y << " " <<
psBondID->_pSysStream[0][i].z << " " << (*psBondID)[i].z << " " <<
psBondID->_pSysStream[0][i].w << " " << (*psBondID)[i].w << " " <<
psBondParameter->_pSysStream[0][i].x << " " << (*psBondParameter)[i].x << " " <<
psBondParameter->_pSysStream[0][i].y << (*psBondParameter)[i].y <<
endl; endl;
#endif #endif
} }
...@@ -164,37 +164,37 @@ void gpuSetBondAngleParameters(gpuContext gpu, const vector<int>& atom1, const v ...@@ -164,37 +164,37 @@ void gpuSetBondAngleParameters(gpuContext gpu, const vector<int>& atom1, const v
{ {
int bond_angles = atom1.size(); int bond_angles = atom1.size();
gpu->sim.bond_angles = bond_angles; gpu->sim.bond_angles = bond_angles;
CUDAStream<int4>* psBondAngleID1 = new CUDAStream<int4>(bond_angles, 1); CUDAStream<int4>* psBondAngleID1 = new CUDAStream<int4>(bond_angles, 1, "BondAngleID1");
gpu->psBondAngleID1 = psBondAngleID1; gpu->psBondAngleID1 = psBondAngleID1;
gpu->sim.pBondAngleID1 = psBondAngleID1->_pDevStream[0]; gpu->sim.pBondAngleID1 = psBondAngleID1->_pDevStream[0];
CUDAStream<int2>* psBondAngleID2 = new CUDAStream<int2>(bond_angles, 1); CUDAStream<int2>* psBondAngleID2 = new CUDAStream<int2>(bond_angles, 1, "BondAngleID2");
gpu->psBondAngleID2 = psBondAngleID2; gpu->psBondAngleID2 = psBondAngleID2;
gpu->sim.pBondAngleID2 = psBondAngleID2->_pDevStream[0]; gpu->sim.pBondAngleID2 = psBondAngleID2->_pDevStream[0];
CUDAStream<float2>* psBondAngleParameter = new CUDAStream<float2>(bond_angles, 1); CUDAStream<float2>* psBondAngleParameter = new CUDAStream<float2>(bond_angles, 1, "BondAngleParameter");
gpu->psBondAngleParameter = psBondAngleParameter; gpu->psBondAngleParameter = psBondAngleParameter;
gpu->sim.pBondAngleParameter = psBondAngleParameter->_pDevStream[0]; gpu->sim.pBondAngleParameter = psBondAngleParameter->_pDevStream[0];
for (int i = 0; i < bond_angles; i++) for (int i = 0; i < bond_angles; i++)
{ {
psBondAngleID1->_pSysStream[0][i].x = atom1[i]; (*psBondAngleID1)[i].x = atom1[i];
psBondAngleID1->_pSysStream[0][i].y = atom2[i]; (*psBondAngleID1)[i].y = atom2[i];
psBondAngleID1->_pSysStream[0][i].z = atom3[i]; (*psBondAngleID1)[i].z = atom3[i];
psBondAngleParameter->_pSysStream[0][i].x = angle[i]; (*psBondAngleParameter)[i].x = angle[i];
psBondAngleParameter->_pSysStream[0][i].y = k[i]; (*psBondAngleParameter)[i].y = k[i];
psBondAngleID1->_pSysStream[0][i].w = gpu->pOutputBufferCounter[psBondAngleID1->_pSysStream[0][i].x]++; psBondAngleID1->_pSysData[i].w = gpu->pOutputBufferCounter[psBondAngleID1->_pSysData[i].x]++;
psBondAngleID2->_pSysStream[0][i].x = gpu->pOutputBufferCounter[psBondAngleID1->_pSysStream[0][i].y]++; psBondAngleID2->_pSysData[i].x = gpu->pOutputBufferCounter[psBondAngleID1->_pSysData[i].y]++;
psBondAngleID2->_pSysStream[0][i].y = gpu->pOutputBufferCounter[psBondAngleID1->_pSysStream[0][i].z]++; psBondAngleID2->_pSysData[i].y = gpu->pOutputBufferCounter[psBondAngleID1->_pSysData[i].z]++;
#if (DUMP_PARAMETERS == 1) #if (DUMP_PARAMETERS == 1)
cout << cout <<
i << " " << i << " " <<
psBondAngleID1->_pSysStream[0][i].x << " " << (*psBondAngleID1)[i].x << " " <<
psBondAngleID1->_pSysStream[0][i].y << " " << (*psBondAngleID1)[i].y << " " <<
psBondAngleID1->_pSysStream[0][i].z << " " << (*psBondAngleID1)[i].z << " " <<
psBondAngleID1->_pSysStream[0][i].w << " " << (*psBondAngleID1)[i].w << " " <<
psBondAngleID2->_pSysStream[0][i].x << " " << (*psBondAngleID2)[i].x << " " <<
psBondAngleID2->_pSysStream[0][i].y << " " << (*psBondAngleID2)[i].y << " " <<
psBondAngleParameter->_pSysStream[0][i].x << " " << (*psBondAngleParameter)[i].x << " " <<
psBondAngleParameter->_pSysStream[0][i].y << (*psBondAngleParameter)[i].y <<
endl; endl;
#endif #endif
} }
...@@ -209,42 +209,42 @@ void gpuSetDihedralParameters(gpuContext gpu, const vector<int>& atom1, const ve ...@@ -209,42 +209,42 @@ void gpuSetDihedralParameters(gpuContext gpu, const vector<int>& atom1, const ve
{ {
int dihedrals = atom1.size(); int dihedrals = atom1.size();
gpu->sim.dihedrals = dihedrals; gpu->sim.dihedrals = dihedrals;
CUDAStream<int4>* psDihedralID1 = new CUDAStream<int4>(dihedrals, 1); CUDAStream<int4>* psDihedralID1 = new CUDAStream<int4>(dihedrals, 1, "DihedralID1");
gpu->psDihedralID1 = psDihedralID1; gpu->psDihedralID1 = psDihedralID1;
gpu->sim.pDihedralID1 = psDihedralID1->_pDevStream[0]; gpu->sim.pDihedralID1 = psDihedralID1->_pDevStream[0];
CUDAStream<int4>* psDihedralID2 = new CUDAStream<int4>(dihedrals, 1); CUDAStream<int4>* psDihedralID2 = new CUDAStream<int4>(dihedrals, 1, "DihedralID2");
gpu->psDihedralID2 = psDihedralID2; gpu->psDihedralID2 = psDihedralID2;
gpu->sim.pDihedralID2 = psDihedralID2->_pDevStream[0]; gpu->sim.pDihedralID2 = psDihedralID2->_pDevStream[0];
CUDAStream<float4>* psDihedralParameter = new CUDAStream<float4>(dihedrals, 1); CUDAStream<float4>* psDihedralParameter = new CUDAStream<float4>(dihedrals, 1, "DihedralParameter");
gpu->psDihedralParameter = psDihedralParameter; gpu->psDihedralParameter = psDihedralParameter;
gpu->sim.pDihedralParameter = psDihedralParameter->_pDevStream[0]; gpu->sim.pDihedralParameter = psDihedralParameter->_pDevStream[0];
for (int i = 0; i < dihedrals; i++) for (int i = 0; i < dihedrals; i++)
{ {
psDihedralID1->_pSysStream[0][i].x = atom1[i]; (*psDihedralID1)[i].x = atom1[i];
psDihedralID1->_pSysStream[0][i].y = atom2[i]; (*psDihedralID1)[i].y = atom2[i];
psDihedralID1->_pSysStream[0][i].z = atom3[i]; (*psDihedralID1)[i].z = atom3[i];
psDihedralID1->_pSysStream[0][i].w = atom4[i]; (*psDihedralID1)[i].w = atom4[i];
psDihedralParameter->_pSysStream[0][i].x = k[i]; (*psDihedralParameter)[i].x = k[i];
psDihedralParameter->_pSysStream[0][i].y = phase[i]; (*psDihedralParameter)[i].y = phase[i];
psDihedralParameter->_pSysStream[0][i].z = (float) periodicity[i]; (*psDihedralParameter)[i].z = (float) periodicity[i];
psDihedralID2->_pSysStream[0][i].x = gpu->pOutputBufferCounter[psDihedralID1->_pSysStream[0][i].x]++; psDihedralID2->_pSysData[i].x = gpu->pOutputBufferCounter[psDihedralID1->_pSysData[i].x]++;
psDihedralID2->_pSysStream[0][i].y = gpu->pOutputBufferCounter[psDihedralID1->_pSysStream[0][i].y]++; psDihedralID2->_pSysData[i].y = gpu->pOutputBufferCounter[psDihedralID1->_pSysData[i].y]++;
psDihedralID2->_pSysStream[0][i].z = gpu->pOutputBufferCounter[psDihedralID1->_pSysStream[0][i].z]++; psDihedralID2->_pSysData[i].z = gpu->pOutputBufferCounter[psDihedralID1->_pSysData[i].z]++;
psDihedralID2->_pSysStream[0][i].w = gpu->pOutputBufferCounter[psDihedralID1->_pSysStream[0][i].w]++; psDihedralID2->_pSysData[i].w = gpu->pOutputBufferCounter[psDihedralID1->_pSysData[i].w]++;
#if (DUMP_PARAMETERS == 1) #if (DUMP_PARAMETERS == 1)
cout << cout <<
i << " " << i << " " <<
psDihedralID1->_pSysStream[0][i].x << " " << (*psDihedralID1)[i].x << " " <<
psDihedralID1->_pSysStream[0][i].y << " " << (*psDihedralID1)[i].y << " " <<
psDihedralID1->_pSysStream[0][i].z << " " << (*psDihedralID1)[i].z << " " <<
psDihedralID1->_pSysStream[0][i].w << " " << (*psDihedralID1)[i].w << " " <<
psDihedralID2->_pSysStream[0][i].x << " " << (*psDihedralID2)[i].x << " " <<
psDihedralID2->_pSysStream[0][i].y << " " << (*psDihedralID2)[i].y << " " <<
psDihedralID2->_pSysStream[0][i].z << " " << (*psDihedralID2)[i].z << " " <<
psDihedralID2->_pSysStream[0][i].w << " " << (*psDihedralID2)[i].w << " " <<
psDihedralParameter->_pSysStream[0][i].x << " " << (*psDihedralParameter)[i].x << " " <<
psDihedralParameter->_pSysStream[0][i].y << " " << (*psDihedralParameter)[i].y << " " <<
psDihedralParameter->_pSysStream[0][i].z << endl; (*psDihedralParameter)[i].z << endl;
#endif #endif
} }
psDihedralID1->Upload(); psDihedralID1->Upload();
...@@ -258,52 +258,52 @@ void gpuSetRbDihedralParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -258,52 +258,52 @@ void gpuSetRbDihedralParameters(gpuContext gpu, const vector<int>& atom1, const
{ {
int rb_dihedrals = atom1.size(); int rb_dihedrals = atom1.size();
gpu->sim.rb_dihedrals = rb_dihedrals; gpu->sim.rb_dihedrals = rb_dihedrals;
CUDAStream<int4>* psRbDihedralID1 = new CUDAStream<int4>(rb_dihedrals, 1); CUDAStream<int4>* psRbDihedralID1 = new CUDAStream<int4>(rb_dihedrals, 1, "RbDihedralID1");
