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 bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble 
        + nCutoffGroups_ * bytesPerCutoffGroup;

      // 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 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:	1965
Committed:	Fri Jan 24 13:53:41 2014 UTC (11 years, 3 months ago) by gezelter
File size:	10407 byte(s)
Log Message:	Memory reporting fix
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	318	*/
42			#include <algorithm>
43			#include "brains/BlockSnapshotManager.hpp"
44	gezelter	1782	//#include "utils/residentMem.h"
45			//#include "utils/physmem.h"
46	tim	324	#include "utils/Algorithm.hpp"
47	tim	318	#include "brains/SimInfo.hpp"
48			#include "io/DumpReader.hpp"
49
50	gezelter	1390	namespace OpenMD {
51	gezelter	1596	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info,
52			const std::string& filename,
53	gezelter	1782	int storageLayout,
54			long long int memSize,
55	gezelter	1596	int blockCapacity)
56	gezelter	1782	: SnapshotManager(storageLayout), info_(info), memSize_(memSize),
57	gezelter	1596	blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1),
58			activeRefCount_(blockCapacity_, 0) {
59	tim	318
60	gezelter	507	nAtoms_ = info->getNGlobalAtoms();
61			nRigidBodies_ = info->getNGlobalRigidBodies();
62	gezelter	1782	nCutoffGroups_ = info->getNCutoffGroups();
63	tim	318
64	gezelter	1596	// eliminate suspect calls to figure out free memory:
65			// RealType physMem = physmem_total();
66			// RealType rssMem = residentMem();
67			// RealType avaliablePhysMem = physMem - rssMem;
68	gezelter	1782
69	gezelter	507	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
70	gezelter	1965	int bytesPerCutoffGroup = DataStorage::getBytesPerStuntDouble(DataStorage::dslPosition);
71			int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble
72			+ nCutoffGroups_ * bytesPerCutoffGroup;
73	tim	318
74	xsun	1215	// total number of frames that can fit in memory
75	gezelter	1596	//RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
76	gezelter	1782	RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame;
77	xsun	1215
78			// number of frames in each block given the need to hold multiple blocks
79			// in memory at the same time:
80			nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
81	gezelter	1963	if (nSnapshotPerBlock_ <= 0) {
82			std::cerr << "not enough memory to hold two configs!" << std::endl;
83			}
84	gezelter	507	reader_ = new DumpReader(info, filename);
85			nframes_ = reader_->getNFrames();
86			int nblocks = nframes_ / nSnapshotPerBlock_;
87	xsun	1215	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
88	tim	318	++nblocks;
89	gezelter	507	}
90	tim	318
91	gezelter	507	for (int i = 0; i < nblocks; ++i) {
92	tim	337	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
93	gezelter	507	}
94			//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
95			blocks_.back().second = nframes_;
96	tim	318
97	gezelter	507	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
98	tim	358
99	xsun	1215	std::cout << "-----------------------------------------------------"<<std::endl;
100			std::cout << "BlockSnapshotManager memory report:" << std::endl;
101			std::cout << "\n";
102	gezelter	1596	// std::cout << " Physical Memory available:\t" << (unsigned long)physMem << " bytes" <<std::endl;
103			//std::cout << " Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
104			//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
105			std::cout << "Memory requested for OpenMD:\t" << (unsigned long)memSize_ << " bytes" <<std::endl;
106	gezelter	1390	std::cout << " Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
107	gezelter	1965	std::cout << " Bytes per Cutoff Group:\t" << (unsigned long)bytesPerCutoffGroup <<std::endl;
108	gezelter	1390	std::cout << " Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
109			std::cout << " Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
110			std::cout << " Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
111			std::cout << " Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
112			std::cout << " Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
113	xsun	1215	std::cout << "-----------------------------------------------------"<<std::endl;
114	tim	318
115	gezelter	507	}
116	tim	318
117
118	gezelter	507	BlockSnapshotManager::~BlockSnapshotManager() {
119	tim	318	currentSnapshot_ = NULL;
120			previousSnapshot_ = NULL;
121
122			delete reader_;
123	tim	324
124			std::vector<int>::iterator i;
125			for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
126	gezelter	507	if (*i != -1) {
127			unloadBlock(*i);
128			}
129	tim	324	}
130	gezelter	507	}
