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tsoc
openmm
Commits
a306aa58
Commit
a306aa58
authored
Aug 29, 2014
by
peastman
Browse files
Minor optimization to CUDA version of CustomManyParticleForce
parent
f5acdd7a
Changes
3
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Showing
3 changed files
with
10 additions
and
14 deletions
+10
-14
platforms/cuda/include/CudaKernels.h
platforms/cuda/include/CudaKernels.h
+2
-2
platforms/cuda/src/CudaKernels.cpp
platforms/cuda/src/CudaKernels.cpp
+6
-12
platforms/cuda/src/kernels/customManyParticle.cu
platforms/cuda/src/kernels/customManyParticle.cu
+2
-0
No files found.
platforms/cuda/include/CudaKernels.h
View file @
a306aa58
...
@@ -931,7 +931,7 @@ private:
...
@@ -931,7 +931,7 @@ private:
class
CudaCalcCustomManyParticleForceKernel
:
public
CalcCustomManyParticleForceKernel
{
class
CudaCalcCustomManyParticleForceKernel
:
public
CalcCustomManyParticleForceKernel
{
public:
public:
CudaCalcCustomManyParticleForceKernel
(
std
::
string
name
,
const
Platform
&
platform
,
CudaContext
&
cu
,
const
System
&
system
)
:
CalcCustomManyParticleForceKernel
(
name
,
platform
),
CudaCalcCustomManyParticleForceKernel
(
std
::
string
name
,
const
Platform
&
platform
,
CudaContext
&
cu
,
const
System
&
system
)
:
CalcCustomManyParticleForceKernel
(
name
,
platform
),
hasInitializedKernel
(
false
),
cu
(
cu
),
params
(
NULL
),
globals
(
NULL
),
particleTypes
(
NULL
),
orderIndex
(
NULL
),
particleOrder
(
NULL
),
exclusions
(
NULL
),
hasInitializedKernel
(
false
),
cu
(
cu
),
params
(
NULL
),
particleTypes
(
NULL
),
orderIndex
(
NULL
),
particleOrder
(
NULL
),
exclusions
(
NULL
),
exclusionStartIndex
(
NULL
),
blockCenter
(
NULL
),
blockBoundingBox
(
NULL
),
neighborPairs
(
NULL
),
numNeighborPairs
(
NULL
),
neighborStartIndex
(
NULL
),
exclusionStartIndex
(
NULL
),
blockCenter
(
NULL
),
blockBoundingBox
(
NULL
),
neighborPairs
(
NULL
),
numNeighborPairs
(
NULL
),
neighborStartIndex
(
NULL
),
numNeighborsForAtom
(
NULL
),
neighbors
(
NULL
),
system
(
system
)
{
numNeighborsForAtom
(
NULL
),
neighbors
(
NULL
),
system
(
system
)
{
}
}
...
@@ -966,7 +966,6 @@ private:
...
@@ -966,7 +966,6 @@ private:
NonbondedMethod
nonbondedMethod
;
NonbondedMethod
nonbondedMethod
;
int
maxNeighborPairs
,
forceWorkgroupSize
,
findNeighborsWorkgroupSize
;
int
maxNeighborPairs
,
forceWorkgroupSize
,
findNeighborsWorkgroupSize
;
CudaParameterSet
*
params
;
CudaParameterSet
*
params
;
CudaArray
*
globals
;
CudaArray
*
particleTypes
;
CudaArray
*
particleTypes
;
CudaArray
*
orderIndex
;
CudaArray
*
orderIndex
;
CudaArray
*
particleOrder
;
CudaArray
*
particleOrder
;
...
@@ -985,6 +984,7 @@ private:
...
