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

Comparing:
trunk/src/brains/BlockSnapshotManager.cpp (file contents), Revision 324 by tim, Sun Feb 13 19:10:25 2005 UTC vs.
branches/development/src/brains/BlockSnapshotManager.cpp (file contents), Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 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]  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/physmem.h"
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 oopse {
51	<	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
52	<	int storageLayout, int blockCapacity)
53	<	: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1) {
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), memSize_(memSize),
57	>	blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1),
58	>	activeRefCount_(blockCapacity_, 0) {
59
60	<	nAtoms_ = info->getNGlobalAtoms();
61	<	nRigidBodies_ = info->getNGlobalRigidBodies();
60	>	nAtoms_ = info->getNGlobalAtoms();
61	>	nRigidBodies_ = info->getNGlobalRigidBodies();
62	>	nCutoffGroups_ = info->getNCutoffGroups();
63
64	<	double avalPhysMem = physmem_available();
64	>	// eliminate suspect calls to figure out free memory:
65	>	// RealType physMem = physmem_total();
66	>	// RealType rssMem = residentMem();
67	>	// RealType avaliablePhysMem = physMem - rssMem;
68
69	<	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
69	>	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
70	>	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
71
72	<	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
72	>	// total number of frames that can fit in memory
73	>	//RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
74	>	RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame;
75
76	<	int frameCapacity = int (avalPhysMem / bytesPerFrame);
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	>	reader_ = new DumpReader(info, filename);
80	>	nframes_ = reader_->getNFrames();
81	>	int nblocks = nframes_ / nSnapshotPerBlock_;
82	>	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
83	>	++nblocks;
84	>	}
85
86	<	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
86	>	for (int i = 0; i < nblocks; ++i) {
87	>	blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
88	>	}
89	>	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
90	>	blocks_.back().second = nframes_;
91
92	<	reader_ = new DumpReader(info, filename);
67	<	nframes_ = reader_->getNFrames();
92	>	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
93
94	<	int nblocks = nframes_ / nSnapshotPerBlock_;
95	<	if (nframes_ % nSnapshotPerBlock_ != 0) {
96	<	++nblocks;
97	<	}
94	>	std::cout << "-----------------------------------------------------"<<std::endl;
95	>	std::cout << "BlockSnapshotManager memory report:" << std::endl;
96	>	std::cout << "\n";
97	>	// std::cout << "  Physical Memory available:\t" << (unsigned long)physMem <<  " bytes" <<std::endl;
98	>	//std::cout << "     Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
99	>	//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
100	>	std::cout << "Memory requested for OpenMD:\t" << (unsigned long)memSize_ << " bytes" <<std::endl;
101	>	std::cout << "      Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
102	>	std::cout << "            Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
103	>	std::cout << "             Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
104	>	std::cout << "       Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
105	>	std::cout << "        Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
106	>	std::cout << "     Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
107	>	std::cout << "-----------------------------------------------------"<<std::endl;
108
74	–	for (int i = 0; i < nblocks; ++i) {
75	–	blocks_.push_back(SnapshotBlock(i, (i+1)*nSnapshotPerBlock_));
109		}
77	–	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
78	–	blocks_.back().second = nframes_;
110
80	–	snapshots_.insert(snapshots_.begin(), nframes_, NULL);
81	–
82	–	}
111
112	<
85	<	BlockSnapshotManager::~BlockSnapshotManager() {
112	>	BlockSnapshotManager::~BlockSnapshotManager() {
113		currentSnapshot_ = NULL;
114		previousSnapshot_ = NULL;
115
#	Line 90 | Line 117 | BlockSnapshotManager::~BlockSnapshotManager() {
117
118		std::vector<int>::iterator i;
119		for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
120	<	if (*i != -1) {
121	<	unloadBlock(*i);
122	<	}
120	>	if (*i != -1) {
121	>	unloadBlock(*i);
122	>	}
123		}
124	<	}
124	>	}
125
126	<	int BlockSnapshotManager::getNActiveBlocks() {
126	>	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
127	>	currentSnapshot_ = snapshots_[id];
128	>	return snapshots_[id];
129	>	}
130	>
131	>	int BlockSnapshotManager::getNActiveBlocks() {
132	>	#ifdef __RWSTD
133	>	int count = 0;
134	>	std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
135	>	return count;
136	>	#else
137		return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
138	<	}
138	>	#endif
139	>	}
140
103	–	bool BlockSnapshotManager::isBlockActive(int block) {
104	–	return std::find(activeBlocks_.begin(), activeBlocks_.end(), block) != activeBlocks_.end() ? true : false;
