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:	2042
Committed:	Thu Feb 17 15:18:36 2005 UTC (19 years, 4 months ago) by tim
File size:	7951 byte(s)
Log Message:	The change of interface of BitSet cause a bug in SelectionEvaluation
#	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	2038	#include "utils/residentMem.h"
44	tim	2006	#include "utils/physmem.h"
45	tim	2008	#include "utils/Algorithm.hpp"
46	tim	2002	#include "brains/SimInfo.hpp"
47			#include "io/DumpReader.hpp"
48
49			namespace oopse {
50	tim	2008	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
51	tim	2002	int storageLayout, int blockCapacity)
52	tim	2035	: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity),
53			activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) {
54	tim	2002
55			nAtoms_ = info->getNGlobalAtoms();
56			nRigidBodies_ = info->getNGlobalRigidBodies();
57
58	tim	2038	double physMem = physmem_total();
59			double rssMem = residentMem();
60	tim	2039	double avaliablePhysMem = physMem - rssMem;
61
62	tim	2002	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
63
64	tim	2007	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
65	tim	2002
66	tim	2039	int frameCapacity = int (avaliablePhysMem / bytesPerFrame);
67	tim	2002
68			nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
69			reader_ = new DumpReader(info, filename);
70	tim	2007	nframes_ = reader_->getNFrames();
71	tim	2002
72	tim	2007	int nblocks = nframes_ / nSnapshotPerBlock_;
73			if (nframes_ % nSnapshotPerBlock_ != 0) {
74	tim	2002	++nblocks;
75			}
76
77			for (int i = 0; i < nblocks; ++i) {
78	tim	2021	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
79	tim	2002	}
80			//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
81	tim	2008	blocks_.back().second = nframes_;
82	tim	2002
83	tim	2031	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
84	tim	2042
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	tim	2002
88			}
89
90
91	tim	2008	BlockSnapshotManager::~BlockSnapshotManager() {
92	tim	2002	currentSnapshot_ = NULL;
93			previousSnapshot_ = NULL;
94
95			delete reader_;
96	tim	2008
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	tim	2002	}
104
105			int BlockSnapshotManager::getNActiveBlocks() {
106	tim	2031	#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	tim	2008	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
112	tim	2031	#endif
113	tim	2002	}
114
115
116	tim	2035
117	tim	2002	bool BlockSnapshotManager::loadBlock(int block) {
118	tim	2035	std::vector<int>::iterator i = findActiveBlock(block);
119	tim	2002	bool loadSuccess;
120	tim	2035	if (i != activeBlocks_.end()) {
121			//if block is already in memory, just increast the reference count
122			++activeRefCount_[i - activeBlocks_.begin()];
123	tim	2002	loadSuccess = true;
124			} else if (getNActiveBlocks() < blockCapacity_){
125	tim	2035	//if number of active blocks is less than the block capacity, just load it
126			internalLoad(block);
127	tim	2002	loadSuccess = true;
128	tim	2035	} 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	tim	2002	loadSuccess = false;
137			}
138	tim	2035
139	tim	2002	return loadSuccess;
140			}
141
142			bool BlockSnapshotManager::unloadBlock(int block) {
143			bool unloadSuccess;
144	tim	2035	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	tim	2002	}
152	tim	2035
153	tim	2008	unloadSuccess = true;
154	tim	2035	} else {
155			unloadSuccess = false;
156	tim	2002	}
157	tim	2008
158			return unloadSuccess;
159	tim	2002	}
160
161	tim	2035	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	tim	2036	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false;
187	tim	2035	}
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	tim	2002	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
195			std::vector<int> result;
196	tim	2008	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
197			std::bind2nd(std::not_equal_to<int>(), -1));
198			return result;
199	tim	2002	}
200
201			Snapshot* BlockSnapshotManager::loadFrame(int frame){
202			Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
203			snapshot->setID(frame);
204	tim	2008
205			/** @todo fixed me */
206			Snapshot* oldSnapshot = currentSnapshot_;
207			currentSnapshot_ = snapshot;
208	tim	2002	reader_->readFrame(frame);
209	tim	2008	currentSnapshot_ = oldSnapshot;
210	tim	2002	return snapshot;
211			}
212
213	tim	2006	int BlockSnapshotManager::getNFrames() {
214			return reader_->getNFrames();
215	tim	2002	}
216	tim	2006
217			}