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root/OpenMD/branches/development/src/brains/BlockSnapshotManager.cpp

Comparing:
trunk/src/brains/BlockSnapshotManager.cpp (file contents), Revision 355 by tim, Wed Feb 16 20:43:10 2005 UTC vs.
branches/development/src/brains/BlockSnapshotManager.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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"
#	Line 46 | Line 46
46		#include "brains/SimInfo.hpp"
47		#include "io/DumpReader.hpp"
48
49	<	namespace oopse {
50	<	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
51	<	int storageLayout, int blockCapacity)
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();
55	>	nAtoms_ = info->getNGlobalAtoms();
56	>	nRigidBodies_ = info->getNGlobalRigidBodies();
57
58	<	double physMem = physmem_total();
59	<	double rssMem = residentMem();
60	<	double avaliablePhysMem = physMem - rssMem;
61	<
62	<	std::cout << "physmem = " << int(physMem) << "\trssMem =  "<< rssMem << "\t availablePhysMem = " << avaliablePhysMem <<std::endl;
63	<	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
58	>	RealType physMem = physmem_total();
59	>	RealType rssMem = residentMem();
60	>	RealType avaliablePhysMem = physMem - rssMem;
61
65	–	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
66	–
67	–	int frameCapacity = int (avaliablePhysMem / bytesPerFrame);
62
63	<	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
63	>	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
64
65	<	reader_ = new DumpReader(info, filename);
72	<	nframes_ = reader_->getNFrames();
65	>	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
66
67	<	int nblocks = nframes_ / nSnapshotPerBlock_;
68	<	if (nframes_ % nSnapshotPerBlock_ != 0) {
67	>	// total number of frames that can fit in memory
68	>	RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
69	>
70	>	// number of frames in each block given the need to hold multiple blocks
71	>	// in memory at the same time:
72	>	nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
73	>	reader_ = new DumpReader(info, filename);
74	>	nframes_ = reader_->getNFrames();
75	>	int nblocks = nframes_ / nSnapshotPerBlock_;
76	>	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
77		++nblocks;
78	<	}
78	>	}
79
80	<	for (int i = 0; i < nblocks; ++i) {
80	>	for (int i = 0; i < nblocks; ++i) {
81		blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
82	<	}
83	<	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
84	<	blocks_.back().second = nframes_;
82	>	}
83	>	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
84	>	blocks_.back().second = nframes_;
85
86	<	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
86	>	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
87	>
88	>	std::cout << "-----------------------------------------------------"<<std::endl;
89	>	std::cout << "BlockSnapshotManager memory report:" << std::endl;
90	>	std::cout << "\n";
91	>	std::cout << "  Physical Memory available:\t" << (unsigned long)physMem <<  " bytes" <<std::endl;
92	>	std::cout << "     Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
93	>	std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
94	>	std::cout << "      Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
95	>	std::cout << "            Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
96	>	std::cout << "             Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
97	>	std::cout << "       Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
98	>	std::cout << "        Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
99	>	std::cout << "     Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
100	>	std::cout << "-----------------------------------------------------"<<std::endl;
101
102	<	}
102	>	}
103
104
105	<	BlockSnapshotManager::~BlockSnapshotManager() {
105	>	BlockSnapshotManager::~BlockSnapshotManager() {
106		currentSnapshot_ = NULL;
107		previousSnapshot_ = NULL;
108
#	Line 95 | Line 110 | BlockSnapshotManager::~BlockSnapshotManager() {
110
111		std::vector<int>::iterator i;
112		for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
113	<	if (*i != -1) {
114	<	unloadBlock(*i);
115	<	}
113	>	if (*i != -1) {
114	>	unloadBlock(*i);
115	>	}
116		}
117	<	}
117	>	}
118
119	<	int BlockSnapshotManager::getNActiveBlocks() {
119	>	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
120	>	currentSnapshot_ = snapshots_[id];
121	>	return snapshots_[id];
122	>	}
123	>
124	>	int BlockSnapshotManager::getNActiveBlocks() {
125		#ifdef __RWSTD
126		int count = 0;
127		std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
#	Line 109 | Line 129 | int BlockSnapshotManager::getNActiveBlocks() {
129		#else
130		return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
131		#endif
132	<	}
132	>	}
133
134
135
136	<	bool BlockSnapshotManager::loadBlock(int block) {
136	>	bool BlockSnapshotManager::loadBlock(int block) {
137		std::vector<int>::iterator i = findActiveBlock(block);
138		bool loadSuccess;
139		if (i != activeBlocks_.end()) {
140	<	//if block is already in memory, just increast the reference count
141	<	++activeRefCount_[i - activeBlocks_.begin()];
142	<	loadSuccess = true;
140	>	//if block is already in memory, just increast the reference count