gpu->psRbDihedralID1 = psRbDihedralID1; gpu->psRbDihedralID1 = psRbDihedralID1;
gpu->sim.pRbDihedralID1 = psRbDihedralID1->_pDevStream[0]; gpu->sim.pRbDihedralID1 = psRbDihedralID1->_pDevStream[0];
CUDAStream<int4>* psRbDihedralID2 = new CUDAStream<int4>(rb_dihedrals, 1); CUDAStream<int4>* psRbDihedralID2 = new CUDAStream<int4>(rb_dihedrals, 1, "RbDihedralID2");
gpu->psRbDihedralID2 = psRbDihedralID2; gpu->psRbDihedralID2 = psRbDihedralID2;
gpu->sim.pRbDihedralID2 = psRbDihedralID2->_pDevStream[0]; gpu->sim.pRbDihedralID2 = psRbDihedralID2->_pDevStream[0];
CUDAStream<float4>* psRbDihedralParameter1 = new CUDAStream<float4>(rb_dihedrals, 1); CUDAStream<float4>* psRbDihedralParameter1 = new CUDAStream<float4>(rb_dihedrals, 1, "RbDihedralParameter1");
gpu->psRbDihedralParameter1 = psRbDihedralParameter1; gpu->psRbDihedralParameter1 = psRbDihedralParameter1;
gpu->sim.pRbDihedralParameter1 = psRbDihedralParameter1->_pDevStream[0]; gpu->sim.pRbDihedralParameter1 = psRbDihedralParameter1->_pDevStream[0];
CUDAStream<float2>* psRbDihedralParameter2 = new CUDAStream<float2>(rb_dihedrals, 1); CUDAStream<float2>* psRbDihedralParameter2 = new CUDAStream<float2>(rb_dihedrals, 1, "RbDihedralParameter2");
gpu->psRbDihedralParameter2 = psRbDihedralParameter2; gpu->psRbDihedralParameter2 = psRbDihedralParameter2;
gpu->sim.pRbDihedralParameter2 = psRbDihedralParameter2->_pDevStream[0]; gpu->sim.pRbDihedralParameter2 = psRbDihedralParameter2->_pDevStream[0];
for (int i = 0; i < rb_dihedrals; i++) for (int i = 0; i < rb_dihedrals; i++)
{ {
psRbDihedralID1->_pSysStream[0][i].x = atom1[i]; (*psRbDihedralID1)[i].x = atom1[i];
psRbDihedralID1->_pSysStream[0][i].y = atom2[i]; (*psRbDihedralID1)[i].y = atom2[i];
psRbDihedralID1->_pSysStream[0][i].z = atom3[i]; (*psRbDihedralID1)[i].z = atom3[i];
psRbDihedralID1->_pSysStream[0][i].w = atom4[i]; (*psRbDihedralID1)[i].w = atom4[i];
psRbDihedralParameter1->_pSysStream[0][i].x = c0[i]; (*psRbDihedralParameter1)[i].x = c0[i];
psRbDihedralParameter1->_pSysStream[0][i].y = c1[i]; (*psRbDihedralParameter1)[i].y = c1[i];
psRbDihedralParameter1->_pSysStream[0][i].z = c2[i]; (*psRbDihedralParameter1)[i].z = c2[i];
psRbDihedralParameter1->_pSysStream[0][i].w = c3[i]; (*psRbDihedralParameter1)[i].w = c3[i];
psRbDihedralParameter2->_pSysStream[0][i].x = c4[i]; (*psRbDihedralParameter2)[i].x = c4[i];
psRbDihedralParameter2->_pSysStream[0][i].y = c5[i]; (*psRbDihedralParameter2)[i].y = c5[i];
psRbDihedralID2->_pSysStream[0][i].x = gpu->pOutputBufferCounter[psRbDihedralID1->_pSysStream[0][i].x]++; psRbDihedralID2->_pSysData[i].x = gpu->pOutputBufferCounter[psRbDihedralID1->_pSysData[i].x]++;
psRbDihedralID2->_pSysStream[0][i].y = gpu->pOutputBufferCounter[psRbDihedralID1->_pSysStream[0][i].y]++; psRbDihedralID2->_pSysData[i].y = gpu->pOutputBufferCounter[psRbDihedralID1->_pSysData[i].y]++;
psRbDihedralID2->_pSysStream[0][i].z = gpu->pOutputBufferCounter[psRbDihedralID1->_pSysStream[0][i].z]++; psRbDihedralID2->_pSysData[i].z = gpu->pOutputBufferCounter[psRbDihedralID1->_pSysData[i].z]++;
psRbDihedralID2->_pSysStream[0][i].w = gpu->pOutputBufferCounter[psRbDihedralID1->_pSysStream[0][i].w]++; psRbDihedralID2->_pSysData[i].w = gpu->pOutputBufferCounter[psRbDihedralID1->_pSysData[i].w]++;
#if (DUMP_PARAMETERS == 1) #if (DUMP_PARAMETERS == 1)
cout << cout <<
i << " " << i << " " <<
psRbDihedralID1->_pSysStream[0][i].x << " " << (*psRbDihedralID1)[i].x << " " <<
psRbDihedralID1->_pSysStream[0][i].y << " " << (*psRbDihedralID1)[i].y << " " <<
psRbDihedralID1->_pSysStream[0][i].z << " " << (*psRbDihedralID1)[i].z << " " <<
psRbDihedralID1->_pSysStream[0][i].w <<" " << (*psRbDihedralID1)[i].w <<" " <<
psRbDihedralID2->_pSysStream[0][i].x << " " << (*psRbDihedralID2)[i].x << " " <<
psRbDihedralID2->_pSysStream[0][i].y << " " << (*psRbDihedralID2)[i].y << " " <<
psRbDihedralID2->_pSysStream[0][i].z << " " << (*psRbDihedralID2)[i].z << " " <<
psRbDihedralID2->_pSysStream[0][i].w <<" " << (*psRbDihedralID2)[i].w <<" " <<
psRbDihedralParameter1->_pSysStream[0][i].x << " " << (*psRbDihedralParameter1)[i].x << " " <<
psRbDihedralParameter1->_pSysStream[0][i].y << " " << (*psRbDihedralParameter1)[i].y << " " <<
psRbDihedralParameter1->_pSysStream[0][i].z << " " << (*psRbDihedralParameter1)[i].z << " " <<
psRbDihedralParameter1->_pSysStream[0][i].w << " " << (*psRbDihedralParameter1)[i].w << " " <<
psRbDihedralParameter2->_pSysStream[0][i].x << " " << (*psRbDihedralParameter2)[i].x << " " <<
psRbDihedralParameter2->_pSysStream[0][i].y << (*psRbDihedralParameter2)[i].y <<
endl; endl;
#endif #endif
} }
...@@ -321,19 +321,19 @@ void gpuSetLJ14Parameters(gpuContext gpu, float epsfac, float fudge, const vecto ...@@ -321,19 +321,19 @@ void gpuSetLJ14Parameters(gpuContext gpu, float epsfac, float fudge, const vecto
float scale = epsfac * fudge; float scale = epsfac * fudge;
gpu->sim.LJ14s = LJ14s; gpu->sim.LJ14s = LJ14s;
CUDAStream<int4>* psLJ14ID = new CUDAStream<int4>(LJ14s, 1); CUDAStream<int4>* psLJ14ID = new CUDAStream<int4>(LJ14s, 1, "LJ14ID");
gpu->psLJ14ID = psLJ14ID; gpu->psLJ14ID = psLJ14ID;
gpu->sim.pLJ14ID = psLJ14ID->_pDevStream[0]; gpu->sim.pLJ14ID = psLJ14ID->_pDevStream[0];
CUDAStream<float4>* psLJ14Parameter = new CUDAStream<float4>(LJ14s, 1); CUDAStream<float4>* psLJ14Parameter = new CUDAStream<float4>(LJ14s, 1, "LJ14Parameter");
gpu->psLJ14Parameter = psLJ14Parameter; gpu->psLJ14Parameter = psLJ14Parameter;
gpu->sim.pLJ14Parameter = psLJ14Parameter->_pDevStream[0]; gpu->sim.pLJ14Parameter = psLJ14Parameter->_pDevStream[0];
for (int i = 0; i < LJ14s; i++) for (int i = 0; i < LJ14s; i++)
{ {
psLJ14ID->_pSysStream[0][i].x = atom1[i]; (*psLJ14ID)[i].x = atom1[i];
psLJ14ID->_pSysStream[0][i].y = atom2[i]; (*psLJ14ID)[i].y = atom2[i];
psLJ14ID->_pSysStream[0][i].z = gpu->pOutputBufferCounter[psLJ14ID->_pSysStream[0][i].x]++; psLJ14ID->_pSysData[i].z = gpu->pOutputBufferCounter[psLJ14ID->_pSysData[i].x]++;
psLJ14ID->_pSysStream[0][i].w = gpu->pOutputBufferCounter[psLJ14ID->_pSysStream[0][i].y]++; psLJ14ID->_pSysData[i].w = gpu->pOutputBufferCounter[psLJ14ID->_pSysData[i].y]++;
float p0, p1, p2; float p0, p1, p2;
if (c12[i] == 0.0f) if (c12[i] == 0.0f)
{ {
...@@ -346,20 +346,20 @@ void gpuSetLJ14Parameters(gpuContext gpu, float epsfac, float fudge, const vecto ...@@ -346,20 +346,20 @@ void gpuSetLJ14Parameters(gpuContext gpu, float epsfac, float fudge, const vecto
p1 = pow(c12[i] / c6[i], 1.0f / 6.0f); p1 = pow(c12[i] / c6[i], 1.0f / 6.0f);
} }
p2 = scale * q1[i] * q2[i]; p2 = scale * q1[i] * q2[i];
psLJ14Parameter->_pSysStream[0][i].x = p0; (*psLJ14Parameter)[i].x = p0;
psLJ14Parameter->_pSysStream[0][i].y = p1; (*psLJ14Parameter)[i].y = p1;
psLJ14Parameter->_pSysStream[0][i].z = p2; (*psLJ14Parameter)[i].z = p2;
} }
#if (DUMP_PARAMETERS == 1) #if (DUMP_PARAMETERS == 1)
cout << cout <<
i << " " << i << " " <<
psLJ14ID->_pSysStream[0][i].x << " " << (*psLJ14ID)[i].x << " " <<
psLJ14ID->_pSysStream[0][i].y << " " << (*psLJ14ID)[i].y << " " <<
psLJ14ID->_pSysStream[0][i].z << " " << (*psLJ14ID)[i].z << " " <<
psLJ14ID->_pSysStream[0][i].w << " " << (*psLJ14ID)[i].w << " " <<
psLJ14Parameter->_pSysStream[0][i].x << " " << (*psLJ14Parameter)[i].x << " " <<
psLJ14Parameter->_pSysStream[0][i].y << " " << (*psLJ14Parameter)[i].y << " " <<
psLJ14Parameter->_pSysStream[0][i].z << " " << (*psLJ14Parameter)[i].z << " " <<
p0 << " " << p0 << " " <<
p1 << " " << p1 << " " <<
p2 << " " << p2 << " " <<
...@@ -389,20 +389,20 @@ void gpuSetCoulombParameters(gpuContext gpu, float epsfac, const vector<int>& at ...@@ -389,20 +389,20 @@ void gpuSetCoulombParameters(gpuContext gpu, float epsfac, const vector<int>& at
} }
if (symbol.size() > 0) if (symbol.size() > 0)
gpu->pAtomSymbol[i] = symbol[i]; gpu->pAtomSymbol[i] = symbol[i];
gpu->psPosq4->_pSysStream[0][i].w = p0; (*gpu->psPosq4)[i].w = p0;
gpu->psSigEps2->_pSysStream[0][i].x = p1; (*gpu->psSigEps2)[i].x = p1;
gpu->psSigEps2->_pSysStream[0][i].y = p2; (*gpu->psSigEps2)[i].y = p2;
} }