131	tim	318
132	gezelter	1249	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
133			currentSnapshot_ = snapshots_[id];
134			return snapshots_[id];
135			}
136	xsun	1215
137	gezelter	507	int BlockSnapshotManager::getNActiveBlocks() {
138	tim	347	#ifdef __RWSTD
139			int count = 0;
140			std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
141			return count;
142			#else
143	tim	324	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
144	tim	347	#endif
145	gezelter	507	}
146	tim	318
147
148	tim	351
149	gezelter	507	bool BlockSnapshotManager::loadBlock(int block) {
150	tim	351	std::vector<int>::iterator i = findActiveBlock(block);
151	tim	318	bool loadSuccess;
152	tim	351	if (i != activeBlocks_.end()) {
153	gezelter	507	//if block is already in memory, just increast the reference count
154			++activeRefCount_[i - activeBlocks_.begin()];
155			loadSuccess = true;
156	tim	318	} else if (getNActiveBlocks() < blockCapacity_){
157	gezelter	507	//if number of active blocks is less than the block capacity, just load it
158			internalLoad(block);
159			loadSuccess = true;
160	gezelter	1782	} else if ( hasZeroRefBlock() ) {
161	gezelter	507	//if already reach the block capacity, need to unload a block with 0 reference
162			int zeroRefBlock = getFirstZeroRefBlock();
163			assert(zeroRefBlock != -1);
164			internalUnload(zeroRefBlock);
165			internalLoad(block);
166	tim	351	} else {
167	gezelter	507	//reach the capacity and all blocks in memory are not zero reference
168			loadSuccess = false;
169	tim	318	}
170	tim	351
171	tim	318	return loadSuccess;
172	gezelter	507	}
173	tim	318
174	gezelter	507	bool BlockSnapshotManager::unloadBlock(int block) {
175	tim	318	bool unloadSuccess;
176	tim	351	std::vector<int>::iterator i = findActiveBlock(block);
177
178			if (i != activeBlocks_.end()){
179	gezelter	507	--activeRefCount_[i - activeBlocks_.begin()];
180			if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
181			//in case, unloadBlock called multiple times
182			activeRefCount_[i - activeBlocks_.begin()] = 0;
183			}
184	gezelter	1964
185			if (activeRefCount_[i-activeBlocks_.begin()] == 0) {
186			internalUnload(block);
187			}
188	tim	351
189	gezelter	507	unloadSuccess = true;
190	tim	351	} else {
191	gezelter	507	unloadSuccess = false;
192	tim	318	}
193	tim	324
194			return unloadSuccess;
195	gezelter	507	}
196	tim	318
197	gezelter	507	void BlockSnapshotManager::internalLoad(int block) {
198	tim	351
199			for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
200	gezelter	507	snapshots_[i] = loadFrame(i);
201	tim	351	}
202
203			std::vector<int>::iterator j;
204			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
205			assert(j != activeBlocks_.end());
206			*j = block;
207			++activeRefCount_[j - activeBlocks_.begin()];
208	gezelter	507	}
209	tim	351
210	gezelter	507	void BlockSnapshotManager::internalUnload(int block) {
211	gezelter	1964	std::cerr << "called internal unload for block "<< block << "\n";
212	tim	351	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
213	gezelter	507	delete snapshots_[i];
214			snapshots_[i] = NULL;
215	tim	351	}
216			std::vector<int>::iterator j;
217			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
218			assert(j != activeBlocks_.end());
219			*j = -1;
220	gezelter	507	}
221	tim	351
222	gezelter	507	bool BlockSnapshotManager::hasZeroRefBlock(){
223	tim	352	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false;
224	gezelter	507	}
225	tim	351
226	gezelter	507	int BlockSnapshotManager::getFirstZeroRefBlock(){
227			std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
228			return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
229			}
230	tim	351
231	gezelter	507	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
232	tim	318	std::vector<int> result;
233	gezelter	1390	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
234	gezelter	507	std::bind2nd(std::not_equal_to<int>(), -1));
235	tim	324	return result;
236	gezelter	507	}
237	tim	318
238	gezelter	507	Snapshot* BlockSnapshotManager::loadFrame(int frame){
239	gezelter	1879	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_,
240	gezelter	1793	getStorageLayout());
241	tim	318	snapshot->setID(frame);
242	gezelter	1782	snapshot->clearDerivedProperties();
243	tim	324
244			currentSnapshot_ = snapshot;
245	tim	318	reader_->readFrame(frame);
246	xsun	1215
247	tim	318	return snapshot;
248	gezelter	507	}
249	tim	318
250	gezelter	507	int BlockSnapshotManager::getNFrames() {
251	tim	322	return reader_->getNFrames();
252	gezelter	507	}
253	tim	322
254	gezelter	1106	void BlockSnapshotManager::needCOMprops(bool ncp) {
255			reader_->setNeedCOMprops(ncp);
256			}
257
258	tim	322	}