| 6 |
|
* redistribute this software in source and binary code form, provided |
| 7 |
|
* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
#include <algorithm> |
| 43 |
|
#include "brains/BlockSnapshotManager.hpp" |
| 44 |
< |
#include "utils/residentMem.h" |
| 45 |
< |
#include "utils/physmem.h" |
| 44 |
> |
//#include "utils/residentMem.h" |
| 45 |
> |
//#include "utils/physmem.h" |
| 46 |
|
#include "utils/Algorithm.hpp" |
| 47 |
|
#include "brains/SimInfo.hpp" |
| 48 |
|
#include "io/DumpReader.hpp" |
| 49 |
|
|
| 50 |
< |
namespace oopse { |
| 51 |
< |
BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename, |
| 52 |
< |
int storageLayout, int blockCapacity) |
| 53 |
< |
: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), |
| 54 |
< |
activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) { |
| 50 |
> |
namespace OpenMD { |
| 51 |
> |
BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, |
| 52 |
> |
const std::string& filename, |
| 53 |
> |
int storageLayout, |
| 54 |
> |
long long int memSize, |
| 55 |
> |
int blockCapacity) |
| 56 |
> |
: SnapshotManager(storageLayout), info_(info), |
| 57 |
> |
blockCapacity_(blockCapacity), memSize_(memSize), |
| 58 |
> |
activeBlocks_(blockCapacity_, -1), |
| 59 |
> |
activeRefCount_(blockCapacity_, 0) { |
| 60 |
|
|
| 61 |
|
nAtoms_ = info->getNGlobalAtoms(); |
| 62 |
|
nRigidBodies_ = info->getNGlobalRigidBodies(); |
| 63 |
+ |
nCutoffGroups_ = info->getNCutoffGroups(); |
| 64 |
|
|
| 65 |
< |
RealType physMem = physmem_total(); |
| 66 |
< |
RealType rssMem = residentMem(); |
| 67 |
< |
RealType avaliablePhysMem = physMem - rssMem; |
| 65 |
> |
// eliminate suspect calls to figure out free memory: |
| 66 |
> |
// RealType physMem = physmem_total(); |
| 67 |
> |
// RealType rssMem = residentMem(); |
| 68 |
> |
// RealType avaliablePhysMem = physMem - rssMem; |
| 69 |
|
|
| 70 |
|
int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout); |
| 71 |
+ |
int bytesPerCutoffGroup = DataStorage::getBytesPerStuntDouble(DataStorage::dslPosition); |
| 72 |
|
|
| 73 |
< |
int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble; |
| 73 |
> |
int bytesPerFrameData = Snapshot::getFrameDataSize(); |
| 74 |
> |
int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble |
| 75 |
> |
+ nCutoffGroups_ * bytesPerCutoffGroup |
| 76 |
> |
+ bytesPerFrameData; |
| 77 |
|
|
| 78 |
< |
int frameCapacity = int (avaliablePhysMem / bytesPerFrame); |
| 79 |
< |
|
| 80 |
< |
nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ; |
| 78 |
> |
// total number of frames that can fit in memory |
| 79 |
> |
//RealType frameCapacity = avaliablePhysMem / bytesPerFrame; |
| 80 |
> |
RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame; |
| 81 |
> |
|
| 82 |
> |
// number of frames in each block given the need to hold multiple blocks |
| 83 |
> |
// in memory at the same time: |
| 84 |
> |
nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_; |
| 85 |
> |
if (nSnapshotPerBlock_ <= 0) { |
| 86 |
> |
std::cerr << "not enough memory to hold two configs!" << std::endl; |
| 87 |
> |
} |
| 88 |
|
reader_ = new DumpReader(info, filename); |
