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;

      // total number of frames that can fit in memory
      RealType frameCapacity = avaliablePhysMem / bytesPerFrame;

      // number of frames in each block given the need to hold multiple blocks 
      // in memory at the same time:
      nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
      reader_ = new DumpReader(info, filename);
      nframes_ = reader_->getNFrames();
      int nblocks = nframes_ / nSnapshotPerBlock_;
      if (nframes_ % int(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 << "-----------------------------------------------------"<<std::endl;
      std::cout << "BlockSnapshotManager memory report:" << std::endl;
      std::cout << "\n";
      std::cout << " Physical Memory available:\t" << (unsigned long)physMem <<  " bytes" <<std::endl;
      std::cout << "    Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
      std::cout << "Memory available for OOPSE:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
      std::cout << "     Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
      std::cout << "           Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
      std::cout << "            Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
      std::cout << "      Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
      std::cout << "       Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
      std::cout << "    Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
      std::cout << "-----------------------------------------------------"<<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);
      }
    }
  }

   Snapshot* BlockSnapshotManager::getSnapshot(int id) { 
    currentSnapshot_ = snapshots_[id]; 
    return snapshots_[id]; 
  }

  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);

    // What was this for?  It doesn't make sense!
    //currentSnapshot_ = oldSnapshot;

    return snapshot;
  }

  int BlockSnapshotManager::getNFrames() {
    return reader_->getNFrames();
  }

  void BlockSnapshotManager::needCOMprops(bool ncp) {
    reader_->setNeedCOMprops(ncp);
  }

