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root/OpenMD/trunk/src/brains/BlockSnapshotManager.cpp

Comparing trunk/src/brains/BlockSnapshotManager.cpp (file contents):
Revision 323 by tim, Sun Feb 13 15:56:10 2005 UTC vs.
Revision 1965 by gezelter, Fri Jan 24 13:53:41 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/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	<	BlockSnapshotMananger::BlockSnapshotMananger(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 bytesPerCutoffGroup = DataStorage::getBytesPerStuntDouble(DataStorage::dslPosition);
71	>	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble
72	>	+ nCutoffGroups_ * bytesPerCutoffGroup;
73
74	<	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
74	>	// total number of frames that can fit in memory
75	>	//RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
76	>	RealType frameCapacity = (RealType) memSize_ / (RealType) bytesPerFrame;
77
78	<	int frameCapacity = int (avalPhysMem / bytesPerFrame);
78	>	// number of frames in each block given the need to hold multiple blocks
79	>	// in memory at the same time:
80	>	nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
81	>	if (nSnapshotPerBlock_ <= 0) {
82	>	std::cerr << "not enough memory to hold two configs!" << std::endl;
83	>	}
84	>	reader_ = new DumpReader(info, filename);
85	>	nframes_ = reader_->getNFrames();
86	>	int nblocks = nframes_ / nSnapshotPerBlock_;
87	>	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
88	>	++nblocks;
89	>	}
90
91	<	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
91	>	for (int i = 0; i < nblocks; ++i) {
92	>	blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
93	>	}
94	>	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
95	>	blocks_.back().second = nframes_;
96
97	<	reader_ = new DumpReader(info, filename);
66	<	nframes_ = reader_->getNFrames();
97	>	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
98
99	<	int nblocks = nframes_ / nSnapshotPerBlock_;
100	<	if (nframes_ % nSnapshotPerBlock_ != 0) {
101	<	++nblocks;
102	<	}
99	>	std::cout << "-----------------------------------------------------"<<std::endl;
100	>	std::cout << "BlockSnapshotManager memory report:" << std::endl;
101	>	std::cout << "\n";
102	>	// std::cout << "  Physical Memory available:\t" << (unsigned long)physMem <<  " bytes" <<std::endl;
103	>	//std::cout << "     Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
104	>	//std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
105	>	std::cout << "Memory requested for OpenMD:\t" << (unsigned long)memSize_ << " bytes" <<std::endl;
106	>	std::cout << "      Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
107	>	std::cout << "     Bytes per Cutoff Group:\t" << (unsigned long)bytesPerCutoffGroup <<std::endl;
108	>	std::cout << "            Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
109	>	std::cout << "             Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
110	>	std::cout << "       Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
111	>	std::cout << "        Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
112	>	std::cout << "     Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
113	>	std::cout << "-----------------------------------------------------"<<std::endl;
114
73	–	for (int i = 0; i < nblocks; ++i) {
74	–	blocks_.push_back(SnapshotBlock(i, (i+1)*nSnapshotPerBlock_);
115		}
76	–	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
77	–	blocks_.back.second = nframes_;
116
79	–	snapshots_.insert(snapshots_.begin(), nframes_, NULL);
80	–
81	–	}
117
118	<
84	<	BlockSnapshotMananger::~BlockSnapshotMananger() {
118	>	BlockSnapshotManager::~BlockSnapshotManager() {
119		currentSnapshot_ = NULL;
120		previousSnapshot_ = NULL;
121
122		delete reader_;
89	–	std::for_each(activeBlocks_.begin(), activeBlocks_.end(), unloadBlock);
90	–	}
123
124	<	int BlockSnapshotManager::getNActiveBlocks() {
125	<	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::not);
126	<	}
124	>	std::vector<int>::iterator i;
125	>	for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
126	>	if (*i != -1) {
127	>	unloadBlock(*i);
128	>	}
129	>	}
130	>	}
131
132	<	bool BlockSnapshotManager::isBlockActive(int block) {
133	<	return std::find(activeBlocks_.begin(), activeBlocks_.end(), block) != activeBlocks_.end() ? true : false;
134	<	}
132	>	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
133	>	currentSnapshot_ = snapshots_[id];
134	>	return snapshots_[id];
135	>	}
136
137	<	bool BlockSnapshotManager::loadBlock(int block) {
137	>	int BlockSnapshotManager::getNActiveBlocks() {
138	>	#ifdef __RWSTD
139	>	int count = 0;
140	>	std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
141	>	return count;
142	>	#else
143	>	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
144	>	#endif
145	>	}
146	>
147	>
148	>
149	>	bool BlockSnapshotManager::loadBlock(int block) {