// Dummy out extra atom data // Dummy out extra atom data
for (unsigned int i = coulombs; i < gpu->sim.paddedNumberOfAtoms; i++) for (unsigned int i = coulombs; i < gpu->sim.paddedNumberOfAtoms; i++)
{ {
gpu->psPosq4->_pSysStream[0][i].x = 100000.0f + i * 10.0f; (*gpu->psPosq4)[i].x = 100000.0f + i * 10.0f;
gpu->psPosq4->_pSysStream[0][i].y = 100000.0f + i * 10.0f; (*gpu->psPosq4)[i].y = 100000.0f + i * 10.0f;
gpu->psPosq4->_pSysStream[0][i].z = 100000.0f + i * 10.0f; (*gpu->psPosq4)[i].z = 100000.0f + i * 10.0f;
gpu->psPosq4->_pSysStream[0][i].w = 0.0f; (*gpu->psPosq4)[i].w = 0.0f;
gpu->psSigEps2->_pSysStream[0][i].x = 0.0f; (*gpu->psSigEps2)[i].x = 0.0f;
gpu->psSigEps2->_pSysStream[0][i].y = 0.0f; (*gpu->psSigEps2)[i].y = 0.0f;
} }
gpu->psPosq4->Upload(); gpu->psPosq4->Upload();
...@@ -432,23 +432,23 @@ void gpuSetObcParameters(gpuContext gpu, float innerDielectric, float solventDie ...@@ -432,23 +432,23 @@ void gpuSetObcParameters(gpuContext gpu, float innerDielectric, float solventDie
gpu->bIncludeGBSA = true; gpu->bIncludeGBSA = true;
for (unsigned int i = 0; i < atoms; i++) for (unsigned int i = 0; i < atoms; i++)
{ {
gpu->psObcData->_pSysStream[0][i].x = radius[i] - dielectricOffset; (*gpu->psObcData)[i].x = radius[i] - dielectricOffset;
gpu->psObcData->_pSysStream[0][i].y = scale[i] * gpu->psObcData->_pSysStream[0][i].x; (*gpu->psObcData)[i].y = scale[i] * (*gpu->psObcData)[i].x;
#if (DUMP_PARAMETERS == 1) #if (DUMP_PARAMETERS == 1)
cout << cout <<
i << " " << i << " " <<
gpu->psObcData->_pSysStream[0][i].x << " " << (*gpu->psObcData)[i].x << " " <<
gpu->psObcData->_pSysStream[0][i].y; (*gpu->psObcData)[i].y;
#endif #endif
} }
// Dummy out extra atom data // Dummy out extra atom data
for (unsigned int i = atoms; i < gpu->sim.paddedNumberOfAtoms; i++) for (unsigned int i = atoms; i < gpu->sim.paddedNumberOfAtoms; i++)
{ {
gpu->psBornRadii->_pSysStream[0][i] = 0.2f; (*gpu->psBornRadii)[i] = 0.2f;
gpu->psObcData->_pSysStream[0][i].x = 0.01f; (*gpu->psObcData)[i].x = 0.01f;
gpu->psObcData->_pSysStream[0][i].y = 0.01f; (*gpu->psObcData)[i].y = 0.01f;
} }
gpu->psBornRadii->Upload(); gpu->psBornRadii->Upload();
...@@ -515,10 +515,10 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -515,10 +515,10 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
// Record the actual SETTLE clusters. // Record the actual SETTLE clusters.
CUDAStream<int4>* psSettleID = new CUDAStream<int4>((int) settleClusters.size(), 1); CUDAStream<int4>* psSettleID = new CUDAStream<int4>((int) settleClusters.size(), 1, "SettleID");
gpu->psSettleID = psSettleID; gpu->psSettleID = psSettleID;
gpu->sim.pSettleID = psSettleID->_pDevStream[0]; gpu->sim.pSettleID = psSettleID->_pDevStream[0];
CUDAStream<float2>* psSettleParameter = new CUDAStream<float2>((int) settleClusters.size(), 1); CUDAStream<float2>* psSettleParameter = new CUDAStream<float2>((int) settleClusters.size(), 1, "SettleParameter");
gpu->psSettleParameter = psSettleParameter; gpu->psSettleParameter = psSettleParameter;
gpu->sim.pSettleParameter = psSettleParameter->_pDevStream[0]; gpu->sim.pSettleParameter = psSettleParameter->_pDevStream[0];
gpu->sim.settleConstraints = settleClusters.size(); gpu->sim.settleConstraints = settleClusters.size();
...@@ -530,25 +530,25 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -530,25 +530,25 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
float dist13 = settleConstraints[atom1].find(atom3)->second; float dist13 = settleConstraints[atom1].find(atom3)->second;
float dist23 = settleConstraints[atom2].find(atom3)->second; float dist23 = settleConstraints[atom2].find(atom3)->second;
if (dist12 == dist13) { // atom1 is the central atom if (dist12 == dist13) { // atom1 is the central atom
psSettleID->_pSysData[i].x = atom1; (*psSettleID)[i].x = atom1;
psSettleID->_pSysData[i].y = atom2; (*psSettleID)[i].y = atom2;
psSettleID->_pSysData[i].z = atom3; (*psSettleID)[i].z = atom3;
psSettleParameter->_pSysData[i].x = dist12; (*psSettleParameter)[i].x = dist12;
psSettleParameter->_pSysData[i].y = dist23; (*psSettleParameter)[i].y = dist23;
} }
else if (dist12 == dist23) { // atom2 is the central atom else if (dist12 == dist23) { // atom2 is the central atom
psSettleID->_pSysData[i].x = atom2; (*psSettleID)[i].x = atom2;
psSettleID->_pSysData[i].y = atom1; (*psSettleID)[i].y = atom1;
psSettleID->_pSysData[i].z = atom3; (*psSettleID)[i].z = atom3;
psSettleParameter->_pSysData[i].x = dist12; (*psSettleParameter)[i].x = dist12;
psSettleParameter->_pSysData[i].y = dist13; (*psSettleParameter)[i].y = dist13;
} }
else if (dist13 == dist23) { // atom3 is the central atom else if (dist13 == dist23) { // atom3 is the central atom
psSettleID->_pSysData[i].x = atom3; (*psSettleID)[i].x = atom3;
psSettleID->_pSysData[i].y = atom1; (*psSettleID)[i].y = atom1;
psSettleID->_pSysData[i].z = atom2; (*psSettleID)[i].z = atom2;
psSettleParameter->_pSysData[i].x = dist13; (*psSettleParameter)[i].x = dist13;
psSettleParameter->_pSysData[i].y = dist12; (*psSettleParameter)[i].y = dist12;
} }
else else
throw OpenMMException("Two of the three distances constrained with SETTLE must be the same."); throw OpenMMException("Two of the three distances constrained with SETTLE must be the same.");
...@@ -627,10 +627,10 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -627,10 +627,10 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
// Fill in the Cuda streams. // Fill in the Cuda streams.
CUDAStream<int4>* psShakeID = new CUDAStream<int4>(validShakeClusters, 1); CUDAStream<int4>* psShakeID = new CUDAStream<int4>(validShakeClusters, 1, "ShakeID");
gpu->psShakeID = psShakeID; gpu->psShakeID = psShakeID;
gpu->sim.pShakeID = psShakeID->_pDevStream[0]; gpu->sim.pShakeID = psShakeID->_pDevStream[0];
CUDAStream<float4>* psShakeParameter = new CUDAStream<float4>(validShakeClusters, 1); CUDAStream<float4>* psShakeParameter = new CUDAStream<float4>(validShakeClusters, 1, "ShakeParameter");
gpu->psShakeParameter = psShakeParameter; gpu->psShakeParameter = psShakeParameter;
gpu->sim.pShakeParameter = psShakeParameter->_pDevStream[0]; gpu->sim.pShakeParameter = psShakeParameter->_pDevStream[0];
gpu->sim.ShakeConstraints = validShakeClusters; gpu->sim.ShakeConstraints = validShakeClusters;
...@@ -639,14 +639,14 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -639,14 +639,14 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
const ShakeCluster& cluster = iter->second; const ShakeCluster& cluster = iter->second;
if (!cluster.valid) if (!cluster.valid)
continue; continue;
psShakeID->_pSysStream[0][index].x = cluster.centralID; (*psShakeID)[index].x = cluster.centralID;
psShakeID->_pSysStream[0][index].y = cluster.peripheralID[0]; (*psShakeID)[index].y = cluster.peripheralID[0];
psShakeID->_pSysStream[0][index].z = cluster.size > 1 ? cluster.peripheralID[1] : -1; (*psShakeID)[index].z = cluster.size > 1 ? cluster.peripheralID[1] : -1;
psShakeID->_pSysStream[0][index].w = cluster.size > 2 ? cluster.peripheralID[2] : -1; (*psShakeID)[index].w = cluster.size > 2 ? cluster.peripheralID[2] : -1;
psShakeParameter->_pSysStream[0][index].x = cluster.centralInvMass; (*psShakeParameter)[index].x = cluster.centralInvMass;
psShakeParameter->_pSysStream[0][index].y = 0.5f/(cluster.centralInvMass+cluster.peripheralInvMass); (*psShakeParameter)[index].y = 0.5f/(cluster.centralInvMass+cluster.peripheralInvMass);
psShakeParameter->_pSysStream[0][index].z = cluster.distance*cluster.distance; (*psShakeParameter)[index].z = cluster.distance*cluster.distance;
psShakeParameter->_pSysStream[0][index].w = cluster.peripheralInvMass; (*psShakeParameter)[index].w = cluster.peripheralInvMass;
isShakeAtom[cluster.centralID] = true; isShakeAtom[cluster.centralID] = true;
isShakeAtom[cluster.peripheralID[0]] = true; isShakeAtom[cluster.peripheralID[0]] = true;
if (cluster.size > 1) if (cluster.size > 1)
...@@ -691,64 +691,64 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -691,64 +691,64 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
// Fill in the CUDA streams. // Fill in the CUDA streams.
