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root/OpenMD/trunk/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.
Revision 1963 by gezelter, Thu Jan 16 15:15:17 2014 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, 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"
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),
54	<	activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) {
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 physMem = physmem_total();
65	<	double rssMem = residentMem();
66	<	double avaliablePhysMem = physMem - rssMem;
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	<	std::cout << "physmem = " << int(physMem) << "\trssMem =  "<< rssMem << "\t availablePhysMem = " << avaliablePhysMem <<std::endl;
70	<	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 (avaliablePhysMem / 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	>	if (nSnapshotPerBlock_ <= 0) {
80	>	std::cerr << "not enough memory to hold two configs!" << std::endl;
81	>	}
82	>	reader_ = new DumpReader(info, filename);
83	>	nframes_ = reader_->getNFrames();
84	>	int nblocks = nframes_ / nSnapshotPerBlock_;
85	>	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
86	>	++nblocks;
87	>	}
88
89	<	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
89	>	for (int i = 0; i < nblocks; ++i) {
90	>	blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
91	>	}
92	>	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
93	>	blocks_.back().second = nframes_;
94
95	<	reader_ = new DumpReader(info, filename);
72	<	nframes_ = reader_->getNFrames();
95	>	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
96
97	<	int nblocks = nframes_ / nSnapshotPerBlock_;
98	<	if (nframes_ % nSnapshotPerBlock_ != 0) {
99	<	++nblocks;
100	<	}
97	>	std::cout << "-----------------------------------------------------"<<std::endl;
98	>	std::cout << "BlockSnapshotManager memory report:" << std::endl;
99	>	std::cout << "\n";
100	>	// std::cout << "  Physical Memory available:\t" << (unsigned long)physMem <<  " bytes" <<std::endl;
101	>	//std::cout << "     Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
102	>	//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
103	>	std::cout << "Memory requested for OpenMD:\t" << (unsigned long)memSize_ << " bytes" <<std::endl;
104	>	std::cout << "      Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
105	>	std::cout << "            Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
106	>	std::cout << "             Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
107	>	std::cout << "       Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
108	>	std::cout << "        Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
109	>	std::cout << "     Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
110	>	std::cout << "-----------------------------------------------------"<<std::endl;
111
79	–	for (int i = 0; i < nblocks; ++i) {
80	–	blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
112		}
82	–	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
83	–	blocks_.back().second = nframes_;
113
85	–	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
86	–
87	–	}
114
115	<
90	<	BlockSnapshotManager::~BlockSnapshotManager() {
115	>	BlockSnapshotManager::~BlockSnapshotManager() {
116		currentSnapshot_ = NULL;
117		previousSnapshot_ = NULL;
118
#	Line 95 | Line 120 | BlockSnapshotManager::~BlockSnapshotManager() {
120
121		std::vector<int>::iterator i;
122		for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
123	<	if (*i != -1) {
124	<	unloadBlock(*i);
125	<	}
123	>	if (*i != -1) {
124	>	unloadBlock(*i);
125	>	}
126		}
127	<	}
127	>	}
128
129	<	int BlockSnapshotManager::getNActiveBlocks() {
129	>	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
130	>	currentSnapshot_ = snapshots_[id];
131	>	return snapshots_[id];
132	>	}
133	>
134	>	int BlockSnapshotManager::getNActiveBlocks() {
135		#ifdef __RWSTD
136		int count = 0;
137		std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
#	Line 109 | Line 139 | int BlockSnapshotManager::getNActiveBlocks() {
139		#else
140		return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
141		#endif
142	<	}
142	>	}
143
144
145
146	<	bool BlockSnapshotManager::loadBlock(int block) {
146	>	bool BlockSnapshotManager::loadBlock(int block) {
147		std::vector<int>::iterator i = findActiveBlock(block);
148		bool loadSuccess;
149		if (i != activeBlocks_.end()) {
150	<	//if block is already in memory, just increast the reference count
151	<	++activeRefCount_[i - activeBlocks_.begin()];
152	<	loadSuccess = true;
150	>	//if block is already in memory, just increast the reference count
151	>	++activeRefCount_[i - activeBlocks_.begin()];
152	>	loadSuccess = true;
153		} else if (getNActiveBlocks() < blockCapacity_){
154	<	//if number of active blocks is less than the block capacity, just load it
155	<	internalLoad(block);
156	<	loadSuccess = true;
