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();

      RealType physMem = physmem_total();
      RealType rssMem = residentMem();
      RealType 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:	963
Committed:	Wed May 17 21:51:42 2006 UTC (18 years, 11 months ago) by tim
Original Path:	*trunk/src/brains/BlockSnapshotManager.cpp*
File size:	7971 byte(s)
Log Message:	Adding single precision capabilities to c++ side
#	User	Rev	Content
1	tim	318	/*
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	354	#include "utils/residentMem.h"
44	tim	322	#include "utils/physmem.h"
45	tim	324	#include "utils/Algorithm.hpp"
46	tim	318	#include "brains/SimInfo.hpp"
47			#include "io/DumpReader.hpp"
48
49			namespace oopse {
50	gezelter	507	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
51			int storageLayout, int blockCapacity)
52	tim	351	: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity),
53			activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) {
54	tim	318
55	gezelter	507	nAtoms_ = info->getNGlobalAtoms();
56			nRigidBodies_ = info->getNGlobalRigidBodies();
57	tim	318
58	tim	963	RealType physMem = physmem_total();
59			RealType rssMem = residentMem();
60			RealType avaliablePhysMem = physMem - rssMem;
61	tim	355
62	gezelter	507	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
63	tim	318
64	gezelter	507	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
65	tim	318
66	gezelter	507	int frameCapacity = int (avaliablePhysMem / bytesPerFrame);
67	tim	318
68	gezelter	507	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
69			reader_ = new DumpReader(info, filename);
70			nframes_ = reader_->getNFrames();
71	tim	318
72	gezelter	507	int nblocks = nframes_ / nSnapshotPerBlock_;
73			if (nframes_ % nSnapshotPerBlock_ != 0) {
74	tim	318	++nblocks;
75	gezelter	507	}
76	tim	318
77	gezelter	507	for (int i = 0; i < nblocks; ++i) {
78	tim	337	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
79	gezelter	507	}
80			//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
81			blocks_.back().second = nframes_;
82	tim	318
83	gezelter	507	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
84	tim	358
85	gezelter	507	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	318
88	gezelter	507	}
89	tim	318
90
91	gezelter	507	BlockSnapshotManager::~BlockSnapshotManager() {
92	tim	318	currentSnapshot_ = NULL;
93			previousSnapshot_ = NULL;
94
95			delete reader_;
96	tim	324
97			std::vector<int>::iterator i;
98			for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
99	gezelter	507	if (*i != -1) {
100			unloadBlock(*i);
101			}
102	tim	324	}
103	gezelter	507	}
104	tim	318
105	gezelter	507	int BlockSnapshotManager::getNActiveBlocks() {
106	tim	347	#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	324	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
112	tim	347	#endif
113	gezelter	507	}
114	tim	318
115
116	tim	351
117	gezelter	507	bool BlockSnapshotManager::loadBlock(int block) {
118	tim	351	std::vector<int>::iterator i = findActiveBlock(block);
119	tim	318	bool loadSuccess;
120	tim	351	if (i != activeBlocks_.end()) {
121	gezelter	507	//if block is already in memory, just increast the reference count
122			++activeRefCount_[i - activeBlocks_.begin()];
123			loadSuccess = true;
124	tim	318	} else if (getNActiveBlocks() < blockCapacity_){
125	gezelter	507	//if number of active blocks is less than the block capacity, just load it
126			internalLoad(block);
127			loadSuccess = true;
128	tim	351	} else if (hasZeroRefBlock() > 0) {
129	gezelter	507	//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	tim	351	} else {
135	gezelter	507	//reach the capacity and all blocks in memory are not zero reference
136			loadSuccess = false;
137	tim	318	}
138	tim	351
139	tim	318	return loadSuccess;
140	gezelter	507	}
141	tim	318
142	gezelter	507	bool BlockSnapshotManager::unloadBlock(int block) {
143	tim	318	bool unloadSuccess;
144	tim	351	std::vector<int>::iterator i = findActiveBlock(block);
145
146			if (i != activeBlocks_.end()){
147	gezelter	507	--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	tim	351
153	gezelter	507	unloadSuccess = true;
154	tim	351	} else {
155	gezelter	507	unloadSuccess = false;
156	tim	318	}
157	tim	324
158			return unloadSuccess;
159	gezelter	507	}
160	tim	318
161	gezelter	507	void BlockSnapshotManager::internalLoad(int block) {
162	tim	351
163			for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
164	gezelter	507	snapshots_[i] = loadFrame(i);
165	tim	351	}
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	gezelter	507	}
173	tim	351
174	gezelter	507	void BlockSnapshotManager::internalUnload(int block) {
175	tim	351	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
176	gezelter	507	delete snapshots_[i];
177			snapshots_[i] = NULL;
178	tim	351	}
179			std::vector<int>::iterator j;
180			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
181			assert(j != activeBlocks_.end());
182			*j = -1;
183	gezelter	507	}
184	tim	351
185	gezelter	507	bool BlockSnapshotManager::hasZeroRefBlock(){
186	tim	352	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false;
187	gezelter	507	}
188	tim	351
189	gezelter	507	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	tim	351
194	gezelter	507	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
195	tim	318	std::vector<int> result;
196	tim	324	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
197	gezelter	507	std::bind2nd(std::not_equal_to<int>(), -1));
198	tim	324	return result;
199	gezelter	507	}
200	tim	318
201	gezelter	507	Snapshot* BlockSnapshotManager::loadFrame(int frame){
202	tim	318	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
203			snapshot->setID(frame);
204	tim	324
205			/** @todo fixed me */
206			Snapshot* oldSnapshot = currentSnapshot_;
207			currentSnapshot_ = snapshot;
208	tim	318	reader_->readFrame(frame);
209	tim	324	currentSnapshot_ = oldSnapshot;
210	tim	318	return snapshot;
211	gezelter	507	}
212	tim	318
213	gezelter	507	int BlockSnapshotManager::getNFrames() {
214	tim	322	return reader_->getNFrames();
215	gezelter	507	}
216	tim	322
217			}