@@ -985,6 +984,7 @@ private:
std
::
vector
<
void
*>
forceArgs
,
blockBoundsArgs
,
neighborsArgs
,
startIndicesArgs
,
copyPairsArgs
;
std
::
vector
<
void
*>
forceArgs
,
blockBoundsArgs
,
neighborsArgs
,
startIndicesArgs
,
copyPairsArgs
;
const
System
&
system
;
const
System
&
system
;
CUfunction
forceKernel
,
blockBoundsKernel
,
neighborsKernel
,
startIndicesKernel
,
copyPairsKernel
;
CUfunction
forceKernel
,
blockBoundsKernel
,
neighborsKernel
,
startIndicesKernel
,
copyPairsKernel
;
CUdeviceptr
globalsPtr
;
CUevent
event
;
CUevent
event
;
};
};
...
...
platforms/cuda/src/CudaKernels.cpp
View file @
a306aa58
...
@@ -4440,8 +4440,6 @@ CudaCalcCustomManyParticleForceKernel::~CudaCalcCustomManyParticleForceKernel()
...
@@ -4440,8 +4440,6 @@ CudaCalcCustomManyParticleForceKernel::~CudaCalcCustomManyParticleForceKernel()
cu
.
setAsCurrent
();
cu
.
setAsCurrent
();
if
(
params
!=
NULL
)
if
(
params
!=
NULL
)
delete
params
;
delete
params
;
if
(
globals
!=
NULL
)
delete
globals
;
if
(
orderIndex
!=
NULL
)
if
(
orderIndex
!=
NULL
)
delete
orderIndex
;
delete
orderIndex
;
if
(
particleOrder
!=
NULL
)
if
(
particleOrder
!=
NULL
)
...
@@ -4481,8 +4479,6 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
...
@@ -4481,8 +4479,6 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
// Record parameter values.
// Record parameter values.
params
=
new
CudaParameterSet
(
cu
,
force
.
getNumPerParticleParameters
(),
numParticles
,
"customManyParticleParameters"
);
params
=
new
CudaParameterSet
(
cu
,
force
.
getNumPerParticleParameters
(),
numParticles
,
"customManyParticleParameters"
);
if
(
force
.
getNumGlobalParameters
()
>
0
)
globals
=
CudaArray
::
create
<
float
>
(
cu
,
force
.
getNumGlobalParameters
(),
"customManyParticleGlobals"
);
vector
<
vector
<
float
>
>
paramVector
(
numParticles
);
vector
<
vector
<
float
>
>
paramVector
(
numParticles
);
for
(
int
i
=
0
;
i
<
numParticles
;
i
++
)
{
for
(
int
i
=
0
;
i
<
numParticles
;
i
++
)
{
vector
<
double
>
parameters
;
vector
<
double
>
parameters
;
...
@@ -4540,8 +4536,6 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
...
@@ -4540,8 +4536,6 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
}
}
}
}
if
(
force
.
getNumGlobalParameters
()
>
0
)
{
if
(
force
.
getNumGlobalParameters
()
>
0
)
{
globals
=
CudaArray
::
create
<
float
>
(
cu
,
force
.
getNumGlobalParameters
(),
"customManyParticleGlobals"
);
globals
->
upload
(
globalParamValues
);
for
(
int
i
=
0
;
i
<
force
.
getNumGlobalParameters
();
i
++
)
{
for
(
int
i
=
0
;
i
<
force
.
getNumGlobalParameters
();
i
++
)
{
const
string
&
name
=
force
.
getGlobalParameterName
(
i
);
const
string
&
name
=
force
.
getGlobalParameterName
(
i
);
string
value
=
"globals["
+
cu
.
intToString
(
i
)
+
"]"
;
string
value
=
"globals["
+
cu
.
intToString
(
i
)
+
"]"
;
...
@@ -4838,8 +4832,6 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
...
@@ -4838,8 +4832,6 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
// Create replacements for extra arguments.