CUDAStream<int2>* psLincsAtoms = new CUDAStream<int2>((int) lincsConstraints.size(), 1); CUDAStream<int2>* psLincsAtoms = new CUDAStream<int2>((int) lincsConstraints.size(), 1, "LincsAtoms");
gpu->psLincsAtoms = psLincsAtoms; gpu->psLincsAtoms = psLincsAtoms;
gpu->sim.pLincsAtoms = psLincsAtoms->_pDevData; gpu->sim.pLincsAtoms = psLincsAtoms->_pDevData;
CUDAStream<float4>* psLincsDistance = new CUDAStream<float4>((int) lincsConstraints.size(), 1); CUDAStream<float4>* psLincsDistance = new CUDAStream<float4>((int) lincsConstraints.size(), 1, "LincsDistance");
gpu->psLincsDistance = psLincsDistance; gpu->psLincsDistance = psLincsDistance;
gpu->sim.pLincsDistance = psLincsDistance->_pDevData; gpu->sim.pLincsDistance = psLincsDistance->_pDevData;
CUDAStream<int>* psLincsConnections = new CUDAStream<int>(totalLinks, 1); CUDAStream<int>* psLincsConnections = new CUDAStream<int>(totalLinks, 1, "LincsConnections");
gpu->psLincsConnections = psLincsConnections; gpu->psLincsConnections = psLincsConnections;
gpu->sim.pLincsConnections = psLincsConnections->_pDevData; gpu->sim.pLincsConnections = psLincsConnections->_pDevData;
CUDAStream<int>* psLincsConnectionsIndex = new CUDAStream<int>((int) lincsConstraints.size()+1, 1); CUDAStream<int>* psLincsConnectionsIndex = new CUDAStream<int>((int) lincsConstraints.size()+1, 1, "LincsConnectionsIndex");
gpu->psLincsConnectionsIndex = psLincsConnectionsIndex; gpu->psLincsConnectionsIndex = psLincsConnectionsIndex;
gpu->sim.pLincsConnectionsIndex = psLincsConnectionsIndex->_pDevData; gpu->sim.pLincsConnectionsIndex = psLincsConnectionsIndex->_pDevData;
CUDAStream<int>* psLincsAtomConstraints = new CUDAStream<int>((int) lincsConstraints.size()*2, 1); CUDAStream<int>* psLincsAtomConstraints = new CUDAStream<int>((int) lincsConstraints.size()*2, 1, "LincsAtomConstraints");
gpu->psLincsAtomConstraints = psLincsAtomConstraints; gpu->psLincsAtomConstraints = psLincsAtomConstraints;
gpu->sim.pLincsAtomConstraints = psLincsAtomConstraints->_pDevData; gpu->sim.pLincsAtomConstraints = psLincsAtomConstraints->_pDevData;
CUDAStream<int>* psLincsAtomConstraintsIndex = new CUDAStream<int>(gpu->natoms+1, 1); CUDAStream<int>* psLincsAtomConstraintsIndex = new CUDAStream<int>(gpu->natoms+1, 1, "LincsAtomConstraintsIndex");
gpu->psLincsAtomConstraintsIndex = psLincsAtomConstraintsIndex; gpu->psLincsAtomConstraintsIndex = psLincsAtomConstraintsIndex;
gpu->sim.pLincsAtomConstraintsIndex = psLincsAtomConstraintsIndex->_pDevData; gpu->sim.pLincsAtomConstraintsIndex = psLincsAtomConstraintsIndex->_pDevData;
CUDAStream<float>* psLincsS = new CUDAStream<float>((int) lincsConstraints.size(), 1); CUDAStream<float>* psLincsS = new CUDAStream<float>((int) lincsConstraints.size(), 1, "LincsS");
gpu->psLincsS = psLincsS; gpu->psLincsS = psLincsS;
gpu->sim.pLincsS = psLincsS->_pDevData; gpu->sim.pLincsS = psLincsS->_pDevData;
CUDAStream<float>* psLincsCoupling = new CUDAStream<float>(totalLinks, 1); CUDAStream<float>* psLincsCoupling = new CUDAStream<float>(totalLinks, 1, "LincsCoupling");
gpu->psLincsCoupling = psLincsCoupling; gpu->psLincsCoupling = psLincsCoupling;
gpu->sim.pLincsCoupling = psLincsCoupling->_pDevData; gpu->sim.pLincsCoupling = psLincsCoupling->_pDevData;
CUDAStream<float>* psLincsRhs1 = new CUDAStream<float>((int) lincsConstraints.size(), 1); CUDAStream<float>* psLincsRhs1 = new CUDAStream<float>((int) lincsConstraints.size(), 1, "LincsRhs1");
gpu->psLincsRhs1 = psLincsRhs1; gpu->psLincsRhs1 = psLincsRhs1;
gpu->sim.pLincsRhs1 = psLincsRhs1->_pDevData; gpu->sim.pLincsRhs1 = psLincsRhs1->_pDevData;
CUDAStream<float>* psLincsRhs2 = new CUDAStream<float>((int) lincsConstraints.size(), 1); CUDAStream<float>* psLincsRhs2 = new CUDAStream<float>((int) lincsConstraints.size(), 1, "LincsRhs2");
gpu->psLincsRhs2 = psLincsRhs2; gpu->psLincsRhs2 = psLincsRhs2;
gpu->sim.pLincsRhs2 = psLincsRhs2->_pDevData; gpu->sim.pLincsRhs2 = psLincsRhs2->_pDevData;
CUDAStream<float>* psLincsSolution = new CUDAStream<float>((int) lincsConstraints.size(), 1); CUDAStream<float>* psLincsSolution = new CUDAStream<float>((int) lincsConstraints.size(), 1, "LincsSolution");
gpu->psLincsSolution = psLincsSolution; gpu->psLincsSolution = psLincsSolution;
gpu->sim.pLincsSolution = psLincsSolution->_pDevData; gpu->sim.pLincsSolution = psLincsSolution->_pDevData;
CUDAStream<unsigned int>* psSyncCounter = new CUDAStream<unsigned int>(2*lincsTerms+2, 1); CUDAStream<unsigned int>* psSyncCounter = new CUDAStream<unsigned int>(2*lincsTerms+2, 1, "SyncCounter");
gpu->psSyncCounter = psSyncCounter; gpu->psSyncCounter = psSyncCounter;
gpu->sim.pSyncCounter = psSyncCounter->_pDevData; gpu->sim.pSyncCounter = psSyncCounter->_pDevData;
gpu->sim.lincsConstraints = lincsConstraints.size(); gpu->sim.lincsConstraints = lincsConstraints.size();
index = 0; index = 0;
for (unsigned int i = 0; i < lincsConstraints.size(); i++) { for (unsigned int i = 0; i < lincsConstraints.size(); i++) {
int c = lincsConstraints[i]; int c = lincsConstraints[i];
psLincsAtoms->_pSysData[i].x = atom1[c]; (*psLincsAtoms)[i].x = atom1[c];
psLincsAtoms->_pSysData[i].y = atom2[c]; (*psLincsAtoms)[i].y = atom2[c];
psLincsDistance->_pSysData[i].w = distance[c]; (*psLincsDistance)[i].w = distance[c];
psLincsS->_pSysData[i] = 1.0f/sqrt(invMass1[c]+invMass2[c]); (*psLincsS)[i] = 1.0f/sqrt(invMass1[c]+invMass2[c]);
psLincsConnectionsIndex->_pSysData[i] = index; (*psLincsConnectionsIndex)[i] = index;
for (unsigned int j = 0; j < linkedConstraints[i].size(); j++) for (unsigned int j = 0; j < linkedConstraints[i].size(); j++)
psLincsConnections->_pSysData[index++] = linkedConstraints[i][j]; (*psLincsConnections)[index++] = linkedConstraints[i][j];
} }
psLincsConnectionsIndex->_pSysData[lincsConstraints.size()] = index; (*psLincsConnectionsIndex)[lincsConstraints.size()] = index;
for (unsigned int i = 0; i < psSyncCounter->_length; i++) for (unsigned int i = 0; i < psSyncCounter->_length; i++)
psSyncCounter->_pSysData[i] = 0; (*psSyncCounter)[i] = 0;
index = 0; index = 0;
for (unsigned int i = 0; i < atomConstraints.size(); i++) { for (unsigned int i = 0; i < atomConstraints.size(); i++) {
psLincsAtomConstraintsIndex->_pSysData[i] = index; (*psLincsAtomConstraintsIndex)[i] = index;
for (unsigned int j = 0; j < atomConstraints[i].size(); j++) for (unsigned int j = 0; j < atomConstraints[i].size(); j++)
psLincsAtomConstraints->_pSysData[index++] = atomConstraints[i][j]; (*psLincsAtomConstraints)[index++] = atomConstraints[i][j];
} }
psLincsAtomConstraintsIndex->_pSysData[atomConstraints.size()] = index; (*psLincsAtomConstraintsIndex)[atomConstraints.size()] = index;
psLincsAtoms->Upload(); psLincsAtoms->Upload();
psLincsDistance->Upload(); psLincsDistance->Upload();
psLincsS->Upload(); psLincsS->Upload();
...@@ -785,7 +785,7 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -785,7 +785,7 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
gpu->sim.NonShakeConstraints = count; gpu->sim.NonShakeConstraints = count;
if( count || true ){ if( count || true ){
CUDAStream<int>* psNonShakeID = new CUDAStream<int>(count, 1); CUDAStream<int>* psNonShakeID = new CUDAStream<int>(count, 1, "NonShakeID");
gpu->psNonShakeID = psNonShakeID; gpu->psNonShakeID = psNonShakeID;
gpu->sim.pNonShakeID = psNonShakeID->_pDevStream[0]; gpu->sim.pNonShakeID = psNonShakeID->_pDevStream[0];
...@@ -802,7 +802,7 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const ...@@ -802,7 +802,7 @@ void gpuSetConstraintParameters(gpuContext gpu, const vector<int>& atom1, const
count = 0; count = 0;
for (int i = 0; i < gpu->natoms; i++){ for (int i = 0; i < gpu->natoms; i++){
if (!isShakeAtom[i]){ if (!isShakeAtom[i]){
psNonShakeID->_pSysStream[0][count++] = i; (*psNonShakeID)[count++] = i;
} }
} }
psNonShakeID->Upload(); psNonShakeID->Upload();
