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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
#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,
                                             long long int memSize,
                                             int blockCapacity) 
    : SnapshotManager(storageLayout), info_(info), memSize_(memSize), 
      blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1), 
      activeRefCount_(blockCapacity_, 0) {

      nAtoms_ = info->getNGlobalAtoms();
      nRigidBodies_ = info->getNGlobalRigidBodies();
      nCutoffGroups_ = info->getNCutoffGroups();

      // eliminate suspect calls to figure out free memory:
      // RealType physMem = physmem_total();
      // RealType rssMem = residentMem();
      // RealType avaliablePhysMem = physMem - rssMem;
    
      int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
      int bytesPerCutoffGroup = DataStorage::getBytesPerStuntDouble(DataStorage::dslPosition);

      int bytesPerFrameData = Snapshot::getFrameDataSize();
      int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble 
        + nCutoffGroups_ * bytesPerCutoffGroup 
        + bytesPerFrameData;

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

      // number of frames in each block given the need to hold multiple blocks 
      // in memory at the same time:
      nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
      if (nSnapshotPerBlock_ <= 0) {
       std::cerr << "not enough memory to hold two configs!" << std::endl;
      }
      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 << "Memory requested for OpenMD:\t" 
                << (unsigned long)memSize_ << " bytes" << std::endl;
      std::cout << "        Bytes per FrameData:\t" 
                << (unsigned long)bytesPerFrameData << std::endl;
      std::cout << "      Bytes per StuntDouble:\t" 
                << (unsigned long)bytesPerStuntDouble << std::endl;
      std::cout << "     Bytes per Cutoff Group:\t" 
                << (unsigned long)bytesPerCutoffGroup << 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() ) {
      //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;
      }

      if (activeRefCount_[i-activeBlocks_.begin()] == 0) {
        internalUnload(block);
      }
        
      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) {
    std::cerr << "called internal unload for block "<< block << "\n";
    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);
    snapshot->clearDerivedProperties();
    
    currentSnapshot_ = snapshot;   
    reader_->readFrame(frame);

