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 "utlis/physmem.h"
#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 = nStuntDoubles * 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(snapshot_.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;
}

}
Revision:	2002
Committed:	Sun Feb 13 06:57:48 2005 UTC (19 years, 4 months ago) by tim
File size:	5476 byte(s)
Log Message:	adding dynamicProps
#	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 "utlis/physmem.h"
44	#include "brains/SimInfo.hpp"
45	#include "io/DumpReader.hpp"
46
47	namespace oopse {
48	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
49	int storageLayout, int blockCapacity)
50	: SnapshotManager(storageLayout), info_(info),
51	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 = nStuntDoubles * 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(i, (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(snapshot_.begin(), nframes, NULL);
81
82	}
83
84
85	BlockSnapshotMananger::~BlockSnapshotMananger() {
86	currentSnapshot_ = NULL;
87	previousSnapshot_ = NULL;
88
89	delete reader_;
90	std::for_each(activeBlocks_.begin(), activeBlocks_.end(), unloadBlock);
91	}
92
93	int BlockSnapshotManager::getNActiveBlocks() {
94	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::not);
95	}
96
97	bool BlockSnapshotManager::isBlockActive(int block) {
98	return std::find(activeBlocks_.begin(), activeBlocks_.end(), block) != activeBlocks_.end() ? true : false;
99	}
100
101	bool BlockSnapshotManager::loadBlock(int block) {
102	bool loadSuccess;
103	if (isBlockActive(block)) {
104	loadSuccess = true;
105	} else if (getNActiveBlocks() < blockCapacity_){
106
107	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
108	snapshots_[i] = loadFrame(i);
109	}
110
111	std::vector<int>::iterator j;
112	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
113	assert(j != activeBlocks_.end());
114	*j = block;
115	loadSuccess = true;
116	}else {
117	loadSuccess = false;
118	}
119
120	return loadSuccess;
121	}
122
123	bool BlockSnapshotManager::unloadBlock(int block) {
124	bool unloadSuccess;
125	if (!isBlockActive(block)){
126	unloadSuccess = false;
127	} else {
128	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
129	delete snapshots_[i];
130	snapshots_[i] = NULL;
131	}
132	std::vector<int>::iterator j;
133	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
134	assert(j != activeBlocks_.end());
135	*j = -1;
136	}
137	}
138
139	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
140	std::vector<int> result;
141	std::copy_if(activeBlocks_.begin(), activeBlocks_.end());
142	}
143
144	Snapshot* BlockSnapshotManager::loadFrame(int frame){
145	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
146	snapshot->setID(frame);
147	setCurrentSnapshot(snapshot); /** @todo fixed me */
148	reader_->readFrame(frame);
149	return snapshot;
150	}
151
152	}