...@@ -821,7 +821,7 @@ int gpuAllocateInitialBuffers(gpuContext gpu) ...@@ -821,7 +821,7 @@ int gpuAllocateInitialBuffers(gpuContext gpu)
gpu->sim.degreesOfFreedom = 3 * gpu->sim.atoms - 6; gpu->sim.degreesOfFreedom = 3 * gpu->sim.atoms - 6;
gpu->gpAtomTable = NULL; gpu->gpAtomTable = NULL;
gpu->gAtomTypes = 0; gpu->gAtomTypes = 0;
gpu->psPosq4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1); gpu->psPosq4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1, "Posq");
gpu->sim.stride = gpu->psPosq4->_stride; gpu->sim.stride = gpu->psPosq4->_stride;
gpu->sim.stride2 = gpu->sim.stride * 2; gpu->sim.stride2 = gpu->sim.stride * 2;
gpu->sim.stride3 = gpu->sim.stride * 3; gpu->sim.stride3 = gpu->sim.stride * 3;
...@@ -831,29 +831,29 @@ int gpuAllocateInitialBuffers(gpuContext gpu) ...@@ -831,29 +831,29 @@ int gpuAllocateInitialBuffers(gpuContext gpu)
gpu->sim.stride2 = 2 * gpu->sim.stride; gpu->sim.stride2 = 2 * gpu->sim.stride;
gpu->sim.stride3 = 3 * gpu->sim.stride; gpu->sim.stride3 = 3 * gpu->sim.stride;
gpu->sim.stride4 = 4 * gpu->sim.stride; gpu->sim.stride4 = 4 * gpu->sim.stride;
gpu->psPosqP4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1); gpu->psPosqP4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1, "PosqP");
gpu->sim.pPosqP = gpu->psPosqP4->_pDevStream[0]; gpu->sim.pPosqP = gpu->psPosqP4->_pDevStream[0];
gpu->psOldPosq4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1); gpu->psOldPosq4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1, "OldPosq");
gpu->sim.pOldPosq = gpu->psOldPosq4->_pDevStream[0]; gpu->sim.pOldPosq = gpu->psOldPosq4->_pDevStream[0];
gpu->psVelm4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1); gpu->psVelm4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1, "Velm");
gpu->sim.pVelm4 = gpu->psVelm4->_pDevStream[0]; gpu->sim.pVelm4 = gpu->psVelm4->_pDevStream[0];
gpu->psvVector4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1); gpu->psvVector4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1, "vVector");
gpu->sim.pvVector4 = gpu->psvVector4->_pDevStream[0]; gpu->sim.pvVector4 = gpu->psvVector4->_pDevStream[0];
gpu->psxVector4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1); gpu->psxVector4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, 1, "xVector");
gpu->sim.pxVector4 = gpu->psxVector4->_pDevStream[0]; gpu->sim.pxVector4 = gpu->psxVector4->_pDevStream[0];
gpu->psBornRadii = new CUDAStream<float>(gpu->sim.paddedNumberOfAtoms, 1); gpu->psBornRadii = new CUDAStream<float>(gpu->sim.paddedNumberOfAtoms, 1, "BornRadii");
gpu->sim.pBornRadii = gpu->psBornRadii->_pDevStream[0]; gpu->sim.pBornRadii = gpu->psBornRadii->_pDevStream[0];
gpu->psObcChain = new CUDAStream<float>(gpu->sim.paddedNumberOfAtoms, 1); gpu->psObcChain = new CUDAStream<float>(gpu->sim.paddedNumberOfAtoms, 1, "ObcChain");
gpu->sim.pObcChain = gpu->psObcChain->_pDevStream[0]; gpu->sim.pObcChain = gpu->psObcChain->_pDevStream[0];
gpu->psSigEps2 = new CUDAStream<float2>(gpu->sim.paddedNumberOfAtoms, 1); gpu->psSigEps2 = new CUDAStream<float2>(gpu->sim.paddedNumberOfAtoms, 1, "SigEps2");
gpu->sim.pAttr = gpu->psSigEps2->_pDevStream[0]; gpu->sim.pAttr = gpu->psSigEps2->_pDevStream[0];
gpu->psObcData = new CUDAStream<float2>(gpu->sim.paddedNumberOfAtoms, 1); gpu->psObcData = new CUDAStream<float2>(gpu->sim.paddedNumberOfAtoms, 1, "ObcData");
gpu->sim.pObcData = gpu->psObcData->_pDevStream[0]; gpu->sim.pObcData = gpu->psObcData->_pDevStream[0];
gpu->pAtomSymbol = new unsigned char[gpu->natoms]; gpu->pAtomSymbol = new unsigned char[gpu->natoms];
gpu->psAtomIndex = new CUDAStream<int>(gpu->sim.paddedNumberOfAtoms, 1); gpu->psAtomIndex = new CUDAStream<int>(gpu->sim.paddedNumberOfAtoms, 1, "AtomIndex");
gpu->sim.pAtomIndex = gpu->psAtomIndex->_pDevStream[0]; gpu->sim.pAtomIndex = gpu->psAtomIndex->_pDevStream[0];
for (int i = 0; i < (int) gpu->sim.paddedNumberOfAtoms; i++) for (int i = 0; i < (int) gpu->sim.paddedNumberOfAtoms; i++)
gpu->psAtomIndex->_pSysStream[0][i] = i; (*gpu->psAtomIndex)[i] = i;
gpu->psAtomIndex->Upload(); gpu->psAtomIndex->Upload();
// Determine randoms // Determine randoms
gpu->seed = 1; gpu->seed = 1;
...@@ -862,10 +862,10 @@ int gpuAllocateInitialBuffers(gpuContext gpu) ...@@ -862,10 +862,10 @@ int gpuAllocateInitialBuffers(gpuContext gpu)
gpu->sim.randoms = gpu->sim.randomFrames * gpu->sim.paddedNumberOfAtoms - 5 * GRID; gpu->sim.randoms = gpu->sim.randomFrames * gpu->sim.paddedNumberOfAtoms - 5 * GRID;
gpu->sim.totalRandoms = gpu->sim.randoms + gpu->sim.paddedNumberOfAtoms; gpu->sim.totalRandoms = gpu->sim.randoms + gpu->sim.paddedNumberOfAtoms;
gpu->sim.totalRandomsTimesTwo = gpu->sim.totalRandoms * 2; gpu->sim.totalRandomsTimesTwo = gpu->sim.totalRandoms * 2;
gpu->psRandom4 = new CUDAStream<float4>(gpu->sim.totalRandomsTimesTwo, 1); gpu->psRandom4 = new CUDAStream<float4>(gpu->sim.totalRandomsTimesTwo, 1, "Random4");
gpu->psRandom2 = new CUDAStream<float2>(gpu->sim.totalRandomsTimesTwo, 1); gpu->psRandom2 = new CUDAStream<float2>(gpu->sim.totalRandomsTimesTwo, 1, "Random2");
gpu->psRandomPosition = new CUDAStream<int>(gpu->sim.blocks, 1); gpu->psRandomPosition = new CUDAStream<int>(gpu->sim.blocks, 1, "RandomPosition");
gpu->psRandomSeed = new CUDAStream<uint4>(gpu->sim.blocks * gpu->sim.random_threads_per_block, 1); gpu->psRandomSeed = new CUDAStream<uint4>(gpu->sim.blocks * gpu->sim.random_threads_per_block, 1, "RandomSeed");
gpu->sim.pRandom4a = gpu->psRandom4->_pDevStream[0]; gpu->sim.pRandom4a = gpu->psRandom4->_pDevStream[0];
gpu->sim.pRandom2a = gpu->psRandom2->_pDevStream[0]; gpu->sim.pRandom2a = gpu->psRandom2->_pDevStream[0];
gpu->sim.pRandom4b = gpu->psRandom4->_pDevStream[0] + gpu->sim.totalRandoms; gpu->sim.pRandom4b = gpu->psRandom4->_pDevStream[0] + gpu->sim.totalRandoms;
...@@ -874,14 +874,14 @@ int gpuAllocateInitialBuffers(gpuContext gpu) ...@@ -874,14 +874,14 @@ int gpuAllocateInitialBuffers(gpuContext gpu)
gpu->sim.pRandomSeed = gpu->psRandomSeed->_pDevStream[0]; gpu->sim.pRandomSeed = gpu->psRandomSeed->_pDevStream[0];
// Allocate and clear linear momentum buffer // Allocate and clear linear momentum buffer
gpu->psLinearMomentum = new CUDAStream<float4>(gpu->sim.blocks, 1); gpu->psLinearMomentum = new CUDAStream<float4>(gpu->sim.blocks, 1, "LinearMomentum");
gpu->sim.pLinearMomentum = gpu->psLinearMomentum->_pDevStream[0]; gpu->sim.pLinearMomentum = gpu->psLinearMomentum->_pDevStream[0];
for (int i = 0; i < (int) gpu->sim.blocks; i++) for (int i = 0; i < (int) gpu->sim.blocks; i++)
{ {
gpu->psLinearMomentum->_pSysStream[0][i].x = 0.0f; (*gpu->psLinearMomentum)[i].x = 0.0f;
gpu->psLinearMomentum->_pSysStream[0][i].y = 0.0f; (*gpu->psLinearMomentum)[i].y = 0.0f;
gpu->psLinearMomentum->_pSysStream[0][i].z = 0.0f; (*gpu->psLinearMomentum)[i].z = 0.0f;
gpu->psLinearMomentum->_pSysStream[0][i].w = 0.0f; (*gpu->psLinearMomentum)[i].w = 0.0f;
} }
gpu->psLinearMomentum->Upload(); gpu->psLinearMomentum->Upload();
...@@ -893,9 +893,9 @@ void gpuSetPositions(gpuContext gpu, const vector<float>& x, const vector<float> ...@@ -893,9 +893,9 @@ void gpuSetPositions(gpuContext gpu, const vector<float>& x, const vector<float>
{ {
for (int i = 0; i < gpu->natoms; i++) for (int i = 0; i < gpu->natoms; i++)
{ {
gpu->psPosq4->_pSysStream[0][i].x = x[i]; (*gpu->psPosq4)[i].x = x[i];
gpu->psPosq4->_pSysStream[0][i].y = y[i]; (*gpu->psPosq4)[i].y = y[i];
gpu->psPosq4->_pSysStream[0][i].z = z[i]; (*gpu->psPosq4)[i].z = z[i];
} }
gpu->psPosq4->Upload(); gpu->psPosq4->Upload();
...@@ -909,9 +909,9 @@ void gpuSetVelocities(gpuContext gpu, const vector<float>& x, const vector<float ...@@ -909,9 +909,9 @@ void gpuSetVelocities(gpuContext gpu, const vector<float>& x, const vector<float
{ {
for (int i = 0; i < gpu->natoms; i++) for (int i = 0; i < gpu->natoms; i++)
{ {