// Create replacements for extra arguments.
stringstream
extraArgs
;
stringstream
extraArgs
;
if
(
force
.
getNumGlobalParameters
()
>
0
)
extraArgs
<<
", const float* __restrict__ globals"
;
for
(
int
i
=
0
;
i
<
(
int
)
params
->
getBuffers
().
size
();
i
++
)
{
for
(
int
i
=
0
;
i
<
(
int
)
params
->
getBuffers
().
size
();
i
++
)
{
CudaNonbondedUtilities
::
ParameterInfo
&
buffer
=
params
->
getBuffers
()[
i
];
CudaNonbondedUtilities
::
ParameterInfo
&
buffer
=
params
->
getBuffers
()[
i
];
extraArgs
<<
", const "
<<
buffer
.
getType
()
<<
"* __restrict__ global_params"
<<
(
i
+
1
);
extraArgs
<<
", const "
<<
buffer
.
getType
()
<<
"* __restrict__ global_params"
<<
(
i
+
1
);
...
@@ -4873,6 +4865,7 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
...
@@ -4873,6 +4865,7 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
defines
[
"CUTOFF_SQUARED"
]
=
cu
.
doubleToString
(
force
.
getCutoffDistance
()
*
force
.
getCutoffDistance
());
defines
[
"CUTOFF_SQUARED"
]
=
cu
.
doubleToString
(
force
.
getCutoffDistance
()
*
force
.
getCutoffDistance
());
defines
[
"TILE_SIZE"
]
=
cu
.
intToString
(
CudaContext
::
TileSize
);
defines
[
"TILE_SIZE"
]
=
cu
.
intToString
(
CudaContext
::
TileSize
);
defines
[
"NUM_BLOCKS"
]
=
cu
.
intToString
(
cu
.
getNumAtomBlocks
());
defines
[
"NUM_BLOCKS"
]
=
cu
.
intToString
(
cu
.
getNumAtomBlocks
());
defines
[
"NUM_GLOBALS"
]
=
cu
.
intToString
(
max
(
1
,
force
.
getNumGlobalParameters
()));
defines
[
"FIND_NEIGHBORS_WORKGROUP_SIZE"
]
=
cu
.
intToString
(
findNeighborsWorkgroupSize
);
defines
[
"FIND_NEIGHBORS_WORKGROUP_SIZE"
]
=
cu
.
intToString
(
findNeighborsWorkgroupSize
);
CUmodule
module
=
cu
.
createModule
(
cu
.
replaceStrings
(
CudaKernelSources
::
vectorOps
+
CudaKernelSources
::
customManyParticle
,
replacements
),
defines
);
CUmodule
module
=
cu
.
createModule
(
cu
.
replaceStrings
(
CudaKernelSources
::
vectorOps
+
CudaKernelSources
::
customManyParticle
,
replacements
),
defines
);
forceKernel
=
cu
.
getKernel
(
module
,
"computeInteraction"
);
forceKernel
=
cu
.
getKernel
(
module
,
"computeInteraction"
);
...
@@ -4882,6 +4875,9 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
...
@@ -4882,6 +4875,9 @@ void CudaCalcCustomManyParticleForceKernel::initialize(const System& system, con
copyPairsKernel
=
cu
.
getKernel
(
module
,
"copyPairsToNeighborList"
);
copyPairsKernel
=
cu
.
getKernel
(
module
,
"copyPairsToNeighborList"
);
cuFuncSetCacheConfig
(
forceKernel
,
CU_FUNC_CACHE_PREFER_L1
);
cuFuncSetCacheConfig
(
forceKernel
,
CU_FUNC_CACHE_PREFER_L1
);
cuFuncSetCacheConfig
(
neighborsKernel
,
CU_FUNC_CACHE_PREFER_L1
);
cuFuncSetCacheConfig
(
neighborsKernel
,
CU_FUNC_CACHE_PREFER_L1
);
size_t
bytes
;
CHECK_RESULT
(
cuModuleGetGlobal
(
&
globalsPtr
,
&
bytes
,
module
,
"globals"
),
"Error getting address for constant memory"
)
cuMemcpyHtoD
(
globalsPtr
,
&
globalParamValues
[
0
],
globalParamValues
.
size
()
*
sizeof
(
float
));
}
}
double
CudaCalcCustomManyParticleForceKernel
::
execute
(
ContextImpl
&
context
,
bool
includeForces
,
bool
includeEnergy
)
{
double
CudaCalcCustomManyParticleForceKernel
::
execute
(
ContextImpl
&
context
,
bool
includeForces
,
bool
includeEnergy
)
{
...