157	<	} else if (hasZeroRefBlock() > 0) {
158	<	//if already reach the block capacity, need to unload a block with 0 reference
159	<	int zeroRefBlock = getFirstZeroRefBlock();
160	<	assert(zeroRefBlock != -1);
161	<	internalUnload(zeroRefBlock);
162	<	internalLoad(block);
154	>	//if number of active blocks is less than the block capacity, just load it
155	>	internalLoad(block);
156	>	loadSuccess = true;
157	>	} else if ( hasZeroRefBlock() ) {
158	>	//if already reach the block capacity, need to unload a block with 0 reference
159	>	int zeroRefBlock = getFirstZeroRefBlock();
160	>	assert(zeroRefBlock != -1);
161	>	internalUnload(zeroRefBlock);
162	>	internalLoad(block);
163		} else {
164	<	//reach the capacity and all blocks in memory are not zero reference
165	<	loadSuccess = false;
164	>	//reach the capacity and all blocks in memory are not zero reference
165	>	loadSuccess = false;
166		}
167
168		return loadSuccess;
169	<	}
169	>	}
170
171	<	bool BlockSnapshotManager::unloadBlock(int block) {
171	>	bool BlockSnapshotManager::unloadBlock(int block) {
172		bool unloadSuccess;
173		std::vector<int>::iterator i = findActiveBlock(block);
174
175		if (i != activeBlocks_.end()){
176	<	--activeRefCount_[i - activeBlocks_.begin()];
177	<	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
178	<	//in case, unloadBlock called multiple times
179	<	activeRefCount_[i - activeBlocks_.begin()]  = 0;
180	<	}
176	>	--activeRefCount_[i - activeBlocks_.begin()];
177	>	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
178	>	//in case, unloadBlock called multiple times
179	>	activeRefCount_[i - activeBlocks_.begin()]  = 0;
180	>	}
181
182	<	unloadSuccess = true;
182	>	unloadSuccess = true;
183		} else {
184	<	unloadSuccess = false;
184	>	unloadSuccess = false;
185		}
186
187		return unloadSuccess;
188	<	}
188	>	}
189
190	<	void BlockSnapshotManager::internalLoad(int block) {
190	>	void BlockSnapshotManager::internalLoad(int block) {
191
192		for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
193	<	snapshots_[i] = loadFrame(i);
193	>	snapshots_[i] = loadFrame(i);
194		}
195
196		std::vector<int>::iterator j;
#	Line 168 | Line 198 | void BlockSnapshotManager::internalLoad(int block) {
198		assert(j != activeBlocks_.end());
199		*j = block;
200		++activeRefCount_[j - activeBlocks_.begin()];
201	<	}
201	>	}
202
203	<	void BlockSnapshotManager::internalUnload(int block) {
203	>	void BlockSnapshotManager::internalUnload(int block) {
204		for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
205	<	delete snapshots_[i];
206	<	snapshots_[i] = NULL;
205	>	delete snapshots_[i];
206	>	snapshots_[i] = NULL;
207		}
208		std::vector<int>::iterator j;
209		j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
210		assert(j != activeBlocks_.end());
211		*j = -1;
212	<	}
212	>	}
213
214	<	bool BlockSnapshotManager::hasZeroRefBlock(){
214	>	bool BlockSnapshotManager::hasZeroRefBlock(){
215		return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ?  true : false;
216	<	}
216	>	}
217
218	<	int BlockSnapshotManager::getFirstZeroRefBlock(){
219	<	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
220	<	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
221	<	}
218	>	int BlockSnapshotManager::getFirstZeroRefBlock(){
219	>	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
220	>	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
221	>	}
222
223	<	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
223	>	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
224		std::vector<int> result;
225	<	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
226	<	std::bind2nd(std::not_equal_to<int>(), -1));
225	>	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
226	>	std::bind2nd(std::not_equal_to<int>(), -1));
227		return result;
228	<	}
228	>	}
229
230	<	Snapshot* BlockSnapshotManager::loadFrame(int frame){
231	<	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
230	>	Snapshot* BlockSnapshotManager::loadFrame(int frame){
231	>	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_,
232	>	getStorageLayout());
233		snapshot->setID(frame);
234	+	snapshot->clearDerivedProperties();
235
204	–	/** @todo fixed me */
205	–	Snapshot* oldSnapshot = currentSnapshot_;
236		currentSnapshot_ = snapshot;
237		reader_->readFrame(frame);
238	<	currentSnapshot_ = oldSnapshot;
238	>
239		return snapshot;
240	<	}
240	>	}
241
242	<	int BlockSnapshotManager::getNFrames() {
242	>	int BlockSnapshotManager::getNFrames() {
243		return reader_->getNFrames();
244	<	}
244	>	}
245
246	+	void BlockSnapshotManager::needCOMprops(bool ncp) {
247	+	reader_->setNeedCOMprops(ncp);
248	+	}
249	+
250		}

Comparing trunk/src/brains/BlockSnapshotManager.cpp (property svn:keywords):
Revision 355 by tim, Wed Feb 16 20:43:10 2005 UTC vs.
Revision 1963 by gezelter, Thu Jan 16 15:15:17 2014 UTC

#	Line 0 | Line 1
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