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), 
      blockCapacity_(blockCapacity), memSize_(memSize), 
      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(false);
    if (i != activeBlocks_.end()) {
      // If the block is already in memory, just increase the
      // reference count:
      ++activeRefCount_[i - activeBlocks_.begin()];
      loadSuccess = true;
    } else if (getNActiveBlocks() < blockCapacity_){
      // If the number of active blocks is less than the block
      // capacity, just load the block:
      internalLoad(block);
      loadSuccess = true;
    } else if ( hasZeroRefBlock() ) {
      // If we have already reached the block capacity, we need to
      // unload a block with 0 references:
      int zeroRefBlock = getFirstZeroRefBlock();
      assert(zeroRefBlock != -1);
      internalUnload(zeroRefBlock);
      internalLoad(block);
    } else {
      // We have reached capacity and all blocks in memory are have
      // non-zero references:
      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:	2071
Committed:	Sat Mar 7 21:41:51 2015 UTC (10 years, 1 month ago) by gezelter
File size:	10892 byte(s)
Log Message:	Reducing the number of warnings when using g++ to compile.
#	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),
57	blockCapacity_(blockCapacity), memSize_(memSize),
58	activeBlocks_(blockCapacity_, -1),
59	activeRefCount_(blockCapacity_, 0) {
60
61	nAtoms_ = info->getNGlobalAtoms();
62	nRigidBodies_ = info->getNGlobalRigidBodies();
63	nCutoffGroups_ = info->getNCutoffGroups();
64
65	// eliminate suspect calls to figure out free memory:
66	// RealType physMem = physmem_total();
67	// RealType rssMem = residentMem();
68	// RealType avaliablePhysMem = physMem - rssMem;
69
70	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
71	int bytesPerCutoffGroup = DataStorage::getBytesPerStuntDouble(DataStorage::dslPosition);
72
73	int bytesPerFrameData = Snapshot::getFrameDataSize();
74	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble
75	+ nCutoffGroups_ * bytesPerCutoffGroup
76	+ bytesPerFrameData;
77
78	// total number of frames that can fit in memory
79	//RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
80	RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame;
81
82	// number of frames in each block given the need to hold multiple blocks
83	// in memory at the same time:
84	nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
85	if (nSnapshotPerBlock_ <= 0) {
86	std::cerr << "not enough memory to hold two configs!" << std::endl;
87	}
88	reader_ = new DumpReader(info, filename);
89	nframes_ = reader_->getNFrames();
90	int nblocks = nframes_ / nSnapshotPerBlock_;
91	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
92	++nblocks;
93	}
94
95	for (int i = 0; i < nblocks; ++i) {
96	blocks_.push_back(SnapshotBlock(inSnapshotPerBlock_, (i+1)nSnapshotPerBlock_));
97	}
98	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
99	blocks_.back().second = nframes_;
100
101	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
102
103	std::cout << "-----------------------------------------------------"
104	<< std::endl;
105	std::cout << "BlockSnapshotManager memory report:" << std::endl;
106	std::cout << "\n";
107	// std::cout << " Physical Memory available:\t" << (unsigned long)physMem << " bytes" <<std::endl;
108	//std::cout << " Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
109	//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
110	std::cout << "Memory requested for OpenMD:\t"
111	<< (unsigned long)memSize_ << " bytes" << std::endl;
112	std::cout << " Bytes per FrameData:\t"
113	<< (unsigned long)bytesPerFrameData << std::endl;
114	std::cout << " Bytes per StuntDouble:\t"
115	<< (unsigned long)bytesPerStuntDouble << std::endl;
116	std::cout << " Bytes per Cutoff Group:\t"
117	<< (unsigned long)bytesPerCutoffGroup << std::endl;
118	std::cout << " Bytes per Frame:\t"
119	<< (unsigned long)bytesPerFrame << std::endl;
120	std::cout << " Frame Capacity:\t"
121	<< (unsigned long)frameCapacity << std::endl;
122	std::cout << " Frames in trajectory:\t"
123	<< (unsigned long)nframes_ << std::endl;
124	std::cout << " Snapshots per Block:\t"
125	<< (unsigned long)nSnapshotPerBlock_ << std::endl;
126	std::cout << " Total number of Blocks:\t"
