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
#	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, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
40	*/
41	#include <algorithm>
42	#include "brains/BlockSnapshotManager.hpp"
43	#include "utils/residentMem.h"
44	#include "utils/physmem.h"
45	#include "utils/Algorithm.hpp"
46	#include "brains/SimInfo.hpp"
47	#include "io/DumpReader.hpp"
48
49	namespace OpenMD {
50	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
51	int storageLayout, int blockCapacity)
52	: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity),
53	activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) {
54
55	nAtoms_ = info->getNGlobalAtoms();
56	nRigidBodies_ = info->getNGlobalRigidBodies();
57	nCutoffGroups_ = info->getNCutoffGroups();
58
59	RealType physMem = physmem_total();
60	RealType rssMem = residentMem();
61	RealType avaliablePhysMem = physMem - rssMem;
62
63
64	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
65
66	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
67
68	// 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	reader_ = new DumpReader(info, filename);
75	nframes_ = reader_->getNFrames();
76	int nblocks = nframes_ / nSnapshotPerBlock_;
77	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
78	++nblocks;
79	}
80
81	for (int i = 0; i < nblocks; ++i) {
82	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
83	}
84	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
85	blocks_.back().second = nframes_;
86
87	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
88
89	std::cout << "-----------------------------------------------------"<<std::endl;
90	std::cout << "BlockSnapshotManager memory report:" << std::endl;
91	std::cout << "\n";
92	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	std::cout << "-----------------------------------------------------"<<std::endl;
102
103	}
104
105
106	BlockSnapshotManager::~BlockSnapshotManager() {
107	currentSnapshot_ = NULL;
108	previousSnapshot_ = NULL;
109
110	delete reader_;
111
112	std::vector<int>::iterator i;
113	for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
114	if (*i != -1) {
115	unloadBlock(*i);
116	}
117	}
118	}
119
120	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
121	currentSnapshot_ = snapshots_[id];
122	return snapshots_[id];
123	}
124
125	int BlockSnapshotManager::getNActiveBlocks() {
126	#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	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
132	#endif
133	}
134
135
136
137	bool BlockSnapshotManager::loadBlock(int block) {
138	std::vector<int>::iterator i = findActiveBlock(block);
139	bool loadSuccess;
140	if (i != activeBlocks_.end()) {
141	//if block is already in memory, just increast the reference count
142	++activeRefCount_[i - activeBlocks_.begin()];
143	loadSuccess = true;
144	} else if (getNActiveBlocks() < blockCapacity_){
145	//if number of active blocks is less than the block capacity, just load it
146	internalLoad(block);
147	loadSuccess = true;
148	} else if (hasZeroRefBlock() > 0) {
149	//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	} else {
155	//reach the capacity and all blocks in memory are not zero reference
156	loadSuccess = false;
157	}
158
159	return loadSuccess;
160	}
161
162	bool BlockSnapshotManager::unloadBlock(int block) {
163	bool unloadSuccess;
164	std::vector<int>::iterator i = findActiveBlock(block);
165
166	if (i != activeBlocks_.end()){
167	--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
173	unloadSuccess = true;
174	} else {
175	unloadSuccess = false;
176	}
177
178	return unloadSuccess;
179	}
180
181	void BlockSnapshotManager::internalLoad(int block) {
182
183	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
184	snapshots_[i] = loadFrame(i);
185	}
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	}
193
194	void BlockSnapshotManager::internalUnload(int block) {
195	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
196	delete snapshots_[i];
197	snapshots_[i] = NULL;
198	}
199	std::vector<int>::iterator j;
200	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
201	assert(j != activeBlocks_.end());
202	*j = -1;
203	}
204
205	bool BlockSnapshotManager::hasZeroRefBlock(){
206	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false;
207	}
208
209	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
214	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
215	std::vector<int> result;
216	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
217	std::bind2nd(std::not_equal_to<int>(), -1));
218	return result;
219	}
220
221	Snapshot* BlockSnapshotManager::loadFrame(int frame){
222	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_, getStorageLayout());
223	snapshot->setID(frame);
224
225	/** @todo fixed me */
226	Snapshot* oldSnapshot = currentSnapshot_;
227	currentSnapshot_ = snapshot;
228	reader_->readFrame(frame);
229
230	// What was this for? It doesn't make sense!
231	//currentSnapshot_ = oldSnapshot;
232
233	return snapshot;
234	}
235
236	int BlockSnapshotManager::getNFrames() {
237	return reader_->getNFrames();
238	}
239
240	void BlockSnapshotManager::needCOMprops(bool ncp) {
241	reader_->setNeedCOMprops(ncp);
242	}
243
244	}