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/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) {

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

    double physMem = physmem_total();
    double rssMem = residentMem();
    double avaliablePhysMem = physMem - rssMem;
    
    int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);

    int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;

    int frameCapacity = int (avaliablePhysMem / 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));   

    std::cout << "physmem = " << int(physMem) << "\trssMem =  "<< int(rssMem) << "\t availablePhysMem = " << int(avaliablePhysMem) <<std::endl;
    std::cout << "nSnapshotPerBlock = " << nSnapshotPerBlock_ << "\t total block = " << nblocks << std::endl;
    
}


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::loadBlock(int block) {
    std::vector<int>::iterator i = findActiveBlock(block);
    bool loadSuccess;
    if (i != activeBlocks_.end()) {
        //if block is already in memory, just increast the reference count
        ++activeRefCount_[i - activeBlocks_.begin()];
        loadSuccess = true;
    } else if (getNActiveBlocks() < blockCapacity_){
        //if number of active blocks is less than the block capacity, just load it
        internalLoad(block);
        loadSuccess = true;
    } else if (hasZeroRefBlock() > 0) {
        //if already reach the block capacity, need to unload a block with 0 reference
        int zeroRefBlock = getFirstZeroRefBlock();
        assert(zeroRefBlock != -1);
        internalUnload(zeroRefBlock);
        internalLoad(block);
    } else {
        //reach the capacity and all blocks in memory are not zero reference
        loadSuccess = false;
    }
    
    return loadSuccess;
}

bool BlockSnapshotManager::unloadBlock(int block) {
    bool unloadSuccess;
    std::vector<int>::iterator i = findActiveBlock(block);
    
    if (i != activeBlocks_.end()){
        --activeRefCount_[i - activeBlocks_.begin()];
        if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
            //in case, unloadBlock called multiple times
            activeRefCount_[i - activeBlocks_.begin()]  = 0;
        }
        
        unloadSuccess = true;
    } else {
        unloadSuccess = false;
    }

    return unloadSuccess;
}

void BlockSnapshotManager::internalLoad(int block) {
        
    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;    
    ++activeRefCount_[j - activeBlocks_.begin()];
}

void BlockSnapshotManager::internalUnload(int block) {
    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;
}

bool BlockSnapshotManager::hasZeroRefBlock(){
    return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ?  true : false;
}

int BlockSnapshotManager::getFirstZeroRefBlock(){
     std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
     return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
}