127	<< (unsigned long)nblocks << std::endl;
128	std::cout << "-----------------------------------------------------"
129	<< std::endl;
130
131	}
132
133
134	BlockSnapshotManager::~BlockSnapshotManager() {
135	currentSnapshot_ = NULL;
136	previousSnapshot_ = NULL;
137
138	delete reader_;
139
140	std::vector<int>::iterator i;
141	for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
142	if (*i != -1) {
143	unloadBlock(*i);
144	}
145	}
146	}
147
148	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
149	currentSnapshot_ = snapshots_[id];
150	return snapshots_[id];
151	}
152
153	int BlockSnapshotManager::getNActiveBlocks() {
154	#ifdef __RWSTD
155	int count = 0;
156	std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
157	return count;
158	#else
159	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
160	#endif
161	}
162
163
164
165	bool BlockSnapshotManager::loadBlock(int block) {
166	std::vector<int>::iterator i = findActiveBlock(block);
167	bool loadSuccess(false);
168	if (i != activeBlocks_.end()) {
169	// If the block is already in memory, just increase the
170	// reference count:
171	++activeRefCount_[i - activeBlocks_.begin()];
172	loadSuccess = true;
173	} else if (getNActiveBlocks() < blockCapacity_){
174	// If the number of active blocks is less than the block
175	// capacity, just load the block:
176	internalLoad(block);
177	loadSuccess = true;
178	} else if ( hasZeroRefBlock() ) {
179	// If we have already reached the block capacity, we need to
180	// unload a block with 0 references:
181	int zeroRefBlock = getFirstZeroRefBlock();
182	assert(zeroRefBlock != -1);
183	internalUnload(zeroRefBlock);
184	internalLoad(block);
185	} else {
186	// We have reached capacity and all blocks in memory are have
187	// non-zero references:
188	loadSuccess = false;
189	}
190	return loadSuccess;
191	}
192
193	bool BlockSnapshotManager::unloadBlock(int block) {
194	bool unloadSuccess;
195	std::vector<int>::iterator i = findActiveBlock(block);
196
197	if (i != activeBlocks_.end()){
198	--activeRefCount_[i - activeBlocks_.begin()];
199	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
200	//in case, unloadBlock called multiple times
201	activeRefCount_[i - activeBlocks_.begin()] = 0;
202	}
203
204	if (activeRefCount_[i-activeBlocks_.begin()] == 0) {
205	internalUnload(block);
206	}
207
208	unloadSuccess = true;
209	} else {
210	unloadSuccess = false;
211	}
212
213	return unloadSuccess;
214	}
215
216	void BlockSnapshotManager::internalLoad(int block) {
217
218	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
219	snapshots_[i] = loadFrame(i);
220	}
221
222	std::vector<int>::iterator j;
223	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
224	assert(j != activeBlocks_.end());
225	*j = block;
226	++activeRefCount_[j - activeBlocks_.begin()];
227	}
228
229	void BlockSnapshotManager::internalUnload(int block) {
230	std::cerr << "called internal unload for block "<< block << "\n";
231	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
232	delete snapshots_[i];
233	snapshots_[i] = NULL;
234	}
235	std::vector<int>::iterator j;
236	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
237	assert(j != activeBlocks_.end());
238	*j = -1;
239	}
240
241	bool BlockSnapshotManager::hasZeroRefBlock(){
242	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false;
243	}
244
245	int BlockSnapshotManager::getFirstZeroRefBlock(){
246	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
247	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
248	}
249
250	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
251	std::vector<int> result;
252	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
253	std::bind2nd(std::not_equal_to<int>(), -1));
254	return result;
255	}
256
257	Snapshot* BlockSnapshotManager::loadFrame(int frame){
258	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_,
259	getStorageLayout());
260	snapshot->setID(frame);
261	snapshot->clearDerivedProperties();
262
263	currentSnapshot_ = snapshot;
264	reader_->readFrame(frame);
265
266	return snapshot;
267	}
268
269	int BlockSnapshotManager::getNFrames() {
270	return reader_->getNFrames();
271	}
272
273	void BlockSnapshotManager::needCOMprops(bool ncp) {
274	reader_->setNeedCOMprops(ncp);
275	}
276
277	}