105	–	}
141
142	<	bool BlockSnapshotManager::loadBlock(int block) {
142	>
143	>	bool BlockSnapshotManager::loadBlock(int block) {
144	>	std::vector<int>::iterator i = findActiveBlock(block);
145		bool loadSuccess;
146	<	if (isBlockActive(block)) {
147	<	loadSuccess = true;
146	>	if (i != activeBlocks_.end()) {
147	>	//if block is already in memory, just increast the reference count
148	>	++activeRefCount_[i - activeBlocks_.begin()];
149	>	loadSuccess = true;
150		} else if (getNActiveBlocks() < blockCapacity_){
151	<
152	<	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
153	<	snapshots_[i] = loadFrame(i);
154	<	}
155	<
156	<	std::vector<int>::iterator j;
157	<	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
158	<	assert(j != activeBlocks_.end());
159	<	*j = block;
160	<	loadSuccess = true;
161	<	}else {
162	<	loadSuccess = false;
151	>	//if number of active blocks is less than the block capacity, just load it
152	>	internalLoad(block);
153	>	loadSuccess = true;
154	>	} else if ( hasZeroRefBlock() ) {
155	>	//if already reach the block capacity, need to unload a block with 0 reference
156	>	int zeroRefBlock = getFirstZeroRefBlock();
157	>	assert(zeroRefBlock != -1);
158	>	internalUnload(zeroRefBlock);
159	>	internalLoad(block);
160	>	} else {
161	>	//reach the capacity and all blocks in memory are not zero reference
162	>	loadSuccess = false;
163		}
164	<
164	>
165		return loadSuccess;
166	<	}
166	>	}
167
168	<	bool BlockSnapshotManager::unloadBlock(int block) {
168	>	bool BlockSnapshotManager::unloadBlock(int block) {
169		bool unloadSuccess;
170	<	if (!isBlockActive(block)){
171	<	unloadSuccess = false;
170	>	std::vector<int>::iterator i = findActiveBlock(block);
171	>
172	>	if (i != activeBlocks_.end()){
173	>	--activeRefCount_[i - activeBlocks_.begin()];
174	>	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
175	>	//in case, unloadBlock called multiple times
176	>	activeRefCount_[i - activeBlocks_.begin()]  = 0;
177	>	}
178	>
179	>	unloadSuccess = true;
180		} else {
181	<	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
135	<	delete snapshots_[i];
136	<	snapshots_[i] = NULL;
137	<	}
138	<	std::vector<int>::iterator j;
139	<	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
140	<	assert(j != activeBlocks_.end());
141	<	*j = -1;
142	<	unloadSuccess = true;
181	>	unloadSuccess = false;
182		}
183
184		return unloadSuccess;
185	<	}
185	>	}
186
187	<	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
187	>	void BlockSnapshotManager::internalLoad(int block) {
188	>
189	>	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
190	>	snapshots_[i] = loadFrame(i);
191	>	}
192	>
193	>	std::vector<int>::iterator j;
194	>	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
195	>	assert(j != activeBlocks_.end());
196	>	*j = block;
197	>	++activeRefCount_[j - activeBlocks_.begin()];
198	>	}
199	>
200	>	void BlockSnapshotManager::internalUnload(int block) {
201	>	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
202	>	delete snapshots_[i];
203	>	snapshots_[i] = NULL;
204	>	}
205	>	std::vector<int>::iterator j;
206	>	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
207	>	assert(j != activeBlocks_.end());
208	>	*j = -1;
209	>	}
210	>
211	>	bool BlockSnapshotManager::hasZeroRefBlock(){
212	>	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ?  true : false;
213	>	}
214	>
215	>	int BlockSnapshotManager::getFirstZeroRefBlock(){
216	>	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
217	>	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
218	>	}
219	>
220	>	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
221		std::vector<int> result;
222	<	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
223	<	std::bind2nd(std::not_equal_to<int>(), -1));
222	>	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
223	>	std::bind2nd(std::not_equal_to<int>(), -1));
224		return result;
225	<	}
225	>	}
226
227	<	Snapshot* BlockSnapshotManager::loadFrame(int frame){
228	<	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
227	>	Snapshot* BlockSnapshotManager::loadFrame(int frame){
228	>	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_,
229	>	getStorageLayout());
230		snapshot->setID(frame);
231	+	snapshot->clearDerivedProperties();
232
159	–	/** @todo fixed me */
160	–	Snapshot* oldSnapshot = currentSnapshot_;
233		currentSnapshot_ = snapshot;
234		reader_->readFrame(frame);
235	<	currentSnapshot_ = oldSnapshot;
235	>
236		return snapshot;
237	<	}
237	>	}
238
239	<	int BlockSnapshotManager::getNFrames() {
239	>	int BlockSnapshotManager::getNFrames() {
240		return reader_->getNFrames();
241	<	}
241	>	}
242
243	+	void BlockSnapshotManager::needCOMprops(bool ncp) {
244	+	reader_->setNeedCOMprops(ncp);
245	+	}
246	+
247		}

Comparing:
trunk/src/brains/BlockSnapshotManager.cpp (property svn:keywords), Revision 324 by tim, Sun Feb 13 19:10:25 2005 UTC vs.
branches/development/src/brains/BlockSnapshotManager.cpp (property svn:keywords), Revision 1825 by gezelter, Wed Jan 9 19:27:52 2013 UTC

#	Line 0 | Line 1
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