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 "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) {

    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*nSnapshotPerBlock_, (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_, static_cast<Snapshot*>(NULL));   
    
}


BlockSnapshotManager::~BlockSnapshotManager() {
    currentSnapshot_ = NULL;
    previousSnapshot_ = NULL;
    
    delete reader_;

    std::vector<int>::iterator i;
    for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
        if (*i != -1) {
            unloadBlock(*i);
        }
    }
}

int BlockSnapshotManager::getNActiveBlocks() {
#ifdef __RWSTD   
    int count = 0;
    std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
    return count;
#else
    return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
#endif
}

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;
        unloadSuccess = true;
    }

    return unloadSuccess;
}

std::vector<int> BlockSnapshotManager::getActiveBlocks() {
    std::vector<int> result;
    oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result), 
        std::bind2nd(std::not_equal_to<int>(), -1));
    return result;    
}

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

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

}
Revision:	2031
Committed:	Tue Feb 15 17:11:35 2005 UTC (19 years, 4 months ago) by tim
File size:	6210 byte(s)
Log Message:	(1) adding #ifdef __RWSTD to make sun compiler happy (2) fix pair density calculation problem when two selections intersect with each other
#	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	2008	#include "utils/Algorithm.hpp"
45	tim	2002	#include "brains/SimInfo.hpp"
46			#include "io/DumpReader.hpp"
47
48			namespace oopse {
49	tim	2008	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
50	tim	2002	int storageLayout, int blockCapacity)
51	tim	2007	: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1) {
52	tim	2002
53			nAtoms_ = info->getNGlobalAtoms();
54			nRigidBodies_ = info->getNGlobalRigidBodies();
55
56			double avalPhysMem = physmem_available();
57
58			int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
59
60	tim	2007	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
61	tim	2002
62			int frameCapacity = int (avalPhysMem / bytesPerFrame);
63
64			nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
65
66			reader_ = new DumpReader(info, filename);
67	tim	2007	nframes_ = reader_->getNFrames();
68	tim	2002
69	tim	2007	int nblocks = nframes_ / nSnapshotPerBlock_;
70			if (nframes_ % nSnapshotPerBlock_ != 0) {
71	tim	2002	++nblocks;
72			}
73
74			for (int i = 0; i < nblocks; ++i) {
75	tim	2021	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
76	tim	2002	}
77			//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
78	tim	2008	blocks_.back().second = nframes_;
79	tim	2002
80	tim	2031	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
81	tim	2002
82			}
83
84
85	tim	2008	BlockSnapshotManager::~BlockSnapshotManager() {
86	tim	2002	currentSnapshot_ = NULL;
87			previousSnapshot_ = NULL;
88
89			delete reader_;
90	tim	2008
91			std::vector<int>::iterator i;
92			for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
93			if (*i != -1) {
94			unloadBlock(*i);
95			}
96			}
97	tim	2002	}
98
99			int BlockSnapshotManager::getNActiveBlocks() {
100	tim	2031	#ifdef __RWSTD
101			int count = 0;
102			std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
103			return count;
104			#else
105	tim	2008	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
106	tim	2031	#endif
107	tim	2002	}
108
109			bool BlockSnapshotManager::isBlockActive(int block) {
110			return std::find(activeBlocks_.begin(), activeBlocks_.end(), block) != activeBlocks_.end() ? true : false;
111			}
112
113			bool BlockSnapshotManager::loadBlock(int block) {
114			bool loadSuccess;
115			if (isBlockActive(block)) {
116			loadSuccess = true;
117			} else if (getNActiveBlocks() < blockCapacity_){
118
119			for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
120			snapshots_[i] = loadFrame(i);
121			}
122
123			std::vector<int>::iterator j;
124			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
125			assert(j != activeBlocks_.end());
126			*j = block;
127			loadSuccess = true;
128			}else {
129			loadSuccess = false;
130			}
131
132			return loadSuccess;
133			}
134
135			bool BlockSnapshotManager::unloadBlock(int block) {
136			bool unloadSuccess;
137			if (!isBlockActive(block)){
138			unloadSuccess = false;
139			} else {
140			for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
141			delete snapshots_[i];
142			snapshots_[i] = NULL;
143			}
144			std::vector<int>::iterator j;
145			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
146			assert(j != activeBlocks_.end());
147			*j = -1;
148	tim	2008	unloadSuccess = true;
149	tim	2002	}
150	tim	2008
151			return unloadSuccess;
152	tim	2002	}
153
154			std::vector<int> BlockSnapshotManager::getActiveBlocks() {
155			std::vector<int> result;
156	tim	2008	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
157			std::bind2nd(std::not_equal_to<int>(), -1));
158			return result;
159	tim	2002	}
160
161			Snapshot* BlockSnapshotManager::loadFrame(int frame){
162			Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
163			snapshot->setID(frame);
164	tim	2008
165			/** @todo fixed me */
166			Snapshot* oldSnapshot = currentSnapshot_;
167			currentSnapshot_ = snapshot;
168	tim	2002	reader_->readFrame(frame);
169	tim	2008	currentSnapshot_ = oldSnapshot;
170	tim	2002	return snapshot;
171			}
172
173	tim	2006	int BlockSnapshotManager::getNFrames() {
174			return reader_->getNFrames();
175	tim	2002	}
176	tim	2006
177			}