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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 2071 by gezelter, Sat Mar 7 21:41:51 2015 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),
57	>	blockCapacity_(blockCapacity), memSize_(memSize),
58	>	activeBlocks_(blockCapacity_, -1),
59	>	activeRefCount_(blockCapacity_, 0) {
60
61	<	nAtoms_ = info->getNGlobalAtoms();
62	<	nRigidBodies_ = info->getNGlobalRigidBodies();
61	>	nAtoms_ = info->getNGlobalAtoms();
62	>	nRigidBodies_ = info->getNGlobalRigidBodies();
63	>	nCutoffGroups_ = info->getNCutoffGroups();
64
65	<	double physMem = physmem_total();
66	<	double rssMem = residentMem();
67	<	double avaliablePhysMem = physMem - rssMem;
65	>	// eliminate suspect calls to figure out free memory:
66	>	// RealType physMem = physmem_total();
67	>	// RealType rssMem = residentMem();
68	>	// RealType avaliablePhysMem = physMem - rssMem;
69
70	<	std::cout << "physmem = " << int(physMem) << "\trssMem =  "<< rssMem << "\t availablePhysMem = " << avaliablePhysMem <<std::endl;
71	<	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
70	>	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
71	>	int bytesPerCutoffGroup = DataStorage::getBytesPerStuntDouble(DataStorage::dslPosition);
72
73	<	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
73	>	int bytesPerFrameData = Snapshot::getFrameDataSize();
74	>	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble
75	>	+ nCutoffGroups_ * bytesPerCutoffGroup
76	>	+ bytesPerFrameData;
77
78	<	int frameCapacity = int (avaliablePhysMem / bytesPerFrame);
79	<
80	<	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
78	>	// total number of frames that can fit in memory
79	>	//RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
80	>	RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame;
81
82	<	reader_ = new DumpReader(info, filename);
83	<	nframes_ = reader_->getNFrames();
84	<
85	<	int nblocks = nframes_ / nSnapshotPerBlock_;
86	<	if (nframes_ % nSnapshotPerBlock_ != 0) {
82	>	// number of frames in each block given the need to hold multiple blocks
83	>	// in memory at the same time:
84	>	nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
85	>	if (nSnapshotPerBlock_ <= 0) {
86	>	std::cerr << "not enough memory to hold two configs!" << std::endl;
87	>	}
88	>	reader_ = new DumpReader(info, filename);
89	>	nframes_ = reader_->getNFrames();
90	>	int nblocks = nframes_ / nSnapshotPerBlock_;
91	>	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
92		++nblocks;
93	<	}
93	>	}
94
95	<	for (int i = 0; i < nblocks; ++i) {
95	>	for (int i = 0; i < nblocks; ++i) {
96		blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
97	<	}
98	<	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
99	<	blocks_.back().second = nframes_;
97	>	}
98	>	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
99	>	blocks_.back().second = nframes_;
100
101	<	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
101	>	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
102	>
103	>	std::cout << "-----------------------------------------------------"
104	>	<< std::endl;
105	>	std::cout << "BlockSnapshotManager memory report:" << std::endl;
106	>	std::cout << "\n";
107	>	// std::cout << "  Physical Memory available:\t" << (unsigned long)physMem <<  " bytes" <<std::endl;
108	>	//std::cout << "     Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
109	>	//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
110	>	std::cout << "Memory requested for OpenMD:\t"
111	>	<< (unsigned long)memSize_ << " bytes" << std::endl;
112	>	std::cout << "        Bytes per FrameData:\t"
113	>	<< (unsigned long)bytesPerFrameData << std::endl;
114	>	std::cout << "      Bytes per StuntDouble:\t"
115	>	<< (unsigned long)bytesPerStuntDouble << std::endl;
116	>	std::cout << "     Bytes per Cutoff Group:\t"
