| 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, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
#include <algorithm> |
| 42 |
|
#include "brains/BlockSnapshotManager.hpp" |
| 43 |
< |
#include "utils/residentMem.h" |
| 44 |
< |
#include "utils/physmem.h" |
| 43 |
> |
// #include "utils/residentMem.h" |
| 44 |
> |
// #include "utils/physmem.h" |
| 45 |
|
#include "utils/Algorithm.hpp" |
| 46 |
|
#include "brains/SimInfo.hpp" |
| 47 |
|
#include "io/DumpReader.hpp" |
| 48 |
|
|
| 49 |
< |
namespace oopse { |
| 50 |
< |
BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename, |
| 51 |
< |
int storageLayout, int blockCapacity) |
| 52 |
< |
: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), |
| 53 |
< |
activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) { |
| 49 |
> |
namespace OpenMD { |
| 50 |
> |
BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, |
| 51 |
> |
const std::string& filename, |
| 52 |
> |
int storageLayout, |
| 53 |
> |
long long int memSize, |
| 54 |
> |
int blockCapacity) |
| 55 |
> |
: SnapshotManager(storageLayout), info_(info), memSize_(memSize), |
| 56 |
> |
blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1), |
| 57 |
> |
activeRefCount_(blockCapacity_, 0) { |
| 58 |
|
|
| 59 |
< |
nAtoms_ = info->getNGlobalAtoms(); |
| 60 |
< |
nRigidBodies_ = info->getNGlobalRigidBodies(); |
| 59 |
> |
nAtoms_ = info->getNGlobalAtoms(); |
| 60 |
> |
nRigidBodies_ = info->getNGlobalRigidBodies(); |
| 61 |
|
|
| 62 |
< |
double physMem = physmem_total(); |
| 63 |
< |
double rssMem = residentMem(); |
| 64 |
< |
double avaliablePhysMem = physMem - rssMem; |
| 65 |
< |
|
| 62 |
< |
int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout); |
| 62 |
> |
// eliminate suspect calls to figure out free memory: |
| 63 |
> |
// RealType physMem = physmem_total(); |
| 64 |
> |
// RealType rssMem = residentMem(); |
| 65 |
> |
// RealType avaliablePhysMem = physMem - rssMem; |
| 66 |
|
|
| 67 |
< |
int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble; |
| 67 |
> |
int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout); |
| 68 |
|
|
| 69 |
< |
int frameCapacity = int (avaliablePhysMem / bytesPerFrame); |
| 67 |
< |
|
| 68 |
< |
nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ; |
| 69 |
< |
reader_ = new DumpReader(info, filename); |
| 70 |
< |
nframes_ = reader_->getNFrames(); |
| 69 |
> |
int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble; |
| 70 |
|
|
| 71 |
< |
int nblocks = nframes_ / nSnapshotPerBlock_; |
| 72 |
< |
if (nframes_ % nSnapshotPerBlock_ != 0) { |
| 71 |
> |
// total number of frames that can fit in memory |
| 72 |
> |
|
| 73 |
> |
//RealType frameCapacity = avaliablePhysMem / bytesPerFrame; |
| 74 |
> |
RealType frameCapacity = memSize_ / bytesPerFrame; |
| 75 |
> |
|
| 76 |
> |
// number of frames in each block given the need to hold multiple blocks |
| 77 |
> |
// in memory at the same time: |
| 78 |
> |
nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_; |
| 79 |
> |
reader_ = new DumpReader(info, filename); |
| 80 |
> |
nframes_ = reader_->getNFrames(); |
| 81 |
> |
int nblocks = nframes_ / nSnapshotPerBlock_; |
| 82 |
> |