@@ -4908,8 +4904,6 @@ double CudaCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
...
@@ -4908,8 +4904,6 @@ double CudaCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
forceArgs
.
push_back
(
&
exclusions
->
getDevicePointer
());
forceArgs
.
push_back
(
&
exclusions
->
getDevicePointer
());
forceArgs
.
push_back
(
&
exclusionStartIndex
->
getDevicePointer
());
forceArgs
.
push_back
(
&
exclusionStartIndex
->
getDevicePointer
());
}
}
if
(
globals
!=
NULL
)
forceArgs
.
push_back
(
&
globals
->
getDevicePointer
());
for
(
int
i
=
0
;
i
<
(
int
)
params
->
getBuffers
().
size
();
i
++
)
{
for
(
int
i
=
0
;
i
<
(
int
)
params
->
getBuffers
().
size
();
i
++
)
{
CudaNonbondedUtilities
::
ParameterInfo
&
buffer
=
params
->
getBuffers
()[
i
];
CudaNonbondedUtilities
::
ParameterInfo
&
buffer
=
params
->
getBuffers
()[
i
];
forceArgs
.
push_back
(
&
buffer
.
getMemory
());
forceArgs
.
push_back
(
&
buffer
.
getMemory
());
...
@@ -4958,7 +4952,7 @@ double CudaCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
...
@@ -4958,7 +4952,7 @@ double CudaCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
copyPairsArgs
.
push_back
(
&
neighborStartIndex
->
getDevicePointer
());
copyPairsArgs
.
push_back
(
&
neighborStartIndex
->
getDevicePointer
());
}
}
}
}
if
(
global
s
!=
NULL
)
{
if
(
global
ParamValues
.
size
()
>
0
)
{
bool
changed
=
false
;
bool
changed
=
false
;
for
(
int
i
=
0
;
i
<
(
int
)
globalParamNames
.
size
();
i
++
)
{
for
(
int
i
=
0
;
i
<
(
int
)
globalParamNames
.
size
();
i
++
)
{
float
value
=
(
float
)
context
.
getParameter
(
globalParamNames
[
i
]);
float
value
=
(
float
)
context
.
getParameter
(
globalParamNames
[
i
]);
...
@@ -4967,7 +4961,7 @@ double CudaCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
...
@@ -4967,7 +4961,7 @@ double CudaCalcCustomManyParticleForceKernel::execute(ContextImpl& context, bool
globalParamValues
[
i
]
=
value
;
globalParamValues
[
i
]
=
value
;
}
}
if
(
changed
)
if
(
changed
)
globals
->
upload
(
globalParamValues
);
cuMemcpyHtoD
(
globalsPtr
,
&
globalParamValues
[
0
],
globalParamValues
.
size
()
*
sizeof
(
float
)
);
}
}
while
(
true
)
{
while
(
true
)
{
int
*
numPairs
=
(
int
*
)
cu
.
getPinnedBuffer
();
int
*
numPairs
=
(
int
*
)
cu
.
getPinnedBuffer
();
...
...
platforms/cuda/src/kernels/customManyParticle.cu
View file @
a306aa58
...
@@ -74,6 +74,8 @@ inline __device__ bool isInteractionExcluded(int atom1, int atom2, int* __restri
...
@@ -74,6 +74,8 @@ inline __device__ bool isInteractionExcluded(int atom1, int atom2, int* __restri
return
false
;
return
false
;
}
}
__constant__
float
globals
[
NUM_GLOBALS
];
/**
/**
* Compute the interaction.
* Compute the interaction.
*/
*/
...
...
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