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

Comparing:
trunk/src/brains/BlockSnapshotManager.cpp (file contents), Revision 347 by tim, Tue Feb 15 17:11:35 2005 UTC vs.
branches/development/src/brains/BlockSnapshotManager.cpp (file contents), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 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"
43	<	#include "utils/physmem.h"
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 oopse {
50	<	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
51	<	int storageLayout, int blockCapacity)
52	<	: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1) {
49	>	namespace OpenMD {
50	>	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info,
51	>	const std::string& filename,
52	>	int storageLayout,
53	>	long long int memSize,
54	>	int blockCapacity)
55	>	: SnapshotManager(storageLayout), info_(info), memSize_(memSize),
56	>	blockCapacity_(blockCapacity), activeBlocks_(blockCapacity_, -1),
57	>	activeRefCount_(blockCapacity_, 0) {
58
59	<	nAtoms_ = info->getNGlobalAtoms();
60	<	nRigidBodies_ = info->getNGlobalRigidBodies();
59	>	nAtoms_ = info->getNGlobalAtoms();
60	>	nRigidBodies_ = info->getNGlobalRigidBodies();
61	>	nCutoffGroups_ = info->getNCutoffGroups();
62
63	<	double avalPhysMem = physmem_available();
63	>	// eliminate suspect calls to figure out free memory:
64	>	// RealType physMem = physmem_total();
65	>	// RealType rssMem = residentMem();
66	>	// RealType avaliablePhysMem = physMem - rssMem;
67
68	<	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
68	>	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
69	>	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
70
71	<	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
71	>	// total number of frames that can fit in memory
72	>	//RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
73	>	RealType frameCapacity = memSize_ / bytesPerFrame;
74
75	<	int frameCapacity = int (avalPhysMem / bytesPerFrame);
75	>	// number of frames in each block given the need to hold multiple blocks
76	>	// in memory at the same time:
77	>	nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
78	>	reader_ = new DumpReader(info, filename);
79	>	nframes_ = reader_->getNFrames();
80	>	int nblocks = nframes_ / nSnapshotPerBlock_;
81	>	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
82	>	++nblocks;
83	>	}
84
85	<	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
85	>	for (int i = 0; i < nblocks; ++i) {
86	>	blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
87	>	}
88	>	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
89	>	blocks_.back().second = nframes_;
90
91	<	reader_ = new DumpReader(info, filename);
67	<	nframes_ = reader_->getNFrames();
91	>	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
92
93	<	int nblocks = nframes_ / nSnapshotPerBlock_;
94	<	if (nframes_ % nSnapshotPerBlock_ != 0) {
95	<	++nblocks;
96	<	}
93	>	std::cout << "-----------------------------------------------------"<<std::endl;
94	>	std::cout << "BlockSnapshotManager memory report:" << std::endl;
95	>	std::cout << "\n";
96	>	// std::cout << "  Physical Memory available:\t" << (unsigned long)physMem <<  " bytes" <<std::endl;
97	>	//std::cout << "     Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
98	>	//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
99	>	std::cout << "Memory requested for OpenMD:\t" << (unsigned long)memSize_ << " bytes" <<std::endl;
100	>	std::cout << "      Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
101	>	std::cout << "            Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
102	>	std::cout << "             Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
103	>	std::cout << "       Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
104	>	std::cout << "        Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
105	>	std::cout << "     Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
106	>	std::cout << "-----------------------------------------------------"<<std::endl;
107
74	–	for (int i = 0; i < nblocks; ++i) {
75	–	blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
108		}
77	–	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
78	–	blocks_.back().second = nframes_;
109
80	–	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
81	–
82	–	}
110
111	<
85	<	BlockSnapshotManager::~BlockSnapshotManager() {
111	>	BlockSnapshotManager::~BlockSnapshotManager() {
112		currentSnapshot_ = NULL;
113		previousSnapshot_ = NULL;
114
#	Line 90 | Line 116 | BlockSnapshotManager::~BlockSnapshotManager() {
116
117		std::vector<int>::iterator i;
118		for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
119	<	if (*i != -1) {
120	<	unloadBlock(*i);
121	<	}
119	>	if (*i != -1) {
120	>	unloadBlock(*i);
121	>	}
122		}
123	<	}
123	>	}
124
125	<	int BlockSnapshotManager::getNActiveBlocks() {
125	>	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
126	>	currentSnapshot_ = snapshots_[id];
127	>	return snapshots_[id];
128	>	}
129	>
130	>	int BlockSnapshotManager::getNActiveBlocks() {
131		#ifdef __RWSTD
132		int count = 0;
133		std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
#	Line 104 | Line 135 | int BlockSnapshotManager::getNActiveBlocks() {
135		#else
136		return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
137		#endif
138	<	}