117	>	<< (unsigned long)bytesPerCutoffGroup << std::endl;
118	>	std::cout << "            Bytes per Frame:\t"
119	>	<< (unsigned long)bytesPerFrame << std::endl;
120	>	std::cout << "             Frame Capacity:\t"
121	>	<< (unsigned long)frameCapacity << std::endl;
122	>	std::cout << "       Frames in trajectory:\t"
123	>	<< (unsigned long)nframes_ << std::endl;
124	>	std::cout << "        Snapshots per Block:\t"
125	>	<< (unsigned long)nSnapshotPerBlock_ << std::endl;
126	>	std::cout << "     Total number of Blocks:\t"
127	>	<< (unsigned long)nblocks << std::endl;
128	>	std::cout << "-----------------------------------------------------"
129	>	<< std::endl;
130
131	<	}
131	>	}
132
133
134	<	BlockSnapshotManager::~BlockSnapshotManager() {
134	>	BlockSnapshotManager::~BlockSnapshotManager() {
135		currentSnapshot_ = NULL;
136		previousSnapshot_ = NULL;
137
#	Line 95 | Line 139 | BlockSnapshotManager::~BlockSnapshotManager() {
139
140		std::vector<int>::iterator i;
141		for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
142	<	if (*i != -1) {
143	<	unloadBlock(*i);
144	<	}
142	>	if (*i != -1) {
143	>	unloadBlock(*i);
144	>	}
145		}
146	<	}
146	>	}
147
148	<	int BlockSnapshotManager::getNActiveBlocks() {
148	>	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
149	>	currentSnapshot_ = snapshots_[id];
150	>	return snapshots_[id];
151	>	}
152	>
153	>	int BlockSnapshotManager::getNActiveBlocks() {
154		#ifdef __RWSTD
155		int count = 0;
156		std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
#	Line 109 | Line 158 | int BlockSnapshotManager::getNActiveBlocks() {
158		#else
159		return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
160		#endif
161	<	}
161	>	}
162
163
164
165	<	bool BlockSnapshotManager::loadBlock(int block) {
165	>	bool BlockSnapshotManager::loadBlock(int block) {
166		std::vector<int>::iterator i = findActiveBlock(block);
167	<	bool loadSuccess;
167	>	bool loadSuccess(false);
168		if (i != activeBlocks_.end()) {
169	<	//if block is already in memory, just increast the reference count
170	<	++activeRefCount_[i - activeBlocks_.begin()];
171	<	loadSuccess = true;
169	>	// If the block is already in memory, just increase the
170	>	// reference count:
171	>	++activeRefCount_[i - activeBlocks_.begin()];
172	>	loadSuccess = true;
173		} else if (getNActiveBlocks() < blockCapacity_){
174	<	//if number of active blocks is less than the block capacity, just load it
175	<	internalLoad(block);
176	<	loadSuccess = true;
177	<	} else if (hasZeroRefBlock() > 0) {
178	<	//if already reach the block capacity, need to unload a block with 0 reference
179	<	int zeroRefBlock = getFirstZeroRefBlock();
180	<	assert(zeroRefBlock != -1);
181	<	internalUnload(zeroRefBlock);
182	<	internalLoad(block);
174	>	// If the number of active blocks is less than the block
175	>	// capacity, just load the block:
176	>	internalLoad(block);
177	>	loadSuccess = true;
178	>	} else if ( hasZeroRefBlock() ) {
179	>	// If we have already reached the block capacity, we need to
180	>	// unload a block with 0 references:
181	>	int zeroRefBlock = getFirstZeroRefBlock();
182	>	assert(zeroRefBlock != -1);
183	>	internalUnload(zeroRefBlock);
184	>	internalLoad(block);
185		} else {
186	<	//reach the capacity and all blocks in memory are not zero reference
187	<	loadSuccess = false;
188	<	}
189	<
186	>	// We have reached capacity and all blocks in memory are have
187	>	// non-zero references:
188	>	loadSuccess = false;
189	>	}
190		return loadSuccess;
191	<	}
191	>	}
192
193	<	bool BlockSnapshotManager::unloadBlock(int block) {
193	>	bool BlockSnapshotManager::unloadBlock(int block) {
194		bool unloadSuccess;
195		std::vector<int>::iterator i = findActiveBlock(block);
196
197		if (i != activeBlocks_.end()){
198	<	--activeRefCount_[i - activeBlocks_.begin()];