gpu->psVelm4->_pSysStream[0][i].x = x[i]; (*gpu->psVelm4)[i].x = x[i];
gpu->psVelm4->_pSysStream[0][i].y = y[i]; (*gpu->psVelm4)[i].y = y[i];
gpu->psVelm4->_pSysStream[0][i].z = z[i]; (*gpu->psVelm4)[i].z = z[i];
} }
gpu->psVelm4->Upload(); gpu->psVelm4->Upload();
} }
...@@ -922,7 +922,7 @@ void gpuSetMass(gpuContext gpu, const vector<float>& mass) ...@@ -922,7 +922,7 @@ void gpuSetMass(gpuContext gpu, const vector<float>& mass)
float totalMass = 0.0f; float totalMass = 0.0f;
for (int i = 0; i < gpu->natoms; i++) for (int i = 0; i < gpu->natoms; i++)
{ {
gpu->psVelm4->_pSysStream[0][i].w = 1.0f/mass[i]; (*gpu->psVelm4)[i].w = 1.0f/mass[i];
totalMass += mass[i]; totalMass += mass[i];
} }
gpu->sim.inverseTotalMass = 1.0f / totalMass; gpu->sim.inverseTotalMass = 1.0f / totalMass;
...@@ -934,16 +934,16 @@ void gpuInitializeRandoms(gpuContext gpu) ...@@ -934,16 +934,16 @@ void gpuInitializeRandoms(gpuContext gpu)
{ {
for (int i = 0; i < (int) gpu->sim.blocks; i++) for (int i = 0; i < (int) gpu->sim.blocks; i++)
{ {
gpu->psRandomPosition->_pSysStream[0][i] = 0; (*gpu->psRandomPosition)[i] = 0;
} }
int seed = gpu->seed | ((gpu->seed ^ 0xffffffff) << 16); int seed = gpu->seed | ((gpu->seed ^ 0xffffffff) << 16);
srand(seed); srand(seed);
for (int i = 0; i < (int) (gpu->sim.blocks * gpu->sim.random_threads_per_block); i++) for (int i = 0; i < (int) (gpu->sim.blocks * gpu->sim.random_threads_per_block); i++)
{ {
gpu->psRandomSeed->_pSysStream[0][i].x = rand(); (*gpu->psRandomSeed)[i].x = rand();
gpu->psRandomSeed->_pSysStream[0][i].y = rand(); (*gpu->psRandomSeed)[i].y = rand();
gpu->psRandomSeed->_pSysStream[0][i].z = rand(); (*gpu->psRandomSeed)[i].z = rand();
gpu->psRandomSeed->_pSysStream[0][i].w = rand(); (*gpu->psRandomSeed)[i].w = rand();
} }
gpu->psRandomPosition->Upload(); gpu->psRandomPosition->Upload();
gpu->psRandomSeed->Upload(); gpu->psRandomSeed->Upload();
...@@ -1046,10 +1046,10 @@ void* gpuInit(int numAtoms) ...@@ -1046,10 +1046,10 @@ void* gpuInit(int numAtoms)
gpuAllocateInitialBuffers(gpu); gpuAllocateInitialBuffers(gpu);
for (int i = 0; i < gpu->natoms; i++) for (int i = 0; i < gpu->natoms; i++)
{ {
gpu->psxVector4->_pSysStream[0][i].x = 0.0f; (*gpu->psxVector4)[i].x = 0.0f;
gpu->psxVector4->_pSysStream[0][i].y = 0.0f; (*gpu->psxVector4)[i].y = 0.0f;
gpu->psxVector4->_pSysStream[0][i].z = 0.0f; (*gpu->psxVector4)[i].z = 0.0f;
gpu->psxVector4->_pSysStream[0][i].w = 0.0f; (*gpu->psxVector4)[i].w = 0.0f;
} }
gpu->psxVector4->Upload(); gpu->psxVector4->Upload();
...@@ -1323,9 +1323,9 @@ int gpuBuildOutputBuffers(gpuContext gpu) ...@@ -1323,9 +1323,9 @@ int gpuBuildOutputBuffers(gpuContext gpu)
} }
} }
gpu->sim.outputBuffers = outputBuffers; gpu->sim.outputBuffers = outputBuffers;
gpu->psForce4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, outputBuffers); gpu->psForce4 = new CUDAStream<float4>(gpu->sim.paddedNumberOfAtoms, outputBuffers, "Force");
gpu->psBornForce = new CUDAStream<float>(gpu->sim.paddedNumberOfAtoms, gpu->sim.nonbondOutputBuffers); gpu->psBornForce = new CUDAStream<float>(gpu->sim.paddedNumberOfAtoms, gpu->sim.nonbondOutputBuffers, "BornForce");
gpu->psBornSum = new CUDAStream<float>(gpu->sim.paddedNumberOfAtoms, gpu->sim.nonbondOutputBuffers); gpu->psBornSum = new CUDAStream<float>(gpu->sim.paddedNumberOfAtoms, gpu->sim.nonbondOutputBuffers, "BornSum");
gpu->sim.pForce4 = gpu->psForce4->_pDevStream[0]; gpu->sim.pForce4 = gpu->psForce4->_pDevStream[0];
gpu->sim.pForce4a = gpu->sim.pForce4; gpu->sim.pForce4a = gpu->sim.pForce4;
gpu->sim.pForce4b = gpu->sim.pForce4 + 1 * gpu->sim.nonbondOutputBuffers * gpu->sim.stride; gpu->sim.pForce4b = gpu->sim.pForce4 + 1 * gpu->sim.nonbondOutputBuffers * gpu->sim.stride;
...@@ -1348,33 +1348,33 @@ int gpuBuildOutputBuffers(gpuContext gpu) ...@@ -1348,33 +1348,33 @@ int gpuBuildOutputBuffers(gpuContext gpu)
int flip = outputBuffers - 1; int flip = outputBuffers - 1;
for (int i = 0; i < (int) gpu->sim.bonds; i++) for (int i = 0; i < (int) gpu->sim.bonds; i++)
{ {
gpu->psBondID->_pSysStream[0][i].z = flip - gpu->psBondID->_pSysStream[0][i].z; (*gpu->psBondID)[i].z = flip - (*gpu->psBondID)[i].z;
gpu->psBondID->_pSysStream[0][i].w = flip - gpu->psBondID->_pSysStream[0][i].w; (*gpu->psBondID)[i].w = flip - (*gpu->psBondID)[i].w;
} }
for (int i = 0; i < (int) gpu->sim.bond_angles; i++) for (int i = 0; i < (int) gpu->sim.bond_angles; i++)
{ {
gpu->psBondAngleID1->_pSysStream[0][i].w = flip - gpu->psBondAngleID1->_pSysStream[0][i].w; (*gpu->psBondAngleID1)[i].w = flip - (*gpu->psBondAngleID1)[i].w;
gpu->psBondAngleID2->_pSysStream[0][i].x = flip - gpu->psBondAngleID2->_pSysStream[0][i].x; (*gpu->psBondAngleID2)[i].x = flip - (*gpu->psBondAngleID2)[i].x;
gpu->psBondAngleID2->_pSysStream[0][i].y = flip - gpu->psBondAngleID2->_pSysStream[0][i].y; (*gpu->psBondAngleID2)[i].y = flip - (*gpu->psBondAngleID2)[i].y;
} }
for (int i = 0; i < (int) gpu->sim.dihedrals; i++) for (int i = 0; i < (int) gpu->sim.dihedrals; i++)
{ {
gpu->psDihedralID2->_pSysStream[0][i].x = flip - gpu->psDihedralID2->_pSysStream[0][i].x; (*gpu->psDihedralID2)[i].x = flip - (*gpu->psDihedralID2)[i].x;
gpu->psDihedralID2->_pSysStream[0][i].y = flip - gpu->psDihedralID2->_pSysStream[0][i].y; (*gpu->psDihedralID2)[i].y = flip - (*gpu->psDihedralID2)[i].y;
gpu->psDihedralID2->_pSysStream[0][i].z = flip - gpu->psDihedralID2->_pSysStream[0][i].z; (*gpu->psDihedralID2)[i].z = flip - (*gpu->psDihedralID2)[i].z;
gpu->psDihedralID2->_pSysStream[0][i].w = flip - gpu->psDihedralID2->_pSysStream[0][i].w; (*gpu->psDihedralID2)[i].w = flip - (*gpu->psDihedralID2)[i].w;
} }
for (int i = 0; i < (int) gpu->sim.rb_dihedrals; i++) for (int i = 0; i < (int) gpu->sim.rb_dihedrals; i++)
{ {
gpu->psRbDihedralID2->_pSysStream[0][i].x = flip - gpu->psRbDihedralID2->_pSysStream[0][i].x; (*gpu->psRbDihedralID2)[i].x = flip - (*gpu->psRbDihedralID2)[i].x;
gpu->psRbDihedralID2->_pSysStream[0][i].y = flip - gpu->psRbDihedralID2->_pSysStream[0][i].y; (*gpu->psRbDihedralID2)[i].y = flip - (*gpu->psRbDihedralID2)[i].y;
gpu->psRbDihedralID2->_pSysStream[0][i].z = flip - gpu->psRbDihedralID2->_pSysStream[0][i].z; (*gpu->psRbDihedralID2)[i].z = flip - (*gpu->psRbDihedralID2)[i].z;
gpu->psRbDihedralID2->_pSysStream[0][i].w = flip - gpu->psRbDihedralID2->_pSysStream[0][i].w; (*gpu->psRbDihedralID2)[i].w = flip - (*gpu->psRbDihedralID2)[i].w;
} }
for (int i = 0; i < (int) gpu->sim.LJ14s; i++) for (int i = 0; i < (int) gpu->sim.LJ14s; i++)
{ {
gpu->psLJ14ID->_pSysStream[0][i].z = flip - gpu->psLJ14ID->_pSysStream[0][i].z; (*gpu->psLJ14ID)[i].z = flip - (*gpu->psLJ14ID)[i].z;
gpu->psLJ14ID->_pSysStream[0][i].w = flip - gpu->psLJ14ID->_pSysStream[0][i].w; (*gpu->psLJ14ID)[i].w = flip - (*gpu->psLJ14ID)[i].w;
} }
gpu->psBondID->Upload(); gpu->psBondID->Upload();
gpu->psBondAngleID1->Upload(); gpu->psBondAngleID1->Upload();
...@@ -1393,23 +1393,23 @@ int gpuBuildThreadBlockWorkList(gpuContext gpu) ...@@ -1393,23 +1393,23 @@ int gpuBuildThreadBlockWorkList(gpuContext gpu)
const unsigned int grid = gpu->grid; const unsigned int grid = gpu->grid;
const unsigned int dim = (atoms + (grid - 1)) / grid; const unsigned int dim = (atoms + (grid - 1)) / grid;
const unsigned int cells = dim * (dim + 1) / 2; const unsigned int cells = dim * (dim + 1) / 2;
CUDAStream<unsigned int>* psWorkUnit = new CUDAStream<unsigned int>(cells, 1u); CUDAStream<unsigned int>* psWorkUnit = new CUDAStream<unsigned int>(cells, 1u, "WorkUnit");
unsigned int* pWorkList = psWorkUnit->_pSysStream[0]; unsigned int* pWorkList = psWorkUnit->_pSysData;
gpu->psWorkUnit = psWorkUnit; gpu->psWorkUnit = psWorkUnit;
gpu->sim.pWorkUnit = psWorkUnit->_pDevStream[0]; gpu->sim.pWorkUnit = psWorkUnit->_pDevStream[0];
CUDAStream<unsigned int>* psInteractingWorkUnit = new CUDAStream<unsigned int>(cells, 1u); CUDAStream<unsigned int>* psInteractingWorkUnit = new CUDAStream<unsigned int>(cells, 1u, "InteractingWorkUnit");