if (nframes_ % int(nSnapshotPerBlock_) != 0) { |
| 83 |
|
++nblocks; |
| 84 |
< |
} |
| 84 |
> |
} |
| 85 |
|
|
| 86 |
< |
for (int i = 0; i < nblocks; ++i) { |
| 86 |
> |
for (int i = 0; i < nblocks; ++i) { |
| 87 |
|
blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_)); |
| 88 |
< |
} |
| 89 |
< |
//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation |
| 90 |
< |
blocks_.back().second = nframes_; |
| 88 |
> |
} |
| 89 |
> |
//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation |
| 90 |
> |
blocks_.back().second = nframes_; |
| 91 |
|
|
| 92 |
< |
snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL)); |
| 92 |
> |
snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL)); |
| 93 |
|
|
| 94 |
< |
std::cout << "physmem = " << int(physMem) << "\trssMem = "<< int(rssMem) << "\t availablePhysMem = " << int(avaliablePhysMem) <<std::endl; |
| 95 |
< |
std::cout << "nSnapshotPerBlock = " << nSnapshotPerBlock_ << "\t total block = " << nblocks << std::endl; |
| 94 |
> |
std::cout << "-----------------------------------------------------"<<std::endl; |
| 95 |
> |
std::cout << "BlockSnapshotManager memory report:" << std::endl; |
| 96 |
> |
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; |
| 100 |
> |
std::cout << "Memory requested for OpenMD:\t" << (unsigned long)memSize_ << " bytes" <<std::endl; |
| 101 |
> |
std::cout << " Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl; |
| 102 |
> |
std::cout << " Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl; |
| 103 |
> |
std::cout << " Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl; |
| 104 |
> |
std::cout << " Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl; |
| 105 |
> |
std::cout << " Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl; |
| 106 |
> |
std::cout << " Total number of Blocks:\t" << (unsigned long)nblocks << std::endl; |
| 107 |
> |
std::cout << "-----------------------------------------------------"<<std::endl; |
| 108 |
|
|
| 109 |
< |
} |
| 109 |
> |
} |
| 110 |
|
|
| 111 |
|
|
| 112 |
< |
BlockSnapshotManager::~BlockSnapshotManager() { |
| 112 |
> |
BlockSnapshotManager::~BlockSnapshotManager() { |
| 113 |
|
currentSnapshot_ = NULL; |
| 114 |
|
previousSnapshot_ = NULL; |
| 115 |
|
|
| 117 |
|
|
| 118 |
|
std::vector<int>::iterator i; |
| 119 |
|
for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) { |
| 120 |
< |
if (*i != -1) { |
| 121 |
< |
unloadBlock(*i); |
| 122 |
< |
} |
| 120 |
> |
if (*i != -1) { |
| 121 |
> |
unloadBlock(*i); |
| 122 |
> |
} |
| 123 |
|
} |
| 124 |
< |
} |
| 124 |
> |
} |
| 125 |
|
|
| 126 |
< |
int BlockSnapshotManager::getNActiveBlocks() { |
| 126 |
> |
Snapshot* BlockSnapshotManager::getSnapshot(int id) { |
| 127 |
> |
currentSnapshot_ = snapshots_[id]; |
| 128 |
> |
return snapshots_[id]; |
| 129 |
> |
} |
| 130 |
> |
|
| 131 |
> |
int BlockSnapshotManager::getNActiveBlocks() { |
| 132 |
|
#ifdef __RWSTD |
| 133 |
|
int count = 0; |
| 134 |
|
std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count); |
| 136 |
|
#else |
| 137 |
|
return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1)); |
| 138 |
|
#endif |
| 139 |
< |
} |
| 139 |
> |
} |
| 140 |
|