| 89 |
|
nframes_ = reader_->getNFrames(); |
| 71 |
– |
|
| 90 |
|
int nblocks = nframes_ / nSnapshotPerBlock_; |
| 91 |
< |
if (nframes_ % nSnapshotPerBlock_ != 0) { |
| 91 |
> |
if (nframes_ % int(nSnapshotPerBlock_) != 0) { |
| 92 |
|
++nblocks; |
| 93 |
|
} |
| 94 |
|
|
| 100 |
|
|
| 101 |
|
snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL)); |
| 102 |
|
|
| 103 |
< |
std::cout << "physmem = " << int(physMem) << "\trssMem = "<< int(rssMem) << "\t availablePhysMem = " << int(avaliablePhysMem) <<std::endl; |
| 104 |
< |
std::cout << "nSnapshotPerBlock = " << nSnapshotPerBlock_ << "\t total block = " << nblocks << std::endl; |
| 103 |
> |
std::cout << "-----------------------------------------------------" |
| 104 |
> |
<< std::endl; |
| 105 |
> |
std::cout << "BlockSnapshotManager memory report:" << std::endl; |
| 106 |
> |
std::cout << "\n"; |
| 107 |
> |
// std::cout << " Physical Memory available:\t" << (unsigned long)physMem << " bytes" <<std::endl; |
| 108 |
> |
//std::cout << " Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl; |
| 109 |
> |
//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl; |
| 110 |
> |
std::cout << "Memory requested for OpenMD:\t" |
| 111 |
> |
<< (unsigned long)memSize_ << " bytes" << std::endl; |
| 112 |
> |
std::cout << " Bytes per FrameData:\t" |
| 113 |
> |
<< (unsigned long)bytesPerFrameData << std::endl; |
| 114 |
> |
std::cout << " Bytes per StuntDouble:\t" |
| 115 |
> |
<< (unsigned long)bytesPerStuntDouble << std::endl; |
| 116 |
> |
std::cout << " Bytes per Cutoff Group:\t" |
| 117 |
> |
<< (unsigned long)bytesPerCutoffGroup << std::endl; |
| 118 |
> |
std::cout << " Bytes per Frame:\t" |
| 119 |
> |
<< (unsigned long)bytesPerFrame << std::endl; |
| 120 |
> |
std::cout << " Frame Capacity:\t" |
| 121 |
> |
<< (unsigned long)frameCapacity << std::endl; |
| 122 |
> |
std::cout << " Frames in trajectory:\t" |
| 123 |
> |
<< (unsigned long)nframes_ << std::endl; |
| 124 |
> |
std::cout << " Snapshots per Block:\t" |
| 125 |
> |
<< (unsigned long)nSnapshotPerBlock_ << std::endl; |
| 126 |
> |
std::cout << " Total number of Blocks:\t" |
| 127 |
> |
<< (unsigned long)nblocks << std::endl; |
| 128 |
> |
std::cout << "-----------------------------------------------------" |
| 129 |
> |
<< std::endl; |
| 130 |
|
|
| 131 |
|
} |
| 132 |
|
|
| 145 |
|
} |
| 146 |
|
} |
| 147 |
|
|
| 148 |
+ |
Snapshot* BlockSnapshotManager::getSnapshot(int id) { |
| 149 |
+ |
currentSnapshot_ = snapshots_[id]; |
| 150 |
+ |
return snapshots_[id]; |
| 151 |
+ |
} |
| 152 |
+ |
|
| 153 |
|
int BlockSnapshotManager::getNActiveBlocks() { |
| 154 |
|
#ifdef __RWSTD |
| 155 |
|
int count = 0; |
| 164 |
|
|
| 165 |
|
bool BlockSnapshotManager::loadBlock(int block) { |
| 166 |
|
std::vector<int>::iterator i = findActiveBlock(block); |
| 167 |
< |
bool loadSuccess; |
| 167 |
> |
bool loadSuccess(false); |
| 168 |
|
if (i != activeBlocks_.end()) { |
| 169 |
< |
//if block is already in memory, just increast the reference count |
| 169 |
> |
// If the block is already in memory, just increase the |
| 170 |
> |
// reference count: |
| 171 |
|