gpu->psInteractingWorkUnit = psInteractingWorkUnit; gpu->psInteractingWorkUnit = psInteractingWorkUnit;
gpu->sim.pInteractingWorkUnit = psInteractingWorkUnit->_pDevStream[0]; gpu->sim.pInteractingWorkUnit = psInteractingWorkUnit->_pDevStream[0];
CUDAStream<unsigned int>* psInteractionFlag = new CUDAStream<unsigned int>(cells, 1u); CUDAStream<unsigned int>* psInteractionFlag = new CUDAStream<unsigned int>(cells, 1u, "InteractionFlag");
gpu->psInteractionFlag = psInteractionFlag; gpu->psInteractionFlag = psInteractionFlag;
gpu->sim.pInteractionFlag = psInteractionFlag->_pDevStream[0]; gpu->sim.pInteractionFlag = psInteractionFlag->_pDevStream[0];
CUDAStream<size_t>* psInteractionCount = new CUDAStream<size_t>(1, 1u); CUDAStream<size_t>* psInteractionCount = new CUDAStream<size_t>(1, 1u, "InteractionCount");
gpu->psInteractionCount = psInteractionCount; gpu->psInteractionCount = psInteractionCount;
gpu->sim.pInteractionCount = psInteractionCount->_pDevStream[0]; gpu->sim.pInteractionCount = psInteractionCount->_pDevStream[0];
CUDAStream<float4>* psGridBoundingBox = new CUDAStream<float4>(dim, 1u); CUDAStream<float4>* psGridBoundingBox = new CUDAStream<float4>(dim, 1u, "GridBoundingBox");
gpu->psGridBoundingBox = psGridBoundingBox; gpu->psGridBoundingBox = psGridBoundingBox;
gpu->sim.pGridBoundingBox = psGridBoundingBox->_pDevStream[0]; gpu->sim.pGridBoundingBox = psGridBoundingBox->_pDevStream[0];
CUDAStream<float4>* psGridCenter = new CUDAStream<float4>(dim, 1u); CUDAStream<float4>* psGridCenter = new CUDAStream<float4>(dim, 1u, "GridCenter");
gpu->psGridCenter = psGridCenter; gpu->psGridCenter = psGridCenter;
gpu->sim.pGridCenter = psGridCenter->_pDevStream[0]; gpu->sim.pGridCenter = psGridCenter->_pDevStream[0];
gpu->sim.nonbond_workBlock = gpu->sim.nonbond_threads_per_block / GRID; gpu->sim.nonbond_workBlock = gpu->sim.nonbond_threads_per_block / GRID;
...@@ -1485,7 +1485,7 @@ void gpuBuildExclusionList(gpuContext gpu) ...@@ -1485,7 +1485,7 @@ void gpuBuildExclusionList(gpuContext gpu)
const unsigned int atoms = gpu->sim.paddedNumberOfAtoms; const unsigned int atoms = gpu->sim.paddedNumberOfAtoms;
const unsigned int grid = gpu->grid; const unsigned int grid = gpu->grid;
const unsigned int dim = atoms/grid; const unsigned int dim = atoms/grid;
unsigned int* pWorkList = gpu->psWorkUnit->_pSysStream[0]; unsigned int* pWorkList = gpu->psWorkUnit->_pSysData;
// Mark which work units have exclusions. // Mark which work units have exclusions.
...@@ -1514,7 +1514,7 @@ void gpuBuildExclusionList(gpuContext gpu) ...@@ -1514,7 +1514,7 @@ void gpuBuildExclusionList(gpuContext gpu)
// Build a list of indexes for the work units with exclusions. // Build a list of indexes for the work units with exclusions.
CUDAStream<unsigned int>* psExclusionIndex = new CUDAStream<unsigned int>(gpu->sim.workUnits, 1u); CUDAStream<unsigned int>* psExclusionIndex = new CUDAStream<unsigned int>(gpu->sim.workUnits, 1u, "ExclusionIndex");
gpu->psExclusionIndex = psExclusionIndex; gpu->psExclusionIndex = psExclusionIndex;
unsigned int* pExclusionIndex = psExclusionIndex->_pSysData; unsigned int* pExclusionIndex = psExclusionIndex->_pSysData;
gpu->sim.pExclusionIndex = psExclusionIndex->_pDevData; gpu->sim.pExclusionIndex = psExclusionIndex->_pDevData;
...@@ -1525,7 +1525,7 @@ void gpuBuildExclusionList(gpuContext gpu) ...@@ -1525,7 +1525,7 @@ void gpuBuildExclusionList(gpuContext gpu)
// Record the exclusion data. // Record the exclusion data.
CUDAStream<unsigned int>* psExclusion = new CUDAStream<unsigned int>(numWithExclusions*grid, 1u); CUDAStream<unsigned int>* psExclusion = new CUDAStream<unsigned int>(numWithExclusions*grid, 1u, "Exclusion");
gpu->psExclusion = psExclusion; gpu->psExclusion = psExclusion;
unsigned int* pExclusion = psExclusion->_pSysData; unsigned int* pExclusion = psExclusion->_pSysData;
gpu->sim.pExclusion = psExclusion->_pDevData; gpu->sim.pExclusion = psExclusion->_pDevData;
...@@ -1619,11 +1619,11 @@ static void findMoleculeGroups(gpuContext gpu) ...@@ -1619,11 +1619,11 @@ static void findMoleculeGroups(gpuContext gpu)
vector<Constraint> constraints; vector<Constraint> constraints;
for (int i = 0; i < gpu->sim.ShakeConstraints; i++) for (int i = 0; i < gpu->sim.ShakeConstraints; i++)
{ {
int atom1 = gpu->psShakeID->_pSysData[i].x; int atom1 = (*gpu->psShakeID)[i].x;
int atom2 = gpu->psShakeID->_pSysData[i].y; int atom2 = (*gpu->psShakeID)[i].y;
int atom3 = gpu->psShakeID->_pSysData[i].z; int atom3 = (*gpu->psShakeID)[i].z;
int atom4 = gpu->psShakeID->_pSysData[i].w; int atom4 = (*gpu->psShakeID)[i].w;
float distance2 = gpu->psShakeParameter->_pSysData[i].z; float distance2 = (*gpu->psShakeParameter)[i].z;
constraints.push_back(Constraint(atom1, atom2, distance2)); constraints.push_back(Constraint(atom1, atom2, distance2));
if (atom3 != -1) if (atom3 != -1)
constraints.push_back(Constraint(atom1, atom3, distance2)); constraints.push_back(Constraint(atom1, atom3, distance2));
...@@ -1632,11 +1632,11 @@ static void findMoleculeGroups(gpuContext gpu) ...@@ -1632,11 +1632,11 @@ static void findMoleculeGroups(gpuContext gpu)
} }
for (int i = 0; i < gpu->sim.settleConstraints; i++) for (int i = 0; i < gpu->sim.settleConstraints; i++)
{ {
int atom1 = gpu->psSettleID->_pSysData[i].x; int atom1 = (*gpu->psSettleID)[i].x;
int atom2 = gpu->psSettleID->_pSysData[i].y; int atom2 = (*gpu->psSettleID)[i].y;
int atom3 = gpu->psSettleID->_pSysData[i].z; int atom3 = (*gpu->psSettleID)[i].z;
float distance12 = gpu->psSettleParameter->_pSysData[i].x; float distance12 = (*gpu->psSettleParameter)[i].x;
float distance23 = gpu->psSettleParameter->_pSysData[i].y; float distance23 = (*gpu->psSettleParameter)[i].y;
constraints.push_back(Constraint(atom1, atom2, distance12*distance12)); constraints.push_back(Constraint(atom1, atom2, distance12*distance12));
constraints.push_back(Constraint(atom1, atom3, distance12*distance12)); constraints.push_back(Constraint(atom1, atom3, distance12*distance12));
constraints.push_back(Constraint(atom2, atom3, distance23*distance23)); constraints.push_back(Constraint(atom2, atom3, distance23*distance23));
...@@ -1648,8 +1648,8 @@ static void findMoleculeGroups(gpuContext gpu) ...@@ -1648,8 +1648,8 @@ static void findMoleculeGroups(gpuContext gpu)
vector<vector<int> > atomBonds(numAtoms); vector<vector<int> > atomBonds(numAtoms);
for (int i = 0; i < gpu->sim.bonds; i++) for (int i = 0; i < gpu->sim.bonds; i++)
{ {
int atom1 = gpu->psBondID->_pSysData[i].x; int atom1 = (*gpu->psBondID)[i].x;
int atom2 = gpu->psBondID->_pSysData[i].y; int atom2 = (*gpu->psBondID)[i].y;
atomBonds[atom1].push_back(atom2); atomBonds[atom1].push_back(atom2);
atomBonds[atom2].push_back(atom1); atomBonds[atom2].push_back(atom1);
} }
...@@ -1679,22 +1679,22 @@ static void findMoleculeGroups(gpuContext gpu) ...@@ -1679,22 +1679,22 @@ static void findMoleculeGroups(gpuContext gpu)
molecules[i].atoms = atomIndices[i]; molecules[i].atoms = atomIndices[i];
for (int i = 0; i < gpu->sim.bonds; i++) for (int i = 0; i < gpu->sim.bonds; i++)
{ {
int atom1 = gpu->psBondID->_pSysData[i].x; int atom1 = (*gpu->psBondID)[i].x;
molecules[atomMolecule[atom1]].bonds.push_back(i); molecules[atomMolecule[atom1]].bonds.push_back(i);
} }
for (int i = 0; i < gpu->sim.bond_angles; i++) for (int i = 0; i < gpu->sim.bond_angles; i++)
{ {
int atom1 = gpu->psBondAngleID1->_pSysData[i].x; int atom1 = (*gpu->psBondAngleID1)[i].x;
molecules[atomMolecule[atom1]].angles.push_back(i); molecules[atomMolecule[atom1]].angles.push_back(i);
} }
for (int i = 0; i < gpu->sim.dihedrals; i++) for (int i = 0; i < gpu->sim.dihedrals; i++)
{ {
int atom1 = gpu->psDihedralID1->_pSysData[i].x; int atom1 = (*gpu->psDihedralID1)[i].x;