|
| 141 |
|
|
| 142 |
|
|
| 143 |
< |
bool BlockSnapshotManager::loadBlock(int block) { |
| 143 |
> |
bool BlockSnapshotManager::loadBlock(int block) { |
| 144 |
|
std::vector<int>::iterator i = findActiveBlock(block); |
| 145 |
|
bool loadSuccess; |
| 146 |
|
if (i != activeBlocks_.end()) { |
| 147 |
< |
//if block is already in memory, just increast the reference count |
| 148 |
< |
++activeRefCount_[i - activeBlocks_.begin()]; |
| 149 |
< |
loadSuccess = true; |
| 147 |
> |
//if block is already in memory, just increast the reference count |
| 148 |
> |
++activeRefCount_[i - activeBlocks_.begin()]; |
| 149 |
> |
loadSuccess = true; |
| 150 |
|
} else if (getNActiveBlocks() < blockCapacity_){ |
| 151 |
< |
//if number of active blocks is less than the block capacity, just load it |
| 152 |
< |
internalLoad(block); |
| 153 |
< |
loadSuccess = true; |
| 151 |
> |
//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) { |
| 155 |
< |
//if already reach the block capacity, need to unload a block with 0 reference |
| 156 |
< |
int zeroRefBlock = getFirstZeroRefBlock(); |
| 157 |
< |
assert(zeroRefBlock != -1); |
| 158 |
< |
internalUnload(zeroRefBlock); |
| 159 |
< |
internalLoad(block); |
| 155 |
> |
//if already reach the block capacity, need to unload a block with 0 reference |
| 156 |
> |
int zeroRefBlock = getFirstZeroRefBlock(); |
| 157 |
> |
assert(zeroRefBlock != -1); |
| 158 |
> |
internalUnload(zeroRefBlock); |
| 159 |
> |
internalLoad(block); |
| 160 |
|
} else { |
| 161 |
< |
//reach the capacity and all blocks in memory are not zero reference |
| 162 |
< |
loadSuccess = false; |
| 161 |
> |
//reach the capacity and all blocks in memory are not zero reference |
| 162 |
> |
loadSuccess = false; |
| 163 |
|
} |
| 164 |
|
|
| 165 |
|
return loadSuccess; |
| 166 |
< |
} |
| 166 |
> |
} |
| 167 |
|
|
| 168 |
< |
bool BlockSnapshotManager::unloadBlock(int block) { |
| 168 |
> |
bool BlockSnapshotManager::unloadBlock(int block) { |
| 169 |
|
bool unloadSuccess; |
| 170 |
|
std::vector<int>::iterator i = findActiveBlock(block); |
| 171 |
|
|
| 172 |
|
if (i != activeBlocks_.end()){ |
| 173 |
< |
--activeRefCount_[i - activeBlocks_.begin()]; |
| 174 |
< |
if (activeRefCount_[i - activeBlocks_.begin()] < 0) { |
| 175 |
< |
//in case, unloadBlock called multiple times |
| 176 |
< |
activeRefCount_[i - activeBlocks_.begin()] = 0; |
| 177 |
< |
} |
| 173 |
> |
--activeRefCount_[i - activeBlocks_.begin()]; |
| 174 |
> |
if (activeRefCount_[i - activeBlocks_.begin()] < 0) { |
| 175 |
> |
//in case, unloadBlock called multiple times |
| 176 |
> |
activeRefCount_[i - activeBlocks_.begin()] = 0; |
| 177 |
> |
} |
| 178 |
|
|
| 179 |
< |
unloadSuccess = true; |
| 179 |
> |
unloadSuccess = true; |
| 180 |
|
} else { |
| 181 |
< |
unloadSuccess = false; |
| 181 |
> |
unloadSuccess = false; |
| 182 |
|
} |
| 183 |
|
|
| 184 |
|
return unloadSuccess; |
| 185 |
< |
} |
| 185 |
> |
} |
| 186 |
|
|
| 187 |
< |
void BlockSnapshotManager::internalLoad(int block) { |
| 187 |
> |
void BlockSnapshotManager::internalLoad(int block) { |
| 188 |
|
|
| 189 |
|
for (int i = blocks_[block].first; i < blocks_[block].second; ++i) { |