}
Revision:	3404
Committed:	Mon Jun 2 02:42:50 2008 UTC (16 years, 11 months ago) by gezelter
File size:	9331 byte(s)
Log Message:	Fixed a bug in BlockSnapshotManager.
#	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	gezelter	2204	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
51			int storageLayout, int blockCapacity)
52	tim	2035	: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity),
53			activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) {
54	tim	2002
55	gezelter	2204	nAtoms_ = info->getNGlobalAtoms();
56			nRigidBodies_ = info->getNGlobalRigidBodies();
57	tim	2002
58	tim	2759	RealType physMem = physmem_total();
59			RealType rssMem = residentMem();
60			RealType avaliablePhysMem = physMem - rssMem;
61	xsun	3324
62	tim	2039
63	gezelter	2204	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
64	tim	2002
65	gezelter	2204	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
66	tim	2002
67	xsun	3324	// total number of frames that can fit in memory
68			RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
69
70			// number of frames in each block given the need to hold multiple blocks
71			// in memory at the same time:
72			nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
73	gezelter	2204	reader_ = new DumpReader(info, filename);
74			nframes_ = reader_->getNFrames();
75			int nblocks = nframes_ / nSnapshotPerBlock_;
76	xsun	3324	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
77	tim	2002	++nblocks;
78	gezelter	2204	}
79	tim	2002
80	gezelter	2204	for (int i = 0; i < nblocks; ++i) {
81	tim	2021	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
82	gezelter	2204	}
83			//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
84			blocks_.back().second = nframes_;
85	tim	2002
86	gezelter	2204	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
87	tim	2042
88	xsun	3324	std::cout << "-----------------------------------------------------"<<std::endl;
89			std::cout << "BlockSnapshotManager memory report:" << std::endl;
90			std::cout << "\n";
91			std::cout << " Physical Memory available:\t" << (unsigned long)physMem << " bytes" <<std::endl;
92			std::cout << " Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
93			std::cout << "Memory available for OOPSE:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
94			std::cout << " Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
95			std::cout << " Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
96			std::cout << " Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
97			std::cout << " Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
98			std::cout << " Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
99			std::cout << " Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
100			std::cout << "-----------------------------------------------------"<<std::endl;
101	tim	2002
102	gezelter	2204	}
103	tim	2002
104
105	gezelter	2204	BlockSnapshotManager::~BlockSnapshotManager() {
106	tim	2002	currentSnapshot_ = NULL;
107			previousSnapshot_ = NULL;
108
109			delete reader_;
110	tim	2008
111			std::vector<int>::iterator i;
112			for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
113	gezelter	2204	if (*i != -1) {
114			unloadBlock(*i);
115			}
116	tim	2008	}
117	gezelter	2204	}
118	tim	2002
119	gezelter	3404	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
120			currentSnapshot_ = snapshots_[id];
121			return snapshots_[id];
122			}
123	xsun	3324
124	gezelter	2204	int BlockSnapshotManager::getNActiveBlocks() {
125	tim	2031	#ifdef __RWSTD
126			int count = 0;
127			std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
128			return count;
129			#else
130	tim	2008	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
131	tim	2031	#endif
132	gezelter	2204	}
133	tim	2002
134
135	tim	2035
136	gezelter	2204	bool BlockSnapshotManager::loadBlock(int block) {
137	tim	2035	std::vector<int>::iterator i = findActiveBlock(block);
138	tim	2002	bool loadSuccess;
139	tim	2035	if (i != activeBlocks_.end()) {
140	gezelter	2204	//if block is already in memory, just increast the reference count
141			++activeRefCount_[i - activeBlocks_.begin()];
142			loadSuccess = true;
143	tim	2002	} else if (getNActiveBlocks() < blockCapacity_){
144	gezelter	2204	//if number of active blocks is less than the block capacity, just load it
145			internalLoad(block);
146			loadSuccess = true;
147	tim	2035	} else if (hasZeroRefBlock() > 0) {
148	gezelter	2204	//if already reach the block capacity, need to unload a block with 0 reference
149			int zeroRefBlock = getFirstZeroRefBlock();
150			assert(zeroRefBlock != -1);
151			internalUnload(zeroRefBlock);
152			internalLoad(block);
153	tim	2035	} else {
154	gezelter	2204	//reach the capacity and all blocks in memory are not zero reference
155			loadSuccess = false;
156	tim	2002	}
157	tim	2035
158	tim	2002	return loadSuccess;
159	gezelter	2204	}
160	tim	2002
161	gezelter	2204	bool BlockSnapshotManager::unloadBlock(int block) {
162	tim	2002	bool unloadSuccess;
163	tim	2035	std::vector<int>::iterator i = findActiveBlock(block);
164
165			if (i != activeBlocks_.end()){
166	gezelter	2204	--activeRefCount_[i - activeBlocks_.begin()];
167			if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
168			//in case, unloadBlock called multiple times
169			activeRefCount_[i - activeBlocks_.begin()] = 0;
170			}
171	tim	2035
172	gezelter	2204	unloadSuccess = true;
173	tim	2035	} else {
174	gezelter	2204	unloadSuccess = false;
175	tim	2002	}
176	tim	2008
177			return unloadSuccess;
178	gezelter	2204	}
179	tim	2002
180	gezelter	2204	void BlockSnapshotManager::internalLoad(int block) {
181	tim	2035
182			for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
183	gezelter	2204	snapshots_[i] = loadFrame(i);
184	tim	2035	}
185
186			std::vector<int>::iterator j;
187			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
188			assert(j != activeBlocks_.end());
189			*j = block;
190			++activeRefCount_[j - activeBlocks_.begin()];
191	gezelter	2204	}
192	tim	2035
193	gezelter	2204	void BlockSnapshotManager::internalUnload(int block) {
194	tim	2035	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
195	gezelter	2204	delete snapshots_[i];
196			snapshots_[i] = NULL;
197	tim	2035	}
198			std::vector<int>::iterator j;
199			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
200			assert(j != activeBlocks_.end());
201			*j = -1;
202	gezelter	2204	}
203	tim	2035
204	gezelter	2204	bool BlockSnapshotManager::hasZeroRefBlock(){
205	tim	2036	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false;
206	gezelter	2204	}
207	tim	2035
208	gezelter	2204	int BlockSnapshotManager::getFirstZeroRefBlock(){
209			std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
210			return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
211			}
212	tim	2035
213	gezelter	2204	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
214	tim	2002	std::vector<int> result;
215	tim	2008	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
216	gezelter	2204	std::bind2nd(std::not_equal_to<int>(), -1));
217	tim	2008	return result;
218	gezelter	2204	}
219	tim	2002
220	gezelter	2204	Snapshot* BlockSnapshotManager::loadFrame(int frame){
221	tim	2002	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
222			snapshot->setID(frame);
223	tim	2008
224			/** @todo fixed me */
225			Snapshot* oldSnapshot = currentSnapshot_;
226			currentSnapshot_ = snapshot;
227	tim	2002	reader_->readFrame(frame);
228	xsun	3324
229			// What was this for? It doesn't make sense!
230			//currentSnapshot_ = oldSnapshot;
231
232	tim	2002	return snapshot;
233	gezelter	2204	}
234	tim	2002
235	gezelter	2204	int BlockSnapshotManager::getNFrames() {
236	tim	2006	return reader_->getNFrames();
237	gezelter	2204	}
238	tim	2006
239	gezelter	3104	void BlockSnapshotManager::needCOMprops(bool ncp) {
240			reader_->setNeedCOMprops(ncp);
241			}
242
243	tim	2006	}