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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 1966 by gezelter, Fri Jan 24 14:17:42 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 bytesPerCutoffGroup = DataStorage::getBytesPerStuntDouble(DataStorage::dslPosition);
71
72	<	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
72	>	int bytesPerFrameData = Snapshot::getFrameDataSize();
73	>	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble
74	>	+ nCutoffGroups_ * bytesPerCutoffGroup
75	>	+ bytesPerFrameData;
76
77	<	int frameCapacity = int (avaliablePhysMem / bytesPerFrame);
78	<
79	<	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
77	>	// total number of frames that can fit in memory
78	>	//RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
79	>	RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame;
80
81	<	reader_ = new DumpReader(info, filename);
82	<	nframes_ = reader_->getNFrames();
83	<
84	<	int nblocks = nframes_ / nSnapshotPerBlock_;
85	<	if (nframes_ % nSnapshotPerBlock_ != 0) {
81	>	// number of frames in each block given the need to hold multiple blocks
82	>	// in memory at the same time:
83	>	nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
84	>	if (nSnapshotPerBlock_ <= 0) {
85	>	std::cerr << "not enough memory to hold two configs!" << std::endl;
86	>	}
87	>	reader_ = new DumpReader(info, filename);
88	>	nframes_ = reader_->getNFrames();
89	>	int nblocks = nframes_ / nSnapshotPerBlock_;
90	>	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
91		++nblocks;
92	<	}
92	>	}
93
94	<	for (int i = 0; i < nblocks; ++i) {
94	>	for (int i = 0; i < nblocks; ++i) {
95		blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
96	<	}
97	<	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
98	<	blocks_.back().second = nframes_;
96	>	}
97	>	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
98	>	blocks_.back().second = nframes_;
99
100	<	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
100	>	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
101	>
102	>	std::cout << "-----------------------------------------------------"
103	>	<< std::endl;
104	>	std::cout << "BlockSnapshotManager memory report:" << std::endl;
105	>	std::cout << "\n";
106	>	// std::cout << "  Physical Memory available:\t" << (unsigned long)physMem <<  " bytes" <<std::endl;
107	>	//std::cout << "     Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
108	>	//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
109	>	std::cout << "Memory requested for OpenMD:\t"
110	>	<< (unsigned long)memSize_ << " bytes" << std::endl;
111	>	std::cout << "        Bytes per FrameData:\t"
112	>	<< (unsigned long)bytesPerFrameData << std::endl;
113	>	std::cout << "      Bytes per StuntDouble:\t"
114	>	<< (unsigned long)bytesPerStuntDouble << std::endl;
115	>	std::cout << "     Bytes per Cutoff Group:\t"
116	>	<< (unsigned long)bytesPerCutoffGroup << std::endl;
117	>	std::cout << "            Bytes per Frame:\t"
118	>	<< (unsigned long)bytesPerFrame << std::endl;
119	>	std::cout << "             Frame Capacity:\t"
120	>	<< (unsigned long)frameCapacity << std::endl;
121	>	std::cout << "       Frames in trajectory:\t"
122	>	<< (unsigned long)nframes_ << std::endl;
123	>	std::cout << "        Snapshots per Block:\t"
124	>	<< (unsigned long)nSnapshotPerBlock_ << std::endl;
125	>	std::cout << "     Total number of Blocks:\t"
126	>	<< (unsigned long)nblocks << std::endl;
127	>	std::cout << "-----------------------------------------------------"
128	>	<< std::endl;
129
130	<	}
130	>	}
131
132
133	<	BlockSnapshotManager::~BlockSnapshotManager() {
133	>	BlockSnapshotManager::~BlockSnapshotManager() {
134		currentSnapshot_ = NULL;
135		previousSnapshot_ = NULL;
136
#	Line 95 | Line 138 | BlockSnapshotManager::~BlockSnapshotManager() {
138
139		std::vector<int>::iterator i;
140		for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
141	<	if (*i != -1) {
142	<	unloadBlock(*i);
143	<	}
141	>	if (*i != -1) {
142	>	unloadBlock(*i);
143	>	}
144		}
145	<	}
145	>	}
146
147	<	int BlockSnapshotManager::getNActiveBlocks() {
147	>	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
148	>	currentSnapshot_ = snapshots_[id];
149	>	return snapshots_[id];
150	>	}
151	>
152	>	int BlockSnapshotManager::getNActiveBlocks() {
153		#ifdef __RWSTD
154		int count = 0;
155		std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
#	Line 109 | Line 157 | int BlockSnapshotManager::getNActiveBlocks() {
157		#else
158		return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
159		#endif
160	<	}
160	>	}
161
162
163
164	<	bool BlockSnapshotManager::loadBlock(int block) {
164	>	bool BlockSnapshotManager::loadBlock(int block) {
165		std::vector<int>::iterator i = findActiveBlock(block);
166		bool loadSuccess;
167		if (i != activeBlocks_.end()) {
168	<	//if block is already in memory, just increast the reference count
169	<	++activeRefCount_[i - activeBlocks_.begin()];
170	<	loadSuccess = true;
168	>	//if block is already in memory, just increast the reference count
169	>	++activeRefCount_[i - activeBlocks_.begin()];
170	>	loadSuccess = true;
171		} else if (getNActiveBlocks() < blockCapacity_){