    return snapshot;
  }

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

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

}
Revision:	1966
Committed:	Fri Jan 24 14:17:42 2014 UTC (11 years, 9 months ago) by gezelter
File size:	10794 byte(s)
Log Message:	More changes for memory management.
#	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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42	#include <algorithm>
43	#include "brains/BlockSnapshotManager.hpp"
44	//#include "utils/residentMem.h"
45	//#include "utils/physmem.h"
46	#include "utils/Algorithm.hpp"
47	#include "brains/SimInfo.hpp"
48	#include "io/DumpReader.hpp"
49
50	namespace OpenMD {
51	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info,
52	const std::string& filename,
53	int storageLayout,
54	long long int memSize,
55	int blockCapacity)
56	: SnapshotManager(storageLayout), info_(info), memSize_(memSize),
57	blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1),
58	activeRefCount_(blockCapacity_, 0) {
59
60	nAtoms_ = info->getNGlobalAtoms();
61	nRigidBodies_ = info->getNGlobalRigidBodies();
62	nCutoffGroups_ = info->getNCutoffGroups();
63
64	// eliminate suspect calls to figure out free memory:
65	// RealType physMem = physmem_total();
66	// RealType rssMem = residentMem();
67	// RealType avaliablePhysMem = physMem - rssMem;
68
69	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
70	int bytesPerCutoffGroup = DataStorage::getBytesPerStuntDouble(DataStorage::dslPosition);
71
72	int bytesPerFrameData = Snapshot::getFrameDataSize();
73	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble
74	+ nCutoffGroups_ * bytesPerCutoffGroup
75	+ bytesPerFrameData;
76
77	// total number of frames that can fit in memory
78	//RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
79	RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame;
80
81	// number of frames in each block given the need to hold multiple blocks
82	// in memory at the same time:
83	nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
84	if (nSnapshotPerBlock_ <= 0) {
85	std::cerr << "not enough memory to hold two configs!" << std::endl;
86	}
87	reader_ = new DumpReader(info, filename);
88	nframes_ = reader_->getNFrames();
89	int nblocks = nframes_ / nSnapshotPerBlock_;
90	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
91	++nblocks;
92	}
93
94	for (int i = 0; i < nblocks; ++i) {
95	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
96	}
97	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
98	blocks_.back().second = nframes_;
99
100	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
101
102	std::cout << "-----------------------------------------------------"
103	<< std::endl;
104	std::cout << "BlockSnapshotManager memory report:" << std::endl;
105	std::cout << "\n";
106	// std::cout << " Physical Memory available:\t" << (unsigned long)physMem << " bytes" <<std::endl;
107	//std::cout << " Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
108	//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
109	std::cout << "Memory requested for OpenMD:\t"
110	<< (unsigned long)memSize_ << " bytes" << std::endl;
111	std::cout << " Bytes per FrameData:\t"
112	<< (unsigned long)bytesPerFrameData << std::endl;
113	std::cout << " Bytes per StuntDouble:\t"
114	<< (unsigned long)bytesPerStuntDouble << std::endl;
115	std::cout << " Bytes per Cutoff Group:\t"
116	<< (unsigned long)bytesPerCutoffGroup << std::endl;
117	std::cout << " Bytes per Frame:\t"
118	<< (unsigned long)bytesPerFrame << std::endl;
119	std::cout << " Frame Capacity:\t"
120	<< (unsigned long)frameCapacity << std::endl;
121	std::cout << " Frames in trajectory:\t"
122	<< (unsigned long)nframes_ << std::endl;
123	std::cout << " Snapshots per Block:\t"
124	<< (unsigned long)nSnapshotPerBlock_ << std::endl;
125	std::cout << " Total number of Blocks:\t"
126	<< (unsigned long)nblocks << std::endl;
127	std::cout << "-----------------------------------------------------"
128	<< std::endl;
129
130	}
131
132
133	BlockSnapshotManager::~BlockSnapshotManager() {
134	currentSnapshot_ = NULL;
135	previousSnapshot_ = NULL;
136
137	delete reader_;
138
139	std::vector<int>::iterator i;
140	for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
141	if (*i != -1) {
142	unloadBlock(*i);
143	}
144	}
145	}
146
147	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
148	currentSnapshot_ = snapshots_[id];
149	return snapshots_[id];
150	}
151
152	int BlockSnapshotManager::getNActiveBlocks() {
153	#ifdef __RWSTD
154	int count = 0;
155	std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
156	return count;
157	#else
158	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
159	#endif
160	}
161
162
163
164	bool BlockSnapshotManager::loadBlock(int block) {
165	std::vector<int>::iterator i = findActiveBlock(block);
166	bool loadSuccess;
167	if (i != activeBlocks_.end()) {
168	//if block is already in memory, just increast the reference count
169	++activeRefCount_[i - activeBlocks_.begin()];
170	loadSuccess = true;
171	} else if (getNActiveBlocks() < blockCapacity_){
172	//if number of active blocks is less than the block capacity, just load it
173	internalLoad(block);
174	loadSuccess = true;
175	} else if ( hasZeroRefBlock() ) {
176	//if already reach the block capacity, need to unload a block with 0 reference
177	int zeroRefBlock = getFirstZeroRefBlock();
178	assert(zeroRefBlock != -1);
179	internalUnload(zeroRefBlock);
180	internalLoad(block);
181	} else {
182	//reach the capacity and all blocks in memory are not zero reference
183	loadSuccess = false;
184	}
185
186	return loadSuccess;
187	}
188
189	bool BlockSnapshotManager::unloadBlock(int block) {
190	bool unloadSuccess;
191	std::vector<int>::iterator i = findActiveBlock(block);
192
193	if (i != activeBlocks_.end()){
194	--activeRefCount_[i - activeBlocks_.begin()];
195	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
196	//in case, unloadBlock called multiple times
197	activeRefCount_[i - activeBlocks_.begin()] = 0;
198	}
199
200	if (activeRefCount_[i-activeBlocks_.begin()] == 0) {
201	internalUnload(block);
202	}
203
204	unloadSuccess = true;
205	} else {
206	unloadSuccess = false;
207	}
208
209	return unloadSuccess;
210	}
211
212	void BlockSnapshotManager::internalLoad(int block) {
213
214	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
215	snapshots_[i] = loadFrame(i);
216	}
217
218	std::vector<int>::iterator j;
219	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
220	assert(j != activeBlocks_.end());
221	*j = block;
222	++activeRefCount_[j - activeBlocks_.begin()];
223	}
224
225	void BlockSnapshotManager::internalUnload(int block) {
226	std::cerr << "called internal unload for block "<< block << "\n";
227	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
228	delete snapshots_[i];
229	snapshots_[i] = NULL;
230	}
231	std::vector<int>::iterator j;
232	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
233	assert(j != activeBlocks_.end());
234	*j = -1;
235	}
236
237	bool BlockSnapshotManager::hasZeroRefBlock(){
238	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false;
239	}
240
241	int BlockSnapshotManager::getFirstZeroRefBlock(){
242	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
243	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
244	}
245
246	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
247	std::vector<int> result;
248	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
249	std::bind2nd(std::not_equal_to<int>(), -1));
250	return result;
251	}
252
253	Snapshot* BlockSnapshotManager::loadFrame(int frame){
254	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_,
255	getStorageLayout());
256	snapshot->setID(frame);
257	snapshot->clearDerivedProperties();
258
259	currentSnapshot_ = snapshot;
260	reader_->readFrame(frame);
261
262	return snapshot;
263	}
264
265	int BlockSnapshotManager::getNFrames() {
266	return reader_->getNFrames();
267	}
268
269	void BlockSnapshotManager::needCOMprops(bool ncp) {
270	reader_->setNeedCOMprops(ncp);
271	}
272
273	}