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 bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;

      // 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 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;
      }
        
      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);
    snapshot->clearDerivedProperties();
    
    currentSnapshot_ = snapshot;   
    reader_->readFrame(frame);

    return snapshot;
  }

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

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

}
Revision:	1963
Committed:	Thu Jan 16 15:15:17 2014 UTC (11 years, 3 months ago) by gezelter
File size:	9999 byte(s)
Log Message:	Report an error if memory requests are very small
#	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			int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
71	tim	318
72	xsun	1215	// total number of frames that can fit in memory
73	gezelter	1596	//RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
74	gezelter	1782	RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame;
75	xsun	1215
76			// number of frames in each block given the need to hold multiple blocks
77			// in memory at the same time:
78			nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
79	gezelter	1963	if (nSnapshotPerBlock_ <= 0) {
80			std::cerr << "not enough memory to hold two configs!" << std::endl;
81			}
82	gezelter	507	reader_ = new DumpReader(info, filename);
83			nframes_ = reader_->getNFrames();
84			int nblocks = nframes_ / nSnapshotPerBlock_;
85	xsun	1215	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
86	tim	318	++nblocks;
87	gezelter	507	}
88	tim	318
89	gezelter	507	for (int i = 0; i < nblocks; ++i) {
90	tim	337	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
91	gezelter	507	}
92			//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
93			blocks_.back().second = nframes_;
94	tim	318
95	gezelter	507	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
96	tim	358
97	xsun	1215	std::cout << "-----------------------------------------------------"<<std::endl;
98			std::cout << "BlockSnapshotManager memory report:" << std::endl;
99			std::cout << "\n";
100	gezelter	1596	// std::cout << " Physical Memory available:\t" << (unsigned long)physMem << " bytes" <<std::endl;
101			//std::cout << " Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
102			//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
103			std::cout << "Memory requested for OpenMD:\t" << (unsigned long)memSize_ << " bytes" <<std::endl;
104	gezelter	1390	std::cout << " Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
105			std::cout << " Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
106			std::cout << " Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
107			std::cout << " Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
108			std::cout << " Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
109			std::cout << " Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
110	xsun	1215	std::cout << "-----------------------------------------------------"<<std::endl;
111	tim	318
112	gezelter	507	}
113	tim	318
114
115	gezelter	507	BlockSnapshotManager::~BlockSnapshotManager() {
116	tim	318	currentSnapshot_ = NULL;
117			previousSnapshot_ = NULL;
118
119			delete reader_;
120	tim	324
121			std::vector<int>::iterator i;
122			for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
123	gezelter	507	if (*i != -1) {
124			unloadBlock(*i);
125			}
126	tim	324	}
127	gezelter	507	}
128	tim	318
129	gezelter	1249	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
130			currentSnapshot_ = snapshots_[id];
131			return snapshots_[id];
132			}
133	xsun	1215
134	gezelter	507	int BlockSnapshotManager::getNActiveBlocks() {
135	tim	347	#ifdef __RWSTD
136			int count = 0;
137			std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
138			return count;
139			#else
140	tim	324	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
141	tim	347	#endif
142	gezelter	507	}
143	tim	318
144
145	tim	351
146	gezelter	507	bool BlockSnapshotManager::loadBlock(int block) {
147	tim	351	std::vector<int>::iterator i = findActiveBlock(block);
148	tim	318	bool loadSuccess;
149	tim	351	if (i != activeBlocks_.end()) {
150	gezelter	507	//if block is already in memory, just increast the reference count
151			++activeRefCount_[i - activeBlocks_.begin()];
152			loadSuccess = true;
153	tim	318	} else if (getNActiveBlocks() < blockCapacity_){
154	gezelter	507	//if number of active blocks is less than the block capacity, just load it
155			internalLoad(block);
156			loadSuccess = true;
157	gezelter	1782	} else if ( hasZeroRefBlock() ) {
158	gezelter	507	//if already reach the block capacity, need to unload a block with 0 reference
159			int zeroRefBlock = getFirstZeroRefBlock();
160			assert(zeroRefBlock != -1);
161			internalUnload(zeroRefBlock);
162			internalLoad(block);
163	tim	351	} else {
164	gezelter	507	//reach the capacity and all blocks in memory are not zero reference
165			loadSuccess = false;
166	tim	318	}
167	tim	351
168	tim	318	return loadSuccess;
169	gezelter	507	}
170	tim	318
171	gezelter	507	bool BlockSnapshotManager::unloadBlock(int block) {
172	tim	318	bool unloadSuccess;
173	tim	351	std::vector<int>::iterator i = findActiveBlock(block);
174
175			if (i != activeBlocks_.end()){
176	gezelter	507	--activeRefCount_[i - activeBlocks_.begin()];
177			if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
178			//in case, unloadBlock called multiple times
179			activeRefCount_[i - activeBlocks_.begin()] = 0;
180			}
181	tim	351
182	gezelter	507	unloadSuccess = true;
183	tim	351	} else {
184	gezelter	507	unloadSuccess = false;
185	tim	318	}
186	tim	324
187			return unloadSuccess;
188	gezelter	507	}
189	tim	318
190	gezelter	507	void BlockSnapshotManager::internalLoad(int block) {
191	tim	351
192			for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
193	gezelter	507	snapshots_[i] = loadFrame(i);
194	tim	351	}
195
196			std::vector<int>::iterator j;
197			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
198			assert(j != activeBlocks_.end());
199			*j = block;
200			++activeRefCount_[j - activeBlocks_.begin()];
201	gezelter	507	}
202	tim	351
203	gezelter	507	void BlockSnapshotManager::internalUnload(int block) {
204	tim	351	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
205	gezelter	507	delete snapshots_[i];
206			snapshots_[i] = NULL;
207	tim	351	}
208			std::vector<int>::iterator j;
209			j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
210			assert(j != activeBlocks_.end());
211			*j = -1;
212	gezelter	507	}
213	tim	351
214	gezelter	507	bool BlockSnapshotManager::hasZeroRefBlock(){
215	tim	352	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false;
216	gezelter	507	}
217	tim	351
218	gezelter	507	int BlockSnapshotManager::getFirstZeroRefBlock(){
219			std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
220			return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
221			}
222	tim	351
223	gezelter	507	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
224	tim	318	std::vector<int> result;
225	gezelter	1390	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
226	gezelter	507	std::bind2nd(std::not_equal_to<int>(), -1));
227	tim	324	return result;
228	gezelter	507	}
229	tim	318
230	gezelter	507	Snapshot* BlockSnapshotManager::loadFrame(int frame){
231	gezelter	1879	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_,
232	gezelter	1793	getStorageLayout());
233	tim	318	snapshot->setID(frame);
234	gezelter	1782	snapshot->clearDerivedProperties();
235	tim	324
236			currentSnapshot_ = snapshot;
237	tim	318	reader_->readFrame(frame);
238	xsun	1215
239	tim	318	return snapshot;
240	gezelter	507	}
241	tim	318
242	gezelter	507	int BlockSnapshotManager::getNFrames() {
243	tim	322	return reader_->getNFrames();
244	gezelter	507	}
245	tim	322
246	gezelter	1106	void BlockSnapshotManager::needCOMprops(bool ncp) {
247			reader_->setNeedCOMprops(ncp);
248			}
249
250	tim	322	}