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:	358
Committed:	Thu Feb 17 15:18:36 2005 UTC (20 years, 8 months ago) by tim
Original Path:	*trunk/src/brains/BlockSnapshotManager.cpp*
File size:	7951 byte(s)
Log Message:	The change of interface of BitSet cause a bug in SelectionEvaluation
#	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/residentMem.h"
44	#include "utils/physmem.h"
45	#include "utils/Algorithm.hpp"
46	#include "brains/SimInfo.hpp"
47	#include "io/DumpReader.hpp"
48
49	namespace oopse {
50	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
51	int storageLayout, int blockCapacity)
52	: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity),
53	activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) {
54
55	nAtoms_ = info->getNGlobalAtoms();
56	nRigidBodies_ = info->getNGlobalRigidBodies();
57
58	double physMem = physmem_total();
59	double rssMem = residentMem();
60	double avaliablePhysMem = physMem - rssMem;
61
62	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
63
64	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
65
66	int frameCapacity = int (avaliablePhysMem / bytesPerFrame);
67
68	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
69	reader_ = new DumpReader(info, filename);
70	nframes_ = reader_->getNFrames();
71
72	int nblocks = nframes_ / nSnapshotPerBlock_;
73	if (nframes_ % nSnapshotPerBlock_ != 0) {
74	++nblocks;
75	}
76
77	for (int i = 0; i < nblocks; ++i) {
78	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
79	}
80	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
81	blocks_.back().second = nframes_;
82
83	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
84
85	std::cout << "physmem = " << int(physMem) << "\trssMem = "<< int(rssMem) << "\t availablePhysMem = " << int(avaliablePhysMem) <<std::endl;
86	std::cout << "nSnapshotPerBlock = " << nSnapshotPerBlock_ << "\t total block = " << nblocks << std::endl;
87
88	}
89
90
91	BlockSnapshotManager::~BlockSnapshotManager() {
92	currentSnapshot_ = NULL;
93	previousSnapshot_ = NULL;
94
95	delete reader_;
96
97	std::vector<int>::iterator i;
98	for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
99	if (*i != -1) {
100	unloadBlock(*i);
101	}
102	}
103	}
104
105	int BlockSnapshotManager::getNActiveBlocks() {
106	#ifdef __RWSTD
107	int count = 0;
108	std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
109	return count;
110	#else
111	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
112	#endif
113	}
114
115
116
117	bool BlockSnapshotManager::loadBlock(int block) {
118	std::vector<int>::iterator i = findActiveBlock(block);
119	bool loadSuccess;
120	if (i != activeBlocks_.end()) {
121	//if block is already in memory, just increast the reference count
122	++activeRefCount_[i - activeBlocks_.begin()];
123	loadSuccess = true;
124	} else if (getNActiveBlocks() < blockCapacity_){
125	//if number of active blocks is less than the block capacity, just load it
126	internalLoad(block);
127	loadSuccess = true;
128	} else if (hasZeroRefBlock() > 0) {
129	//if already reach the block capacity, need to unload a block with 0 reference
130	int zeroRefBlock = getFirstZeroRefBlock();
131	assert(zeroRefBlock != -1);
132	internalUnload(zeroRefBlock);
133	internalLoad(block);
134	} else {
135	//reach the capacity and all blocks in memory are not zero reference
136	loadSuccess = false;
137	}
138
139	return loadSuccess;
140	}
141
142	bool BlockSnapshotManager::unloadBlock(int block) {
143	bool unloadSuccess;
144	std::vector<int>::iterator i = findActiveBlock(block);
145
146	if (i != activeBlocks_.end()){
147	--activeRefCount_[i - activeBlocks_.begin()];
148	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
149	//in case, unloadBlock called multiple times
150	activeRefCount_[i - activeBlocks_.begin()] = 0;
151	}
152
153	unloadSuccess = true;
154	} else {
155	unloadSuccess = false;
156	}
157
158	return unloadSuccess;
159	}
160
161	void BlockSnapshotManager::internalLoad(int block) {
162
163	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
164	snapshots_[i] = loadFrame(i);
165	}
166
167	std::vector<int>::iterator j;
168	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
169	assert(j != activeBlocks_.end());
170	*j = block;
171	++activeRefCount_[j - activeBlocks_.begin()];
172	}
173
174	void BlockSnapshotManager::internalUnload(int block) {
175	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
176	delete snapshots_[i];
177	snapshots_[i] = NULL;
178	}
179	std::vector<int>::iterator j;
180	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
181	assert(j != activeBlocks_.end());
182	*j = -1;
183	}
184
185	bool BlockSnapshotManager::hasZeroRefBlock(){
186	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false;
187	}
188
189	int BlockSnapshotManager::getFirstZeroRefBlock(){
190	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
191	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
192	}
193
194	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
195	std::vector<int> result;
196	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
197	std::bind2nd(std::not_equal_to<int>(), -1));
198	return result;
199	}
200
201	Snapshot* BlockSnapshotManager::loadFrame(int frame){
202	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
203	snapshot->setID(frame);
204
205	/** @todo fixed me */
206	Snapshot* oldSnapshot = currentSnapshot_;
207	currentSnapshot_ = snapshot;
208	reader_->readFrame(frame);
209	currentSnapshot_ = oldSnapshot;
210	return snapshot;
211	}
212
213	int BlockSnapshotManager::getNFrames() {
214	return reader_->getNFrames();
215	}
216
217	}