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
#	Content
1	/*
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	#include "utils/physmem.h"
44	#include "utils/Algorithm.hpp"
45	#include "brains/SimInfo.hpp"
46	#include "io/DumpReader.hpp"
47
48	namespace oopse {
49	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
50	int storageLayout, int blockCapacity)
51	: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1) {
52
53	nAtoms_ = info->getNGlobalAtoms();
54	nRigidBodies_ = info->getNGlobalRigidBodies();
55
56	double avalPhysMem = physmem_available();
57
58	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
59
60	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
61
62	int frameCapacity = int (avalPhysMem / bytesPerFrame);
63
64	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
65
66	reader_ = new DumpReader(info, filename);
67	nframes_ = reader_->getNFrames();
68
69	int nblocks = nframes_ / nSnapshotPerBlock_;
70	if (nframes_ % nSnapshotPerBlock_ != 0) {
71	++nblocks;
72	}
73
74	for (int i = 0; i < nblocks; ++i) {
75	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
76	}
77	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
78	blocks_.back().second = nframes_;
79
80	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
81
82	}
83
84
85	BlockSnapshotManager::~BlockSnapshotManager() {
86	currentSnapshot_ = NULL;
87	previousSnapshot_ = NULL;
88
89	delete reader_;
90
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	}
98
99	int BlockSnapshotManager::getNActiveBlocks() {
100	#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	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
106	#endif
107	}
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	unloadSuccess = true;
149	}
150
151	return unloadSuccess;
152	}
153
154	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
155	std::vector<int> result;
156	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
157	std::bind2nd(std::not_equal_to<int>(), -1));
158	return result;
159	}
160
161	Snapshot* BlockSnapshotManager::loadFrame(int frame){
162	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
163	snapshot->setID(frame);
164
165	/** @todo fixed me */
166	Snapshot* oldSnapshot = currentSnapshot_;
167	currentSnapshot_ = snapshot;
168	reader_->readFrame(frame);
169	currentSnapshot_ = oldSnapshot;
170	return snapshot;
171	}
172
173	int BlockSnapshotManager::getNFrames() {
174	return reader_->getNFrames();
175	}
176
177	}