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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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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, 234107 (2008). |
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* [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/Algorithm.hpp" |
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#include "brains/SimInfo.hpp" |
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#include "io/DumpReader.hpp" |
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namespace OpenMD { |
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BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, |
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const std::string& filename, |
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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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|
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// eliminate suspect calls to figure out free memory: |
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// RealType physMem = physmem_total(); |
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// RealType rssMem = residentMem(); |
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// RealType avaliablePhysMem = physMem - rssMem; |
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|
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int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout); |
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int bytesPerCutoffGroup = DataStorage::getBytesPerStuntDouble(DataStorage::dslPosition); |
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|
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int bytesPerFrameData = Snapshot::getFrameDataSize(); |
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int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble |
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+ nCutoffGroups_ * bytesPerCutoffGroup |
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+ bytesPerFrameData; |
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|
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// total number of frames that can fit in memory |
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//RealType frameCapacity = avaliablePhysMem / bytesPerFrame; |
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RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame; |
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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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nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_; |
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if (nSnapshotPerBlock_ <= 0) { |
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std::cerr << "not enough memory to hold two configs!" << std::endl; |
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} |
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reader_ = new DumpReader(info, filename); |
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nframes_ = reader_->getNFrames(); |
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int nblocks = nframes_ / nSnapshotPerBlock_; |
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if (nframes_ % int(nSnapshotPerBlock_) != 0) { |
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++nblocks; |
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} |
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|
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for (int i = 0; i < nblocks; ++i) { |
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blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_)); |
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} |
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//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation |
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blocks_.back().second = nframes_; |
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|
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snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL)); |
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|
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std::cout << "-----------------------------------------------------" |
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<< std::endl; |
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std::cout << "BlockSnapshotManager memory report:" << std::endl; |
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std::cout << "\n"; |
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// std::cout << " Physical Memory available:\t" << (unsigned long)physMem << " bytes" <<std::endl; |
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//std::cout << " Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl; |
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//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl; |
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std::cout << "Memory requested for OpenMD:\t" |
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<< (unsigned long)memSize_ << " bytes" << std::endl; |
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std::cout << " Bytes per FrameData:\t" |
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<< (unsigned long)bytesPerFrameData << std::endl; |
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std::cout << " Bytes per StuntDouble:\t" |
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<< (unsigned long)bytesPerStuntDouble << std::endl; |
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std::cout << " Bytes per Cutoff Group:\t" |
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<< (unsigned long)bytesPerCutoffGroup << std::endl; |
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std::cout << " Bytes per Frame:\t" |
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<< (unsigned long)bytesPerFrame << std::endl; |
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std::cout << " Frame Capacity:\t" |
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<< (unsigned long)frameCapacity << std::endl; |
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std::cout << " Frames in trajectory:\t" |
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<< (unsigned long)nframes_ << std::endl; |
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std::cout << " Snapshots per Block:\t" |
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<< (unsigned long)nSnapshotPerBlock_ << std::endl; |
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std::cout << " Total number of Blocks:\t" |
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<< (unsigned long)nblocks << std::endl; |
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std::cout << "-----------------------------------------------------" |
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<< std::endl; |
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|
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} |
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BlockSnapshotManager::~BlockSnapshotManager() { |
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currentSnapshot_ = NULL; |
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previousSnapshot_ = NULL; |
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delete reader_; |
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std::vector<int>::iterator i; |
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for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) { |
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if (*i != -1) { |
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unloadBlock(*i); |
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} |
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} |
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} |
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Snapshot* BlockSnapshotManager::getSnapshot(int id) { |
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currentSnapshot_ = snapshots_[id]; |
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return snapshots_[id]; |
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} |
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int BlockSnapshotManager::getNActiveBlocks() { |
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#ifdef __RWSTD |
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int count = 0; |
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std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count); |
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return count; |
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#else |
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return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1)); |
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#endif |
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} |
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bool BlockSnapshotManager::loadBlock(int block) { |
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std::vector<int>::iterator i = findActiveBlock(block); |
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bool loadSuccess; |
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if (i != activeBlocks_.end()) { |
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//if block is already in memory, just increast the reference count |
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++activeRefCount_[i - activeBlocks_.begin()]; |
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loadSuccess = true; |
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} else if (getNActiveBlocks() < blockCapacity_){ |
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//if number of active blocks is less than the block capacity, just load it |
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internalLoad(block); |
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loadSuccess = true; |
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} else if ( hasZeroRefBlock() ) { |
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//if already reach the block capacity, need to unload a block with 0 reference |
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int zeroRefBlock = getFirstZeroRefBlock(); |
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assert(zeroRefBlock != -1); |
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internalUnload(zeroRefBlock); |
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internalLoad(block); |
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} else { |
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//reach the capacity and all blocks in memory are not zero reference |
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loadSuccess = false; |
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} |
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return loadSuccess; |
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} |
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bool BlockSnapshotManager::unloadBlock(int block) { |
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bool unloadSuccess; |
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std::vector<int>::iterator i = findActiveBlock(block); |
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if (i != activeBlocks_.end()){ |
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--activeRefCount_[i - activeBlocks_.begin()]; |
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if (activeRefCount_[i - activeBlocks_.begin()] < 0) { |
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//in case, unloadBlock called multiple times |
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activeRefCount_[i - activeBlocks_.begin()] = 0; |
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} |
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if (activeRefCount_[i-activeBlocks_.begin()] == 0) { |
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internalUnload(block); |
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} |
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unloadSuccess = true; |
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} else { |
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unloadSuccess = false; |
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} |
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return unloadSuccess; |
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} |
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|
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void BlockSnapshotManager::internalLoad(int block) { |
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for (int i = blocks_[block].first; i < blocks_[block].second; ++i) { |
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snapshots_[i] = loadFrame(i); |
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} |
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std::vector<int>::iterator j; |
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j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1); |
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assert(j != activeBlocks_.end()); |
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*j = block; |
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++activeRefCount_[j - activeBlocks_.begin()]; |
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} |
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void BlockSnapshotManager::internalUnload(int block) { |
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std::cerr << "called internal unload for block "<< block << "\n"; |
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for (int i = blocks_[block].first; i < blocks_[block].second; ++i) { |
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delete snapshots_[i]; |
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snapshots_[i] = NULL; |
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} |
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std::vector<int>::iterator j; |
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j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block); |
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assert(j != activeBlocks_.end()); |
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*j = -1; |
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} |
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bool BlockSnapshotManager::hasZeroRefBlock(){ |
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return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false; |
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} |
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int BlockSnapshotManager::getFirstZeroRefBlock(){ |
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std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0); |
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return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1; |
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} |
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std::vector<int> BlockSnapshotManager::getActiveBlocks() { |
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std::vector<int> result; |
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OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result), |
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std::bind2nd(std::not_equal_to<int>(), -1)); |
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return result; |
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} |
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|
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Snapshot* BlockSnapshotManager::loadFrame(int frame){ |
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Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_, |
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getStorageLayout()); |
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snapshot->setID(frame); |
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snapshot->clearDerivedProperties(); |
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currentSnapshot_ = snapshot; |
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reader_->readFrame(frame); |
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return snapshot; |
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} |
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|
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int BlockSnapshotManager::getNFrames() { |
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return reader_->getNFrames(); |
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} |
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void BlockSnapshotManager::needCOMprops(bool ncp) { |
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reader_->setNeedCOMprops(ncp); |
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} |
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} |