| 190 |
< |
snapshots_[i] = loadFrame(i); |
| 190 |
> |
snapshots_[i] = loadFrame(i); |
| 191 |
|
} |
| 192 |
|
|
| 193 |
|
std::vector<int>::iterator j; |
| 195 |
|
assert(j != activeBlocks_.end()); |
| 196 |
|
*j = block; |
| 197 |
|
++activeRefCount_[j - activeBlocks_.begin()]; |
| 198 |
< |
} |
| 198 |
> |
} |
| 199 |
|
|
| 200 |
< |
void BlockSnapshotManager::internalUnload(int block) { |
| 200 |
> |
void BlockSnapshotManager::internalUnload(int block) { |
| 201 |
|
for (int i = blocks_[block].first; i < blocks_[block].second; ++i) { |
| 202 |
< |
delete snapshots_[i]; |
| 203 |
< |
snapshots_[i] = NULL; |
| 202 |
> |
delete snapshots_[i]; |
| 203 |
> |
snapshots_[i] = NULL; |
| 204 |
|
} |
| 205 |
|
std::vector<int>::iterator j; |
| 206 |
|
j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block); |
| 207 |
|
assert(j != activeBlocks_.end()); |
| 208 |
|
*j = -1; |
| 209 |
< |
} |
| 209 |
> |
} |
| 210 |
|
|
| 211 |
< |
bool BlockSnapshotManager::hasZeroRefBlock(){ |
| 211 |
> |
bool BlockSnapshotManager::hasZeroRefBlock(){ |
| 212 |
|
return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false; |
| 213 |
< |
} |
| 213 |
> |
} |
| 214 |
|
|
| 215 |
< |
int BlockSnapshotManager::getFirstZeroRefBlock(){ |
| 216 |
< |
std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0); |
| 217 |
< |
return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1; |
| 218 |
< |
} |
| 215 |
> |
int BlockSnapshotManager::getFirstZeroRefBlock(){ |
| 216 |
> |
std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0); |
| 217 |
> |
return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1; |
| 218 |
> |
} |
| 219 |
|
|
| 220 |
< |
std::vector<int> BlockSnapshotManager::getActiveBlocks() { |
| 220 |
> |
std::vector<int> BlockSnapshotManager::getActiveBlocks() { |
| 221 |
|
std::vector<int> result; |
| 222 |
< |
oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result), |
| 223 |
< |
std::bind2nd(std::not_equal_to<int>(), -1)); |
| 222 |
> |
OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result), |
| 223 |
> |
std::bind2nd(std::not_equal_to<int>(), -1)); |
| 224 |
|
return result; |
| 225 |
< |
} |
| 225 |
> |
} |
| 226 |
|
|
| 227 |
< |
Snapshot* BlockSnapshotManager::loadFrame(int frame){ |
| 227 |
> |
Snapshot* BlockSnapshotManager::loadFrame(int frame){ |
| 228 |
|
Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout()); |
| 229 |
|
snapshot->setID(frame); |
| 230 |
|
|
| 232 |
|
Snapshot* oldSnapshot = currentSnapshot_; |
| 233 |
|
currentSnapshot_ = snapshot; |
| 234 |
|
reader_->readFrame(frame); |
| 235 |
< |
currentSnapshot_ = oldSnapshot; |
| 235 |
> |
|
| 236 |
> |
// What was this for? It doesn't make sense! |
| 237 |
> |
//currentSnapshot_ = oldSnapshot; |
| 238 |
> |
|
| 239 |
|
return snapshot; |
| 240 |
< |
} |
| 240 |
> |
} |
| 241 |
|
|
| 242 |
< |
int BlockSnapshotManager::getNFrames() { |
| 242 |
> |
int BlockSnapshotManager::getNFrames() { |
| 243 |
|
return reader_->getNFrames(); |
| 244 |
< |
} |
| 244 |
> |
} |
| 245 |
|
|
| 246 |
+ |
void BlockSnapshotManager::needCOMprops(bool ncp) { |
| 247 |
+ |
reader_->setNeedCOMprops(ncp); |
| 248 |
+ |
} |
| 249 |
+ |
|
| 250 |
|
} |
