| 36 |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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< |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include <algorithm> |
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#include "brains/BlockSnapshotManager.hpp" |
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< |
#include "utils/residentMem.h" |
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< |
#include "utils/physmem.h" |
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> |
//#include "utils/residentMem.h" |
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> |
//#include "utils/physmem.h" |
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#include "utils/Algorithm.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "io/DumpReader.hpp" |
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|
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namespace OpenMD { |
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< |
BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename, |
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< |
int storageLayout, int blockCapacity) |
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< |
: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), |
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< |
activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) { |
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> |
BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, |
| 52 |
> |
const std::string& filename, |
| 53 |
> |
int storageLayout, |
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> |
long long int memSize, |
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> |
int blockCapacity) |
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> |
: SnapshotManager(storageLayout), info_(info), memSize_(memSize), |
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> |
blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1), |
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> |
activeRefCount_(blockCapacity_, 0) { |
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|
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nAtoms_ = info->getNGlobalAtoms(); |
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nRigidBodies_ = info->getNGlobalRigidBodies(); |
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+ |
nCutoffGroups_ = info->getNCutoffGroups(); |
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|
| 64 |
< |
RealType physMem = physmem_total(); |
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< |
RealType rssMem = residentMem(); |
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< |
RealType avaliablePhysMem = physMem - rssMem; |
| 67 |
< |
|
| 64 |
> |
// eliminate suspect calls to figure out free memory: |
| 65 |
> |
// RealType physMem = physmem_total(); |
| 66 |
> |
// RealType rssMem = residentMem(); |
| 67 |
> |
// RealType avaliablePhysMem = physMem - rssMem; |
| 68 |
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|
| 69 |
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int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout); |
| 64 |
– |
|
| 70 |
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int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble; |
| 71 |
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|
| 72 |
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// total number of frames that can fit in memory |
| 73 |
< |
RealType frameCapacity = avaliablePhysMem / bytesPerFrame; |
| 73 |
> |
//RealType frameCapacity = avaliablePhysMem / bytesPerFrame; |
| 74 |
> |
RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame; |
| 75 |
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|
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// number of frames in each block given the need to hold multiple blocks |
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// in memory at the same time: |
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std::cout << "-----------------------------------------------------"<<std::endl; |
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std::cout << "BlockSnapshotManager memory report:" << std::endl; |
| 96 |
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std::cout << "\n"; |
| 97 |
< |
std::cout << " Physical Memory available:\t" << (unsigned long)physMem << " bytes" <<std::endl; |
| 98 |
< |
std::cout << " Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl; |
| 99 |
< |
std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl; |
| 97 |
> |
// std::cout << " Physical Memory available:\t" << (unsigned long)physMem << " bytes" <<std::endl; |
| 98 |
> |
//std::cout << " Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl; |
| 99 |
> |
//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl; |
| 100 |
> |
std::cout << "Memory requested for OpenMD:\t" << (unsigned long)memSize_ << " bytes" <<std::endl; |
| 101 |
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std::cout << " Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl; |
| 102 |
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std::cout << " Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl; |
| 103 |
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std::cout << " Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl; |
| 151 |
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//if number of active blocks is less than the block capacity, just load it |
| 152 |
|
internalLoad(block); |
| 153 |
|
loadSuccess = true; |
| 154 |
< |
} else if (hasZeroRefBlock() > 0) { |
| 154 |
> |
} else if ( hasZeroRefBlock() ) { |
| 155 |
|
//if already reach the block capacity, need to unload a block with 0 reference |
| 156 |
|
int zeroRefBlock = getFirstZeroRefBlock(); |
| 157 |
|
assert(zeroRefBlock != -1); |
| 225 |
|
} |
| 226 |
|
|
| 227 |
|
Snapshot* BlockSnapshotManager::loadFrame(int frame){ |
| 228 |
< |
Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout()); |
| 228 |
> |
Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_, getStorageLayout()); |
| 229 |
|
snapshot->setID(frame); |
| 230 |
+ |
snapshot->clearDerivedProperties(); |
| 231 |
|
|
| 232 |
|
/** @todo fixed me */ |
| 233 |
|
Snapshot* oldSnapshot = currentSnapshot_; |
