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root/OpenMD/trunk/src/brains/BlockSnapshotManager.cpp
Revision: 1966
Committed: Fri Jan 24 14:17:42 2014 UTC (11 years, 3 months ago) by gezelter
File size: 10794 byte(s)
Log Message:
More changes for memory management.

File Contents

# 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 gezelter 1966
72     int bytesPerFrameData = Snapshot::getFrameDataSize();
73 gezelter 1965 int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble
74 gezelter 1966 + nCutoffGroups_ * bytesPerCutoffGroup
75     + bytesPerFrameData;
76 tim 318
77 xsun 1215 // total number of frames that can fit in memory
78 gezelter 1596 //RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
79 gezelter 1782 RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame;
80 xsun 1215
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 gezelter 1963 if (nSnapshotPerBlock_ <= 0) {
85     std::cerr << "not enough memory to hold two configs!" << std::endl;
86     }
87 gezelter 507 reader_ = new DumpReader(info, filename);
88     nframes_ = reader_->getNFrames();
89     int nblocks = nframes_ / nSnapshotPerBlock_;
90 xsun 1215 if (nframes_ % int(nSnapshotPerBlock_) != 0) {
91 tim 318 ++nblocks;
92 gezelter 507 }
93 tim 318
94 gezelter 507 for (int i = 0; i < nblocks; ++i) {
95 tim 337 blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
96 gezelter 507 }
97     //the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
98     blocks_.back().second = nframes_;
99 tim 318
100 gezelter 507 snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
101 tim 358
102 gezelter 1966 std::cout << "-----------------------------------------------------"
103     << std::endl;
104 xsun 1215 std::cout << "BlockSnapshotManager memory report:" << std::endl;
105     std::cout << "\n";
106 gezelter 1596 // 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 gezelter 1966 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 tim 318
130 gezelter 507 }
131 tim 318
132    
133 gezelter 507 BlockSnapshotManager::~BlockSnapshotManager() {
134 tim 318 currentSnapshot_ = NULL;
135     previousSnapshot_ = NULL;
136    
137     delete reader_;
138 tim 324
139     std::vector<int>::iterator i;
140     for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
141 gezelter 507 if (*i != -1) {
142     unloadBlock(*i);
143     }
144 tim 324 }
145 gezelter 507 }
146 tim 318
147 gezelter 1249 Snapshot* BlockSnapshotManager::getSnapshot(int id) {
148     currentSnapshot_ = snapshots_[id];
149     return snapshots_[id];
150     }
151 xsun 1215
152 gezelter 507 int BlockSnapshotManager::getNActiveBlocks() {
153 tim 347 #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 tim 324 return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
159 tim 347 #endif
160 gezelter 507 }
161 tim 318
162    
163 tim 351
164 gezelter 507 bool BlockSnapshotManager::loadBlock(int block) {
165 tim 351 std::vector<int>::iterator i = findActiveBlock(block);
166 tim 318 bool loadSuccess;
167 tim 351 if (i != activeBlocks_.end()) {
168 gezelter 507 //if block is already in memory, just increast the reference count
169     ++activeRefCount_[i - activeBlocks_.begin()];
170     loadSuccess = true;
171 tim 318 } else if (getNActiveBlocks() < blockCapacity_){
172 gezelter 507 //if number of active blocks is less than the block capacity, just load it
173     internalLoad(block);
174     loadSuccess = true;
175 gezelter 1782 } else if ( hasZeroRefBlock() ) {
176 gezelter 507 //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 tim 351 } else {
182 gezelter 507 //reach the capacity and all blocks in memory are not zero reference
183     loadSuccess = false;
184 tim 318 }
185 tim 351
186 tim 318 return loadSuccess;
187 gezelter 507 }
188 tim 318
189 gezelter 507 bool BlockSnapshotManager::unloadBlock(int block) {
190 tim 318 bool unloadSuccess;
191 tim 351 std::vector<int>::iterator i = findActiveBlock(block);
192    
193     if (i != activeBlocks_.end()){
194 gezelter 507 --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 gezelter 1964
200     if (activeRefCount_[i-activeBlocks_.begin()] == 0) {
201     internalUnload(block);
202     }
203 tim 351
204 gezelter 507 unloadSuccess = true;
205 tim 351 } else {
206 gezelter 507 unloadSuccess = false;
207 tim 318 }
208 tim 324
209     return unloadSuccess;
210 gezelter 507 }
211 tim 318
212 gezelter 507 void BlockSnapshotManager::internalLoad(int block) {
213 tim 351
214     for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
215 gezelter 507 snapshots_[i] = loadFrame(i);
216 tim 351 }
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 gezelter 507 }
224 tim 351
225 gezelter 507 void BlockSnapshotManager::internalUnload(int block) {
226 gezelter 1964 std::cerr << "called internal unload for block "<< block << "\n";
227 tim 351 for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
228 gezelter 507 delete snapshots_[i];
229     snapshots_[i] = NULL;
230 tim 351 }
231     std::vector<int>::iterator j;
232     j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
233     assert(j != activeBlocks_.end());
234     *j = -1;
235 gezelter 507 }
236 tim 351
237 gezelter 507 bool BlockSnapshotManager::hasZeroRefBlock(){
238 tim 352 return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ? true : false;
239 gezelter 507 }
240 tim 351
241 gezelter 507 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 tim 351
246 gezelter 507 std::vector<int> BlockSnapshotManager::getActiveBlocks() {
247 tim 318 std::vector<int> result;
248 gezelter 1390 OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
249 gezelter 507 std::bind2nd(std::not_equal_to<int>(), -1));
250 tim 324 return result;
251 gezelter 507 }
252 tim 318
253 gezelter 507 Snapshot* BlockSnapshotManager::loadFrame(int frame){
254 gezelter 1879 Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_,
255 gezelter 1793 getStorageLayout());
256 tim 318 snapshot->setID(frame);
257 gezelter 1782 snapshot->clearDerivedProperties();
258 tim 324
259     currentSnapshot_ = snapshot;
260 tim 318 reader_->readFrame(frame);
261 xsun 1215
262 tim 318 return snapshot;
263 gezelter 507 }
264 tim 318
265 gezelter 507 int BlockSnapshotManager::getNFrames() {
266 tim 322 return reader_->getNFrames();
267 gezelter 507 }
268 tim 322
269 gezelter 1106 void BlockSnapshotManager::needCOMprops(bool ncp) {
270     reader_->setNeedCOMprops(ncp);
271     }
272    
273 tim 322 }

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