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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
#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 OpenMD {
  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();
      nCutoffGroups_ = info->getNCutoffGroups();

      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 OpenMD:\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;
    OpenMD::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_, nCutoffGroups_, 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:	1540
Committed:	Mon Jan 17 21:34:36 2011 UTC (14 years, 3 months ago) by gezelter
File size:	9448 byte(s)
Log Message:	changes for new parallel architecture
#	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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	tim	318	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	318	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	tim	318	*/
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	gezelter	1390	namespace OpenMD {
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	gezelter	1540	nCutoffGroups_ = info->getNCutoffGroups();
58	tim	318
59	tim	963	RealType physMem = physmem_total();
60			RealType rssMem = residentMem();
61			RealType avaliablePhysMem = physMem - rssMem;
62	xsun	1215
63	tim	355
64	gezelter	507	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
65	tim	318
66	gezelter	507	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
67	tim	318
68	xsun	1215	// total number of frames that can fit in memory
69			RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
70
71			// number of frames in each block given the need to hold multiple blocks
72			// in memory at the same time:
73			nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
74	gezelter	507	reader_ = new DumpReader(info, filename);
75			nframes_ = reader_->getNFrames();
76			int nblocks = nframes_ / nSnapshotPerBlock_;
77	xsun	1215	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
78	tim	318	++nblocks;
79	gezelter	507	}
80	tim	318
81	gezelter	507	for (int i = 0; i < nblocks; ++i) {
82	tim	337	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
83	gezelter	507	}
84			//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
85			blocks_.back().second = nframes_;
86	tim	318
87	gezelter	507	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
88	tim	358
89	xsun	1215	std::cout << "-----------------------------------------------------"<<std::endl;
90			std::cout << "BlockSnapshotManager memory report:" << std::endl;
91			std::cout << "\n";
92	gezelter	1390	std::cout << " Physical Memory available:\t" << (unsigned long)physMem << " bytes" <<std::endl;
93			std::cout << " Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
94			std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
95			std::cout << " Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
96			std::cout << " Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
97			std::cout << " Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
98			std::cout << " Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
99			std::cout << " Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
100			std::cout << " Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
101	xsun	1215	std::cout << "-----------------------------------------------------"<<std::endl;
102	tim	318
103	gezelter	507	}
104	tim	318
105
106	gezelter	507	BlockSnapshotManager::~BlockSnapshotManager() {
107	tim	318	currentSnapshot_ = NULL;
108			previousSnapshot_ = NULL;
109
110			delete reader_;
111	tim	324
112			std::vector<int>::iterator i;
113			for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
114	gezelter	507	if (*i != -1) {
115			unloadBlock(*i);
116			}
117	tim	324	}
118	gezelter	507	}
119	tim	318
120	gezelter	1249	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
121			currentSnapshot_ = snapshots_[id];
122			return snapshots_[id];
123			}
124	xsun	1215
125	gezelter	507	int BlockSnapshotManager::getNActiveBlocks() {
126	tim	347	#ifdef __RWSTD
127			int count = 0;
128			std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
129			return count;
130			#else
131	tim	324	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
132	tim	347	#endif
133	gezelter	507	}
134	tim	318
135
136	tim	351
137	gezelter	507	bool BlockSnapshotManager::loadBlock(int block) {
138	tim	351	std::vector<int>::iterator i = findActiveBlock(block);
139	tim	318	bool loadSuccess;
140	tim	351	if (i != activeBlocks_.end()) {
141	gezelter	507	//if block is already in memory, just increast the reference count
142			++activeRefCount_[i - activeBlocks_.begin()];
143			loadSuccess = true;
144	tim	318	} else if (getNActiveBlocks() < blockCapacity_){
145	gezelter	507	//if number of active blocks is less than the block capacity, just load it
146			internalLoad(block);
147			loadSuccess = true;
148	tim	351	} else if (hasZeroRefBlock() > 0) {
149	gezelter	507	//if already reach the block capacity, need to unload a block with 0 reference
150			int zeroRefBlock = getFirstZeroRefBlock();
151			assert(zeroRefBlock != -1);
152			internalUnload(zeroRefBlock);
153			internalLoad(block);
154	tim	351	} else {
155	gezelter	507	//reach the capacity and all blocks in memory are not zero reference
156			loadSuccess = false;
157	tim	318	}
158	tim	351
159	tim	318	return loadSuccess;
160	gezelter	507	}
161	tim	318
162	gezelter	507	bool BlockSnapshotManager::unloadBlock(int block) {
163	tim	318	bool unloadSuccess;
164	tim	351	std::vector<int>::iterator i = findActiveBlock(block);
165
166			if (i != activeBlocks_.end()){
167	gezelter	507	--activeRefCount_[i - activeBlocks_.begin()];
168			if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
169			//in case, unloadBlock called multiple times
170			activeRefCount_[i - activeBlocks_.begin()] = 0;
171			}
172	tim	351
173	gezelter	507	unloadSuccess = true;
174	tim	351	} else {
175	gezelter	507	unloadSuccess = false;
176	tim	318	}
177	tim	324
178			return unloadSuccess;
179	gezelter	507	}
180	tim	318
181	gezelter	507	void BlockSnapshotManager::internalLoad(int block) {
182	tim	351
183			for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
184	gezelter	507	snapshots_[i] = loadFrame(i);
185	tim	351	}
186
187			std::vector<int>::iterator j;
188			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
189			assert(j != activeBlocks_.end());
190			*j = block;
191			++activeRefCount_[j - activeBlocks_.begin()];
192	gezelter	507	}
193	tim	351
194	gezelter	507	void BlockSnapshotManager::internalUnload(int block) {
195	tim	351	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
196	gezelter	507	delete snapshots_[i];
197			snapshots_[i] = NULL;
198	tim	351	}
199			std::vector<int>::iterator j;
200			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
201			assert(j != activeBlocks_.end());
202			*j = -1;
203	gezelter	507	}
204	tim	351
205	gezelter	507	bool BlockSnapshotManager::hasZeroRefBlock(){
206	tim	352	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false;
207	gezelter	507	}
208	tim	351
209	gezelter	507	int BlockSnapshotManager::getFirstZeroRefBlock(){
210			std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
211			return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
212			}
213	tim	351
214	gezelter	507	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
215	tim	318	std::vector<int> result;
216	gezelter	1390	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
217	gezelter	507	std::bind2nd(std::not_equal_to<int>(), -1));
218	tim	324	return result;
219	gezelter	507	}
220	tim	318
221	gezelter	507	Snapshot* BlockSnapshotManager::loadFrame(int frame){
222	gezelter	1540	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_, getStorageLayout());
223	tim	318	snapshot->setID(frame);
224	tim	324
225			/** @todo fixed me */
226			Snapshot* oldSnapshot = currentSnapshot_;
227			currentSnapshot_ = snapshot;
228	tim	318	reader_->readFrame(frame);
229	xsun	1215
230			// What was this for? It doesn't make sense!
231			//currentSnapshot_ = oldSnapshot;
232
233	tim	318	return snapshot;
234	gezelter	507	}
235	tim	318
236	gezelter	507	int BlockSnapshotManager::getNFrames() {
237	tim	322	return reader_->getNFrames();
238	gezelter	507	}
239	tim	322
240	gezelter	1106	void BlockSnapshotManager::needCOMprops(bool ncp) {
241			reader_->setNeedCOMprops(ncp);
242			}
243
244	tim	322	}