172	<	//if number of active blocks is less than the block capacity, just load it
173	<	internalLoad(block);
174	<	loadSuccess = true;
175	<	} else if (hasZeroRefBlock() > 0) {
176	<	//if already reach the block capacity, need to unload a block with 0 reference
177	<	int zeroRefBlock = getFirstZeroRefBlock();
178	<	assert(zeroRefBlock != -1);
179	<	internalUnload(zeroRefBlock);
180	<	internalLoad(block);
172	>	//if number of active blocks is less than the block capacity, just load it
173	>	internalLoad(block);
174	>	loadSuccess = true;
175	>	} else if ( hasZeroRefBlock() ) {
176	>	//if already reach the block capacity, need to unload a block with 0 reference
177	>	int zeroRefBlock = getFirstZeroRefBlock();
178	>	assert(zeroRefBlock != -1);
179	>	internalUnload(zeroRefBlock);
180	>	internalLoad(block);
181		} else {
182	<	//reach the capacity and all blocks in memory are not zero reference
183	<	loadSuccess = false;
182	>	//reach the capacity and all blocks in memory are not zero reference
183	>	loadSuccess = false;
184		}
185
186		return loadSuccess;
187	<	}
187	>	}
188
189	<	bool BlockSnapshotManager::unloadBlock(int block) {
189	>	bool BlockSnapshotManager::unloadBlock(int block) {
190		bool unloadSuccess;
191		std::vector<int>::iterator i = findActiveBlock(block);
192
193		if (i != activeBlocks_.end()){
194	<	--activeRefCount_[i - activeBlocks_.begin()];
195	<	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
196	<	//in case, unloadBlock called multiple times
197	<	activeRefCount_[i - activeBlocks_.begin()]  = 0;
198	<	}
194	>	--activeRefCount_[i - activeBlocks_.begin()];
195	>	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
196	>	//in case, unloadBlock called multiple times
197	>	activeRefCount_[i - activeBlocks_.begin()]  = 0;
198	>	}
199	>
200	>	if (activeRefCount_[i-activeBlocks_.begin()] == 0) {
201	>	internalUnload(block);
202	>	}
203
204	<	unloadSuccess = true;
204	>	unloadSuccess = true;
205		} else {
206	<	unloadSuccess = false;
206	>	unloadSuccess = false;
207		}
208
209		return unloadSuccess;
210	<	}
210	>	}
211
212	<	void BlockSnapshotManager::internalLoad(int block) {
212	>	void BlockSnapshotManager::internalLoad(int block) {
213
214		for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
215	<	snapshots_[i] = loadFrame(i);
215	>	snapshots_[i] = loadFrame(i);
216		}
217
218		std::vector<int>::iterator j;
#	Line 168 | Line 220 | void BlockSnapshotManager::internalLoad(int block) {
220		assert(j != activeBlocks_.end());
221		*j = block;
222		++activeRefCount_[j - activeBlocks_.begin()];
223	<	}
223	>	}
224
225	<	void BlockSnapshotManager::internalUnload(int block) {
225	>	void BlockSnapshotManager::internalUnload(int block) {
226	>	std::cerr << "called internal unload for block "<< block << "\n";
227		for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
228	<	delete snapshots_[i];
229	<	snapshots_[i] = NULL;
228	>	delete snapshots_[i];
229	>	snapshots_[i] = NULL;
230		}
231		std::vector<int>::iterator j;
232		j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
233		assert(j != activeBlocks_.end());
234		*j = -1;
235	<	}
235	>	}
236
237	<	bool BlockSnapshotManager::hasZeroRefBlock(){
237	>	bool BlockSnapshotManager::hasZeroRefBlock(){
238		return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ?  true : false;
239	<	}
239	>	}
240
241	<	int BlockSnapshotManager::getFirstZeroRefBlock(){
242	<	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
243	<	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
244	<	}
241	>	int BlockSnapshotManager::getFirstZeroRefBlock(){
242	>	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
243	>	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
244	>	}
245
246	<	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
246	>	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
247		std::vector<int> result;
248	<	oopse::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
249	<	std::bind2nd(std::not_equal_to<int>(), -1));
248	>	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
249	>	std::bind2nd(std::not_equal_to<int>(), -1));
250		return result;
251	<	}
251	>	}
252
253	<	Snapshot* BlockSnapshotManager::loadFrame(int frame){
254	<	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
253	>	Snapshot* BlockSnapshotManager::loadFrame(int frame){
254	>	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_,
255	>	getStorageLayout());
256		snapshot->setID(frame);
257	+	snapshot->clearDerivedProperties();
258
204	–	/** @todo fixed me */
205	–	Snapshot* oldSnapshot = currentSnapshot_;
259		currentSnapshot_ = snapshot;
260		reader_->readFrame(frame);
261	<	currentSnapshot_ = oldSnapshot;
261	>
262		return snapshot;
263	<	}
263	>	}
264
265	<	int BlockSnapshotManager::getNFrames() {
265	>	int BlockSnapshotManager::getNFrames() {
266		return reader_->getNFrames();
267	<	}
267	>	}
268
269	+	void BlockSnapshotManager::needCOMprops(bool ncp) {
270	+	reader_->setNeedCOMprops(ncp);
271	+	}
272	+
273		}

Comparing trunk/src/brains/BlockSnapshotManager.cpp (property svn:keywords):
Revision 355 by tim, Wed Feb 16 20:43:10 2005 UTC vs.
Revision 1966 by gezelter, Fri Jan 24 14:17:42 2014 UTC

#	Line 0 | Line 1
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