molecules[atomMolecule[atom1]].periodicTorsions.push_back(i); molecules[atomMolecule[atom1]].periodicTorsions.push_back(i);
} }
for (int i = 0; i < gpu->sim.rb_dihedrals; i++) for (int i = 0; i < gpu->sim.rb_dihedrals; i++)
{ {
int atom1 = gpu->psRbDihedralID1->_pSysData[i].x; int atom1 = (*gpu->psRbDihedralID1)[i].x;
molecules[atomMolecule[atom1]].rbTorsions.push_back(i); molecules[atomMolecule[atom1]].rbTorsions.push_back(i);
} }
for (int i = 0; i < constraints.size(); i++) for (int i = 0; i < constraints.size(); i++)
...@@ -1937,7 +1937,7 @@ void gpuReorderAtoms(gpuContext gpu) ...@@ -1937,7 +1937,7 @@ void gpuReorderAtoms(gpuContext gpu)
{ {
int oldIndex = mol.instances[molBins[i].second]+atoms[j]; int oldIndex = mol.instances[molBins[i].second]+atoms[j];
int newIndex = mol.instances[i]+atoms[j]; int newIndex = mol.instances[i]+atoms[j];
originalIndex[newIndex] = gpu->psAtomIndex->_pSysStream[0][oldIndex]; originalIndex[newIndex] = (*gpu->psAtomIndex)[oldIndex];
newPosq[newIndex] = posq[oldIndex]; newPosq[newIndex] = posq[oldIndex];
newVelm[newIndex] = velm[oldIndex]; newVelm[newIndex] = velm[oldIndex];
} }
...@@ -1953,6 +1953,6 @@ void gpuReorderAtoms(gpuContext gpu) ...@@ -1953,6 +1953,6 @@ void gpuReorderAtoms(gpuContext gpu)
velm[i] = newVelm[i]; velm[i] = newVelm[i];
gpu->psVelm4->Upload(); gpu->psVelm4->Upload();
for (int i = 0; i < numAtoms; i++) for (int i = 0; i < numAtoms; i++)
gpu->psAtomIndex->_pSysData[i] = originalIndex[i]; (*gpu->psAtomIndex)[i] = originalIndex[i];
gpu->psAtomIndex->Upload(); gpu->psAtomIndex->Upload();
} }
platforms/cuda/tests/TestCudaNonbondedForce.cpp
View file @ 306d99e8
...@@ -428,8 +428,8 @@ void testBlockInteractions(bool periodic) { ...@@ -428,8 +428,8 @@ void testBlockInteractions(bool periodic) {
data.gpu->psGridBoundingBox->Download(); data.gpu->psGridBoundingBox->Download();
data.gpu->psGridCenter->Download(); data.gpu->psGridCenter->Download();
for (int i = 0; i < numBlocks; i++) { for (int i = 0; i < numBlocks; i++) {
float4 gridSize = data.gpu->psGridBoundingBox->_pSysData[i]; float4 gridSize = (*data.gpu->psGridBoundingBox)[i];
float4 center = data.gpu->psGridCenter->_pSysData[i]; float4 center = (*data.gpu->psGridCenter)[i];
if (periodic) { if (periodic) {
ASSERT(gridSize.x < 0.5*boxSize); ASSERT(gridSize.x < 0.5*boxSize);
ASSERT(gridSize.y < 0.5*boxSize); ASSERT(gridSize.y < 0.5*boxSize);
...@@ -437,7 +437,7 @@ void testBlockInteractions(bool periodic) { ...@@ -437,7 +437,7 @@ void testBlockInteractions(bool periodic) {
} }
float minx = 0.0, maxx = 0.0, miny = 0.0, maxy = 0.0, minz = 0.0, maxz = 0.0, radius = 0.0; float minx = 0.0, maxx = 0.0, miny = 0.0, maxy = 0.0, minz = 0.0, maxz = 0.0, radius = 0.0;
for (int j = 0; j < blockSize; j++) { for (int j = 0; j < blockSize; j++) {
float4 pos = data.gpu->psPosq4->_pSysData[i*blockSize+j]; float4 pos = (*data.gpu->psPosq4)[i*blockSize+j];
float dx = pos.x-center.x; float dx = pos.x-center.x;
float dy = pos.y-center.y; float dy = pos.y-center.y;
float dz = pos.z-center.z; float dz = pos.z-center.z;
...@@ -467,7 +467,7 @@ void testBlockInteractions(bool periodic) { ...@@ -467,7 +467,7 @@ void testBlockInteractions(bool periodic) {
// Verify that interactions were identified correctly. // Verify that interactions were identified correctly.
data.gpu->psInteractionCount->Download(); data.gpu->psInteractionCount->Download();
int numWithInteractions = data.gpu->psInteractionCount->_pSysData[0]; int numWithInteractions = (*data.gpu->psInteractionCount)[0];
vector<bool> hasInteractions(data.gpu->sim.workUnits, false); vector<bool> hasInteractions(data.gpu->sim.workUnits, false);
data.gpu->psInteractingWorkUnit->Download(); data.gpu->psInteractingWorkUnit->Download();
data.gpu->psInteractionFlag->Download(); data.gpu->psInteractionFlag->Download();
...@@ -475,7 +475,7 @@ void testBlockInteractions(bool periodic) { ...@@ -475,7 +475,7 @@ void testBlockInteractions(bool periodic) {
const unsigned int grid = data.gpu->grid; const unsigned int grid = data.gpu->grid;
const unsigned int dim = (atoms+(grid-1))/grid; const unsigned int dim = (atoms+(grid-1))/grid;
for (int i = 0; i < numWithInteractions; i++) { for (int i = 0; i < numWithInteractions; i++) {
unsigned int workUnit = data.gpu->psInteractingWorkUnit->_pSysData[i]; unsigned int workUnit = (*data.gpu->psInteractingWorkUnit)[i];
unsigned int x = (workUnit >> 17); unsigned int x = (workUnit >> 17);
unsigned int y = ((workUnit >> 2) & 0x7fff); unsigned int y = ((workUnit >> 2) & 0x7fff);
int tile = (x > y ? x+y*dim-y*(y+1)/2 : y+x*dim-x*(x+1)/2); int tile = (x > y ? x+y*dim-y*(y+1)/2 : y+x*dim-x*(x+1)/2);
...@@ -483,10 +483,10 @@ void testBlockInteractions(bool periodic) { ...@@ -483,10 +483,10 @@ void testBlockInteractions(bool periodic) {
// Make sure this tile really should have been flagged based on bounding volumes. // Make sure this tile really should have been flagged based on bounding volumes.
float4 gridSize1 = data.gpu->psGridBoundingBox->_pSysData[x]; float4 gridSize1 = (*data.gpu->psGridBoundingBox)[x];
float4 gridSize2 = data.gpu->psGridBoundingBox->_pSysData[y]; float4 gridSize2 = (*data.gpu->psGridBoundingBox)[y];
float4 center1 = data.gpu->psGridCenter->_pSysData[x]; float4 center1 = (*data.gpu->psGridCenter)[x];
float4 center2 = data.gpu->psGridCenter->_pSysData[y]; float4 center2 = (*data.gpu->psGridCenter)[y];
float dx = center1.x-center2.x; float dx = center1.x-center2.x;
float dy = center1.y-center2.y; float dy = center1.y-center2.y;
float dz = center1.z-center2.z; float dz = center1.z-center2.z;
...@@ -502,12 +502,12 @@ void testBlockInteractions(bool periodic) { ...@@ -502,12 +502,12 @@ void testBlockInteractions(bool periodic) {
// Check the interaction flags. // Check the interaction flags.
unsigned int flags = data.gpu->psInteractionFlag->_pSysData[i]; unsigned int flags = (*data.gpu->psInteractionFlag)[i];
for (int atom2 = 0; atom2 < 32; atom2++) { for (int atom2 = 0; atom2 < 32; atom2++) {
if ((flags & 1) == 0) { if ((flags & 1) == 0) {
float4 pos2 = data.gpu->psPosq4->_pSysData[y*blockSize+atom2]; float4 pos2 = (*data.gpu->psPosq4)[y*blockSize+atom2];
for (int atom1 = 0; atom1 < blockSize; ++atom1) { for (int atom1 = 0; atom1 < blockSize; ++atom1) {
float4 pos1 = data.gpu->psPosq4->_pSysData[x*blockSize+atom1]; float4 pos1 = (*data.gpu->psPosq4)[x*blockSize+atom1];
float dx = pos2.x-pos1.x; float dx = pos2.x-pos1.x;
float dy = pos2.y-pos1.y; float dy = pos2.y-pos1.y;
float dz = pos2.z-pos1.z; float dz = pos2.z-pos1.z;
...@@ -536,13 +536,13 @@ void testBlockInteractions(bool periodic) { ...@@ -536,13 +536,13 @@ void testBlockInteractions(bool periodic) {
data.gpu->psWorkUnit->Download(); data.gpu->psWorkUnit->Download();
for (int i = 0; i < hasInteractions.size(); i++) for (int i = 0; i < hasInteractions.size(); i++)
if (!hasInteractions[i]) { if (!hasInteractions[i]) {
unsigned int workUnit = data.gpu->psWorkUnit->_pSysData[i]; unsigned int workUnit = (*data.gpu->psWorkUnit)[i];
unsigned int x = (workUnit >> 17); unsigned int x = (workUnit >> 17);
unsigned int y = ((workUnit >> 2) & 0x7fff); unsigned int y = ((workUnit >> 2) & 0x7fff);
for (int atom1 = 0; atom1 < blockSize; ++atom1) { for (int atom1 = 0; atom1 < blockSize; ++atom1) {
float4 pos1 = data.gpu->psPosq4->_pSysData[x*blockSize+atom1]; float4 pos1 = (*data.gpu->psPosq4)[x*blockSize+atom1];
for (int atom2 = 0; atom2 < blockSize; ++atom2) { for (int atom2 = 0; atom2 < blockSize; ++atom2) {
float4 pos2 = data.gpu->psPosq4->_pSysData[y*blockSize+atom2]; float4 pos2 = (*data.gpu->psPosq4)[y*blockSize+atom2];
float dx = pos1.x-pos2.x; float dx = pos1.x-pos2.x;
float dy = pos1.y-pos2.y; float dy = pos1.y-pos2.y;
float dz = pos1.z-pos2.z; float dz = pos1.z-pos2.z;
......
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