199	<	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
200	<	//in case, unloadBlock called multiple times
201	<	activeRefCount_[i - activeBlocks_.begin()]  = 0;
202	<	}
198	>	--activeRefCount_[i - activeBlocks_.begin()];
199	>	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
200	>	//in case, unloadBlock called multiple times
201	>	activeRefCount_[i - activeBlocks_.begin()]  = 0;
202	>	}
203	>
204	>	if (activeRefCount_[i-activeBlocks_.begin()] == 0) {
205	>	internalUnload(block);
206	>	}
207
208	<	unloadSuccess = true;
208	>	unloadSuccess = true;
209		} else {
210	<	unloadSuccess = false;
210	>	unloadSuccess = false;
211		}
212
213		return unloadSuccess;
214	<	}
214	>	}
215
216	<	void BlockSnapshotManager::internalLoad(int block) {
216	>	void BlockSnapshotManager::internalLoad(int block) {
217
218		for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
219	<	snapshots_[i] = loadFrame(i);
219	>	snapshots_[i] = loadFrame(i);
220		}
221
222		std::vector<int>::iterator j;
#	Line 168 | Line 224 | void BlockSnapshotManager::internalLoad(int block) {
224		assert(j != activeBlocks_.end());
225		*j = block;
226		++activeRefCount_[j - activeBlocks_.begin()];
227	<	}
227	>	}
228
229	<	void BlockSnapshotManager::internalUnload(int block) {
229	>	void BlockSnapshotManager::internalUnload(int block) {
230	>	std::cerr << "called internal unload for block "<< block << "\n";
231		for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
232	<	delete snapshots_[i];
233	<	snapshots_[i] = NULL;
232	>	delete snapshots_[i];
233	>	snapshots_[i] = NULL;
234		}
235		std::vector<int>::iterator j;
236		j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
237		assert(j != activeBlocks_.end());
238		*j = -1;
239	<	}
239	>	}
240
241	<	bool BlockSnapshotManager::hasZeroRefBlock(){
241	>	bool BlockSnapshotManager::hasZeroRefBlock(){
242		return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ?  true : false;
243	<	}
243	>	}
244
245	<	int BlockSnapshotManager::getFirstZeroRefBlock(){
246	<	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
247	<	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
248	<	}
245	>	int BlockSnapshotManager::getFirstZeroRefBlock(){
246	>	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
247	>	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
248	>	}
249
250	<	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
250	>	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
251		std::vector<int> result;
252	<	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
253	<	std::bind2nd(std::not_equal_to<int>(), -1));
252	>	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
253	>	std::bind2nd(std::not_equal_to<int>(), -1));
254		return result;
255	<	}
255	>	}
256
257	<	Snapshot* BlockSnapshotManager::loadFrame(int frame){
258	<	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
257	>	Snapshot* BlockSnapshotManager::loadFrame(int frame){
258	>	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_,
259	>	getStorageLayout());
260		snapshot->setID(frame);
261	+	snapshot->clearDerivedProperties();
262
204	–	/** @todo fixed me */
205	–	Snapshot* oldSnapshot = currentSnapshot_;
263		currentSnapshot_ = snapshot;
264		reader_->readFrame(frame);
265	<	currentSnapshot_ = oldSnapshot;
265	>
266		return snapshot;
267	<	}
267	>	}
268
269	<	int BlockSnapshotManager::getNFrames() {
269	>	int BlockSnapshotManager::getNFrames() {
270		return reader_->getNFrames();
271	<	}
271	>	}
272
273	+	void BlockSnapshotManager::needCOMprops(bool ncp) {
274	+	reader_->setNeedCOMprops(ncp);
275	+	}
276	+
277		}

Comparing trunk/src/brains/BlockSnapshotManager.cpp (property svn:keywords):
Revision 355 by tim, Wed Feb 16 20:43:10 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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