141	>	++activeRefCount_[i - activeBlocks_.begin()];
142	>	loadSuccess = true;
143		} else if (getNActiveBlocks() < blockCapacity_){
144	<	//if number of active blocks is less than the block capacity, just load it
145	<	internalLoad(block);
146	<	loadSuccess = true;
144	>	//if number of active blocks is less than the block capacity, just load it
145	>	internalLoad(block);
146	>	loadSuccess = true;
147		} else if (hasZeroRefBlock() > 0) {
148	<	//if already reach the block capacity, need to unload a block with 0 reference
149	<	int zeroRefBlock = getFirstZeroRefBlock();
150	<	assert(zeroRefBlock != -1);
151	<	internalUnload(zeroRefBlock);
152	<	internalLoad(block);
148	>	//if already reach the block capacity, need to unload a block with 0 reference
149	>	int zeroRefBlock = getFirstZeroRefBlock();
150	>	assert(zeroRefBlock != -1);
151	>	internalUnload(zeroRefBlock);
152	>	internalLoad(block);
153		} else {
154	<	//reach the capacity and all blocks in memory are not zero reference
155	<	loadSuccess = false;
154	>	//reach the capacity and all blocks in memory are not zero reference
155	>	loadSuccess = false;
156		}
157
158		return loadSuccess;
159	<	}
159	>	}
160
161	<	bool BlockSnapshotManager::unloadBlock(int block) {
161	>	bool BlockSnapshotManager::unloadBlock(int block) {
162		bool unloadSuccess;
163		std::vector<int>::iterator i = findActiveBlock(block);
164
165		if (i != activeBlocks_.end()){
166	<	--activeRefCount_[i - activeBlocks_.begin()];
167	<	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
168	<	//in case, unloadBlock called multiple times
169	<	activeRefCount_[i - activeBlocks_.begin()]  = 0;
170	<	}
166	>	--activeRefCount_[i - activeBlocks_.begin()];
167	>	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
168	>	//in case, unloadBlock called multiple times
169	>	activeRefCount_[i - activeBlocks_.begin()]  = 0;
170	>	}
171
172	<	unloadSuccess = true;
172	>	unloadSuccess = true;
173		} else {
174	<	unloadSuccess = false;
174	>	unloadSuccess = false;
175		}
176
177		return unloadSuccess;
178	<	}
178	>	}
179
180	<	void BlockSnapshotManager::internalLoad(int block) {
180	>	void BlockSnapshotManager::internalLoad(int block) {
181
182		for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
183	<	snapshots_[i] = loadFrame(i);
183	>	snapshots_[i] = loadFrame(i);
184		}
185
186		std::vector<int>::iterator j;
#	Line 168 | Line 188 | void BlockSnapshotManager::internalLoad(int block) {
188		assert(j != activeBlocks_.end());
189		*j = block;
190		++activeRefCount_[j - activeBlocks_.begin()];
191	<	}
191	>	}
192
193	<	void BlockSnapshotManager::internalUnload(int block) {
193	>	void BlockSnapshotManager::internalUnload(int block) {
194		for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
195	<	delete snapshots_[i];
196	<	snapshots_[i] = NULL;
195	>	delete snapshots_[i];
196	>	snapshots_[i] = NULL;
197		}
198		std::vector<int>::iterator j;
199		j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
200		assert(j != activeBlocks_.end());
201		*j = -1;
202	<	}
202	>	}
203
204	<	bool BlockSnapshotManager::hasZeroRefBlock(){
204	>	bool BlockSnapshotManager::hasZeroRefBlock(){
205		return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ?  true : false;
206	<	}
206	>	}
207
208	<	int BlockSnapshotManager::getFirstZeroRefBlock(){
209	<	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
210	<	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
211	<	}
208	>	int BlockSnapshotManager::getFirstZeroRefBlock(){
209	>	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
210	>	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
211	>	}
212
213	<	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
213	>	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
214		std::vector<int> result;
215	<	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
216	<	std::bind2nd(std::not_equal_to<int>(), -1));
215	>	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
216	>	std::bind2nd(std::not_equal_to<int>(), -1));
217		return result;
218	<	}
218	>	}
219
220	<	Snapshot* BlockSnapshotManager::loadFrame(int frame){
220	>	Snapshot* BlockSnapshotManager::loadFrame(int frame){
221		Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
222		snapshot->setID(frame);
223
#	Line 205 | Line 225 | Snapshot* BlockSnapshotManager::loadFrame(int frame){
225		Snapshot* oldSnapshot = currentSnapshot_;
226		currentSnapshot_ = snapshot;
227		reader_->readFrame(frame);
228	<	currentSnapshot_ = oldSnapshot;
228	>
229	>	// What was this for?  It doesn't make sense!
230	>	//currentSnapshot_ = oldSnapshot;
231	>
232		return snapshot;
233	<	}
233	>	}
234
235	<	int BlockSnapshotManager::getNFrames() {
235	>	int BlockSnapshotManager::getNFrames() {
236		return reader_->getNFrames();
237	<	}
237	>	}
238
239	+	void BlockSnapshotManager::needCOMprops(bool ncp) {
240	+	reader_->setNeedCOMprops(ncp);
241	+	}
242	+
243		}

Comparing:
trunk/src/brains/BlockSnapshotManager.cpp (property svn:keywords), Revision 355 by tim, Wed Feb 16 20:43:10 2005 UTC vs.
branches/development/src/brains/BlockSnapshotManager.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 0 | Line 1
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