++activeRefCount_[i - activeBlocks_.begin()]; |
| 172 |
|
loadSuccess = true; |
| 173 |
|
} else if (getNActiveBlocks() < blockCapacity_){ |
| 174 |
< |
//if number of active blocks is less than the block capacity, just load it |
| 174 |
> |
// If the number of active blocks is less than the block |
| 175 |
> |
// capacity, just load the block: |
| 176 |
|
internalLoad(block); |
| 177 |
|
loadSuccess = true; |
| 178 |
< |
} else if (hasZeroRefBlock() > 0) { |
| 179 |
< |
//if already reach the block capacity, need to unload a block with 0 reference |
| 178 |
> |
} else if ( hasZeroRefBlock() ) { |
| 179 |
> |
// If we have already reached the block capacity, we need to |
| 180 |
> |
// unload a block with 0 references: |
| 181 |
|
int zeroRefBlock = getFirstZeroRefBlock(); |
| 182 |
|
assert(zeroRefBlock != -1); |
| 183 |
|
internalUnload(zeroRefBlock); |
| 184 |
|
internalLoad(block); |
| 185 |
|
} else { |
| 186 |
< |
//reach the capacity and all blocks in memory are not zero reference |
| 186 |
> |
// We have reached capacity and all blocks in memory are have |
| 187 |
> |
// non-zero references: |
| 188 |
|
loadSuccess = false; |
| 189 |
< |
} |
| 138 |
< |
|
| 189 |
> |
} |
| 190 |
|
return loadSuccess; |
| 191 |
|
} |
| 192 |
|
|
| 200 |
|
//in case, unloadBlock called multiple times |
| 201 |
|
activeRefCount_[i - activeBlocks_.begin()] = 0; |
| 202 |
|
} |
| 203 |
+ |
|
| 204 |
+ |
if (activeRefCount_[i-activeBlocks_.begin()] == 0) { |
| 205 |
+ |
internalUnload(block); |
| 206 |
+ |
} |
| 207 |
|
|
| 208 |
|
unloadSuccess = true; |
| 209 |
|
} else { |
| 227 |
|
} |
| 228 |
|
|
| 229 |
|
void BlockSnapshotManager::internalUnload(int block) { |
| 230 |
+ |
std::cerr << "called internal unload for block "<< block << "\n"; |
| 231 |
|
for (int i = blocks_[block].first; i < blocks_[block].second; ++i) { |
| 232 |
|
delete snapshots_[i]; |
| 233 |
|
snapshots_[i] = NULL; |
| 249 |
|
|
| 250 |
|
std::vector<int> BlockSnapshotManager::getActiveBlocks() { |
| 251 |
|
std::vector<int> result; |
| 252 |
< |
oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result), |
| 252 |
> |
OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result), |
| 253 |
|
std::bind2nd(std::not_equal_to<int>(), -1)); |
| 254 |
|
return result; |
| 255 |
|
} |
| 256 |
|
|
| 257 |
|
Snapshot* BlockSnapshotManager::loadFrame(int frame){ |
| 258 |
< |
Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout()); |
| 258 |
> |
Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_, |
| 259 |
> |
getStorageLayout()); |
| 260 |
|
snapshot->setID(frame); |
| 261 |
+ |
snapshot->clearDerivedProperties(); |
| 262 |
|
|
| 205 |
– |
/** @todo fixed me */ |
| 206 |
– |
Snapshot* oldSnapshot = currentSnapshot_; |
| 263 |
|
currentSnapshot_ = snapshot; |
| 264 |
|
reader_->readFrame(frame); |
| 265 |
< |
currentSnapshot_ = oldSnapshot; |
| 265 |
> |
|
| 266 |
|
return snapshot; |
| 267 |
|
} |
| 268 |
|
|
| 270 |
|
return reader_->getNFrames(); |
| 271 |
|
} |
| 272 |
|
|
| 273 |
+ |
void BlockSnapshotManager::needCOMprops(bool ncp) { |
| 274 |
+ |
reader_->setNeedCOMprops(ncp); |
| 275 |
+ |
} |
| 276 |
+ |
|
| 277 |
|
} |