150	>	std::vector<int>::iterator i = findActiveBlock(block);
151		bool loadSuccess;
152	<	if (isBlockActive(block)) {
153	<	loadSuccess = true;
152	>	if (i != activeBlocks_.end()) {
153	>	//if block is already in memory, just increast the reference count
154	>	++activeRefCount_[i - activeBlocks_.begin()];
155	>	loadSuccess = true;
156		} else if (getNActiveBlocks() < blockCapacity_){
157	<
158	<	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
159	<	snapshots_[i] = loadFrame(i);
160	<	}
161	<
162	<	std::vector<int>::iterator j;
163	<	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
164	<	assert(j != activeBlocks_.end());
165	<	*j = block;
166	<	loadSuccess = true;
167	<	}else {
168	<	loadSuccess = false;
157	>	//if number of active blocks is less than the block capacity, just load it
158	>	internalLoad(block);
159	>	loadSuccess = true;
160	>	} else if ( hasZeroRefBlock() ) {
161	>	//if already reach the block capacity, need to unload a block with 0 reference
162	>	int zeroRefBlock = getFirstZeroRefBlock();
163	>	assert(zeroRefBlock != -1);
164	>	internalUnload(zeroRefBlock);
165	>	internalLoad(block);
166	>	} else {
167	>	//reach the capacity and all blocks in memory are not zero reference
168	>	loadSuccess = false;
169		}
170	<
170	>
171		return loadSuccess;
172	<	}
172	>	}
173
174	<	bool BlockSnapshotManager::unloadBlock(int block) {
174	>	bool BlockSnapshotManager::unloadBlock(int block) {
175		bool unloadSuccess;
176	<	if (!isBlockActive(block)){
177	<	unloadSuccess = false;
176	>	std::vector<int>::iterator i = findActiveBlock(block);
177	>
178	>	if (i != activeBlocks_.end()){
179	>	--activeRefCount_[i - activeBlocks_.begin()];
180	>	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
181	>	//in case, unloadBlock called multiple times
182	>	activeRefCount_[i - activeBlocks_.begin()]  = 0;
183	>	}
184	>
185	>	if (activeRefCount_[i-activeBlocks_.begin()] == 0) {
186	>	internalUnload(block);
187	>	}
188	>
189	>	unloadSuccess = true;
190		} else {
191	<	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
128	<	delete snapshots_[i];
129	<	snapshots_[i] = NULL;
130	<	}
131	<	std::vector<int>::iterator j;
132	<	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
133	<	assert(j != activeBlocks_.end());
134	<	*j = -1;
191	>	unloadSuccess = false;
192		}
136	–	}
193
194	<	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
194	>	return unloadSuccess;
195	>	}
196	>
197	>	void BlockSnapshotManager::internalLoad(int block) {
198	>
199	>	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
200	>	snapshots_[i] = loadFrame(i);
201	>	}
202	>
203	>	std::vector<int>::iterator j;
204	>	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
205	>	assert(j != activeBlocks_.end());
206	>	*j = block;
207	>	++activeRefCount_[j - activeBlocks_.begin()];
208	>	}
209	>
210	>	void BlockSnapshotManager::internalUnload(int block) {
211	>	std::cerr << "called internal unload for block "<< block << "\n";
212	>	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
213	>	delete snapshots_[i];
214	>	snapshots_[i] = NULL;
215	>	}
216	>	std::vector<int>::iterator j;
217	>	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
218	>	assert(j != activeBlocks_.end());
219	>	*j = -1;
220	>	}
221	>
222	>	bool BlockSnapshotManager::hasZeroRefBlock(){
223	>	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ?  true : false;
224	>	}
225	>
226	>	int BlockSnapshotManager::getFirstZeroRefBlock(){
227	>	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
228	>	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
229	>	}
230	>
231	>	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
232		std::vector<int> result;
233	<	std::copy_if(activeBlocks_.begin(), activeBlocks_.end());
234	<	}
233	>	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
234	>	std::bind2nd(std::not_equal_to<int>(), -1));
235	>	return result;
236	>	}
237
238	<	Snapshot* BlockSnapshotManager::loadFrame(int frame){
239	<	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
238	>	Snapshot* BlockSnapshotManager::loadFrame(int frame){
239	>	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_,
240	>	getStorageLayout());
241		snapshot->setID(frame);
242	<	setCurrentSnapshot(snapshot);   /** @todo fixed me */
242	>	snapshot->clearDerivedProperties();
243	>
244	>	currentSnapshot_ = snapshot;
245		reader_->readFrame(frame);
246	+
247		return snapshot;
248	<	}
248	>	}
249
250	<	int BlockSnapshotManager::getNFrames() {
250	>	int BlockSnapshotManager::getNFrames() {
251		return reader_->getNFrames();
252	<	}
252	>	}
253
254	+	void BlockSnapshotManager::needCOMprops(bool ncp) {
255	+	reader_->setNeedCOMprops(ncp);
256	+	}
257	+
258		}

Comparing trunk/src/brains/BlockSnapshotManager.cpp (property svn:keywords):
Revision 323 by tim, Sun Feb 13 15:56:10 2005 UTC vs.
Revision 1965 by gezelter, Fri Jan 24 13:53:41 2014 UTC

#	Line 0 | Line 1
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