src/brains/BlockSnapshotManager.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * 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
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * 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.
 */
#include <algorithm>
#include "brains/BlockSnapshotManager.hpp"
#include "utils/physmem.h"
#include "brains/SimInfo.hpp"
#include "io/DumpReader.hpp"

namespace oopse {
BlockSnapshotMananger::BlockSnapshotMananger(SimInfo* info, const std::string& filename, 
    int storageLayout, int blockCapacity) 
    : SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1) {

    nAtoms_ = info->getNGlobalAtoms();
    nRigidBodies_ = info->getNGlobalRigidBodies();

    double avalPhysMem = physmem_available();
    
    int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);

    int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;

    int frameCapacity = int (avalPhysMem / bytesPerFrame);
    
    nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;

    reader_ = new DumpReader(info, filename);
    nframes_ = reader_->getNFrames();

    int nblocks = nframes_ / nSnapshotPerBlock_;
    if (nframes_ % nSnapshotPerBlock_ != 0) {
        ++nblocks;
    }  
    
    for (int i = 0; i < nblocks; ++i) {
        blocks_.push_back(SnapshotBlock(i, (i+1)*nSnapshotPerBlock_);    
    }
    //the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
    blocks_.back.second = nframes_;

    snapshots_.insert(snapshots_.begin(), nframes_, NULL);   
    
}


BlockSnapshotMananger::~BlockSnapshotMananger() {
    currentSnapshot_ = NULL;
    previousSnapshot_ = NULL;
    
    delete reader_;
    std::for_each(activeBlocks_.begin(), activeBlocks_.end(), unloadBlock);
}

int BlockSnapshotManager::getNActiveBlocks() {
    return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::not);
}

bool BlockSnapshotManager::isBlockActive(int block) {
    return std::find(activeBlocks_.begin(), activeBlocks_.end(), block) != activeBlocks_.end() ? true : false;
}

bool BlockSnapshotManager::loadBlock(int block) {
    bool loadSuccess;
    if (isBlockActive(block)) {
        loadSuccess = true;
    } else if (getNActiveBlocks() < blockCapacity_){

        for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
            snapshots_[i] = loadFrame(i);
        }
        
        std::vector<int>::iterator j;
        j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
        assert(j != activeBlocks_.end());
        *j = block;    
        loadSuccess = true;
    }else {
        loadSuccess = false;
    }

    return loadSuccess;
}

bool BlockSnapshotManager::unloadBlock(int block) {
    bool unloadSuccess;
    if (!isBlockActive(block)){
        unloadSuccess = false;
    } else {
        for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
            delete snapshots_[i];
            snapshots_[i] = NULL;
        }
        std::vector<int>::iterator j;
        j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
        assert(j != activeBlocks_.end());
        *j = -1;
    }
}

std::vector<int> BlockSnapshotManager::getActiveBlocks() {
    std::vector<int> result;
    std::copy_if(activeBlocks_.begin(), activeBlocks_.end());
}

Snapshot* BlockSnapshotManager::loadFrame(int frame){
    Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
    snapshot->setID(frame);
    setCurrentSnapshot(snapshot);   /** @todo fixed me */
    reader_->readFrame(frame);
    return snapshot;
}

int BlockSnapshotManager::getNFrames() {
    return reader_->getNFrames();
}

}
Revision:	2007
Committed:	Sun Feb 13 15:56:10 2005 UTC (19 years, 4 months ago) by tim
File size:	5570 byte(s)
Log Message:	dynamicProps in progress
#	User	Rev	Content
1	tim	2002	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41			#include <algorithm>
42			#include "brains/BlockSnapshotManager.hpp"
43	tim	2006	#include "utils/physmem.h"
44	tim	2002	#include "brains/SimInfo.hpp"
45			#include "io/DumpReader.hpp"
46
47			namespace oopse {
48	tim	2007	BlockSnapshotMananger::BlockSnapshotMananger(SimInfo* info, const std::string& filename,
49	tim	2002	int storageLayout, int blockCapacity)
50	tim	2007	: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1) {
51	tim	2002
52			nAtoms_ = info->getNGlobalAtoms();
53			nRigidBodies_ = info->getNGlobalRigidBodies();
54
55			double avalPhysMem = physmem_available();
56
57			int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
58
59	tim	2007	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
60	tim	2002
61			int frameCapacity = int (avalPhysMem / bytesPerFrame);
62
63			nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
64
65			reader_ = new DumpReader(info, filename);
66	tim	2007	nframes_ = reader_->getNFrames();
67	tim	2002
68	tim	2007	int nblocks = nframes_ / nSnapshotPerBlock_;
69			if (nframes_ % nSnapshotPerBlock_ != 0) {
70	tim	2002	++nblocks;
71			}
72
73			for (int i = 0; i < nblocks; ++i) {
74			blocks_.push_back(SnapshotBlock(i, (i+1)*nSnapshotPerBlock_);
75			}
76			//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
77	tim	2007	blocks_.back.second = nframes_;
78	tim	2002
79	tim	2007	snapshots_.insert(snapshots_.begin(), nframes_, NULL);
80	tim	2002
81			}
82
83
84			BlockSnapshotMananger::~BlockSnapshotMananger() {
85			currentSnapshot_ = NULL;
86			previousSnapshot_ = NULL;
87
88			delete reader_;
89			std::for_each(activeBlocks_.begin(), activeBlocks_.end(), unloadBlock);
90			}
91
92			int BlockSnapshotManager::getNActiveBlocks() {
93			return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::not);
94			}
95
96			bool BlockSnapshotManager::isBlockActive(int block) {
97			return std::find(activeBlocks_.begin(), activeBlocks_.end(), block) != activeBlocks_.end() ? true : false;
98			}
99
100			bool BlockSnapshotManager::loadBlock(int block) {
101			bool loadSuccess;
102			if (isBlockActive(block)) {
103			loadSuccess = true;
104			} else if (getNActiveBlocks() < blockCapacity_){
105
106			for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
107			snapshots_[i] = loadFrame(i);
108			}
109
110			std::vector<int>::iterator j;
111			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
112			assert(j != activeBlocks_.end());
113			*j = block;
114			loadSuccess = true;
115			}else {
116			loadSuccess = false;
117			}
118
119			return loadSuccess;
120			}
121
122			bool BlockSnapshotManager::unloadBlock(int block) {
123			bool unloadSuccess;
124			if (!isBlockActive(block)){
125			unloadSuccess = false;
126			} else {
127			for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
128			delete snapshots_[i];
129			snapshots_[i] = NULL;
130			}
131			std::vector<int>::iterator j;
132			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
133			assert(j != activeBlocks_.end());
134			*j = -1;
135			}
136			}
137
138			std::vector<int> BlockSnapshotManager::getActiveBlocks() {
139			std::vector<int> result;
140			std::copy_if(activeBlocks_.begin(), activeBlocks_.end());
141			}
142
143			Snapshot* BlockSnapshotManager::loadFrame(int frame){
144			Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
145			snapshot->setID(frame);
146			setCurrentSnapshot(snapshot); /** @todo fixed me */
147			reader_->readFrame(frame);
148			return snapshot;
149			}
150
151	tim	2006	int BlockSnapshotManager::getNFrames() {
152			return reader_->getNFrames();
153	tim	2002	}
154	tim	2006
155			}