138	>	}
139
109	–	bool BlockSnapshotManager::isBlockActive(int block) {
110	–	return std::find(activeBlocks_.begin(), activeBlocks_.end(), block) != activeBlocks_.end() ? true : false;
111	–	}
140
141	<	bool BlockSnapshotManager::loadBlock(int block) {
141	>
142	>	bool BlockSnapshotManager::loadBlock(int block) {
143	>	std::vector<int>::iterator i = findActiveBlock(block);
144		bool loadSuccess;
145	<	if (isBlockActive(block)) {
146	<	loadSuccess = true;
145	>	if (i != activeBlocks_.end()) {
146	>	//if block is already in memory, just increast the reference count
147	>	++activeRefCount_[i - activeBlocks_.begin()];
148	>	loadSuccess = true;
149		} else if (getNActiveBlocks() < blockCapacity_){
150	<
151	<	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
152	<	snapshots_[i] = loadFrame(i);
153	<	}
154	<
155	<	std::vector<int>::iterator j;
156	<	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
157	<	assert(j != activeBlocks_.end());
158	<	*j = block;
159	<	loadSuccess = true;
160	<	}else {
161	<	loadSuccess = false;
150	>	//if number of active blocks is less than the block capacity, just load it
151	>	internalLoad(block);
152	>	loadSuccess = true;
153	>	} else if (hasZeroRefBlock() > 0) {
154	>	//if already reach the block capacity, need to unload a block with 0 reference
155	>	int zeroRefBlock = getFirstZeroRefBlock();
156	>	assert(zeroRefBlock != -1);
157	>	internalUnload(zeroRefBlock);
158	>	internalLoad(block);
159	>	} else {
160	>	//reach the capacity and all blocks in memory are not zero reference
161	>	loadSuccess = false;
162		}
163	<
163	>
164		return loadSuccess;
165	<	}
165	>	}
166
167	<	bool BlockSnapshotManager::unloadBlock(int block) {
167	>	bool BlockSnapshotManager::unloadBlock(int block) {
168		bool unloadSuccess;
169	<	if (!isBlockActive(block)){
170	<	unloadSuccess = false;
169	>	std::vector<int>::iterator i = findActiveBlock(block);
170	>
171	>	if (i != activeBlocks_.end()){
172	>	--activeRefCount_[i - activeBlocks_.begin()];
173	>	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
174	>	//in case, unloadBlock called multiple times
175	>	activeRefCount_[i - activeBlocks_.begin()]  = 0;
176	>	}
177	>
178	>	unloadSuccess = true;
179		} else {
180	<	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
141	<	delete snapshots_[i];
142	<	snapshots_[i] = NULL;
143	<	}
144	<	std::vector<int>::iterator j;
145	<	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
146	<	assert(j != activeBlocks_.end());
147	<	*j = -1;
148	<	unloadSuccess = true;
180	>	unloadSuccess = false;
181		}
182
183		return unloadSuccess;
184	<	}
184	>	}
185
186	<	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
186	>	void BlockSnapshotManager::internalLoad(int block) {
187	>
188	>	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
189	>	snapshots_[i] = loadFrame(i);
190	>	}
191	>
192	>	std::vector<int>::iterator j;
193	>	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
194	>	assert(j != activeBlocks_.end());
195	>	*j = block;
196	>	++activeRefCount_[j - activeBlocks_.begin()];
197	>	}
198	>
199	>	void BlockSnapshotManager::internalUnload(int block) {
200	>	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
201	>	delete snapshots_[i];
202	>	snapshots_[i] = NULL;
203	>	}
204	>	std::vector<int>::iterator j;
205	>	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
206	>	assert(j != activeBlocks_.end());
207	>	*j = -1;
208	>	}
209	>
210	>	bool BlockSnapshotManager::hasZeroRefBlock(){
211	>	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ?  true : false;
212	>	}
213	>
214	>	int BlockSnapshotManager::getFirstZeroRefBlock(){
215	>	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
216	>	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
217	>	}
218	>
219	>	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
220		std::vector<int> result;
221	<	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
222	<	std::bind2nd(std::not_equal_to<int>(), -1));
221	>	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
222	>	std::bind2nd(std::not_equal_to<int>(), -1));
223		return result;
224	<	}
224	>	}
225
226	<	Snapshot* BlockSnapshotManager::loadFrame(int frame){
227	<	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
226	>	Snapshot* BlockSnapshotManager::loadFrame(int frame){
227	>	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_, getStorageLayout());
228		snapshot->setID(frame);
229
230		/** @todo fixed me */
231		Snapshot* oldSnapshot = currentSnapshot_;
232		currentSnapshot_ = snapshot;
233		reader_->readFrame(frame);
234	<	currentSnapshot_ = oldSnapshot;
234	>
235	>	// What was this for?  It doesn't make sense!
236	>	//currentSnapshot_ = oldSnapshot;
237	>
238		return snapshot;
239	<	}
239	>	}
240
241	<	int BlockSnapshotManager::getNFrames() {
241	>	int BlockSnapshotManager::getNFrames() {
242		return reader_->getNFrames();
243	<	}
243	>	}
244
245	+	void BlockSnapshotManager::needCOMprops(bool ncp) {
246	+	reader_->setNeedCOMprops(ncp);
247	+	}
248	+
249		}

Comparing:
trunk/src/brains/BlockSnapshotManager.cpp (property svn:keywords), Revision 347 by tim, Tue Feb 15 17:11:35 2005 UTC vs.
branches/development/src/brains/BlockSnapshotManager.cpp (property svn:keywords), Revision 1629 by gezelter, Wed Sep 14 21:15:17 2011 UTC

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