--- trunk/src/brains/BlockSnapshotManager.cpp 2005/04/15 22:04:00 507 +++ branches/development/src/brains/BlockSnapshotManager.cpp 2013/01/09 19:27:52 1825 @@ -6,19 +6,10 @@ * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,40 +28,58 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include #include "brains/BlockSnapshotManager.hpp" -#include "utils/residentMem.h" -#include "utils/physmem.h" +//#include "utils/residentMem.h" +//#include "utils/physmem.h" #include "utils/Algorithm.hpp" #include "brains/SimInfo.hpp" #include "io/DumpReader.hpp" -namespace oopse { - BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename, - int storageLayout, int blockCapacity) - : SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), - activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) { +namespace OpenMD { + BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, + const std::string& filename, + int storageLayout, + long long int memSize, + int blockCapacity) + : SnapshotManager(storageLayout), info_(info), memSize_(memSize), + blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1), + activeRefCount_(blockCapacity_, 0) { nAtoms_ = info->getNGlobalAtoms(); nRigidBodies_ = info->getNGlobalRigidBodies(); + nCutoffGroups_ = info->getNCutoffGroups(); - double physMem = physmem_total(); - double rssMem = residentMem(); - double avaliablePhysMem = physMem - rssMem; + // eliminate suspect calls to figure out free memory: + // RealType physMem = physmem_total(); + // RealType rssMem = residentMem(); + // RealType avaliablePhysMem = physMem - rssMem; int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout); - int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble; - int frameCapacity = int (avaliablePhysMem / bytesPerFrame); - - nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ; + // total number of frames that can fit in memory + //RealType frameCapacity = avaliablePhysMem / bytesPerFrame; + RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame; + + // number of frames in each block given the need to hold multiple blocks + // in memory at the same time: + nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_; reader_ = new DumpReader(info, filename); nframes_ = reader_->getNFrames(); - int nblocks = nframes_ / nSnapshotPerBlock_; - if (nframes_ % nSnapshotPerBlock_ != 0) { + if (nframes_ % int(nSnapshotPerBlock_) != 0) { ++nblocks; } @@ -82,8 +91,20 @@ namespace oopse { snapshots_.insert(snapshots_.begin(), nframes_, static_cast(NULL)); - std::cout << "physmem = " << int(physMem) << "\trssMem = "<< int(rssMem) << "\t availablePhysMem = " << int(avaliablePhysMem) < 0) { + } else if ( hasZeroRefBlock() ) { //if already reach the block capacity, need to unload a block with 0 reference int zeroRefBlock = getFirstZeroRefBlock(); assert(zeroRefBlock != -1); @@ -193,20 +219,20 @@ namespace oopse { std::vector BlockSnapshotManager::getActiveBlocks() { std::vector result; - oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result), + OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result), std::bind2nd(std::not_equal_to(), -1)); return result; } Snapshot* BlockSnapshotManager::loadFrame(int frame){ - Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout()); + Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_, + getStorageLayout()); snapshot->setID(frame); + snapshot->clearDerivedProperties(); - /** @todo fixed me */ - Snapshot* oldSnapshot = currentSnapshot_; currentSnapshot_ = snapshot; reader_->readFrame(frame); - currentSnapshot_ = oldSnapshot; + return snapshot; } @@ -214,4 +240,8 @@ namespace oopse { return reader_->getNFrames(); } + void BlockSnapshotManager::needCOMprops(bool ncp) { + reader_->setNeedCOMprops(ncp); + } + }