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

Comparing:
trunk/src/brains/BlockSnapshotManager.cpp (file contents), Revision 318 by tim, Sun Feb 13 06:57:48 2005 UTC vs.
branches/development/src/brains/BlockSnapshotManager.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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 "utlis/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),
53	<	blockCapacity_(blockCapacity), activeBlocks(blockCapacity_, -1) {
49	>	namespace OpenMD {
50	>	BlockSnapshotManager::BlockSnapshotManager(SimInfo* info, const std::string& filename,
51	>	int storageLayout, int blockCapacity)
52	>	: SnapshotManager(storageLayout), info_(info), blockCapacity_(blockCapacity),
53	>	activeBlocks_(blockCapacity_, -1), activeRefCount_(blockCapacity_, 0) {
54
55	<	nAtoms_ = info->getNGlobalAtoms();
56	<	nRigidBodies_ = info->getNGlobalRigidBodies();
55	>	nAtoms_ = info->getNGlobalAtoms();
56	>	nRigidBodies_ = info->getNGlobalRigidBodies();
57
58	<	double avalPhysMem = physmem_available();
58	>	RealType physMem = physmem_total();
59	>	RealType rssMem = residentMem();
60	>	RealType avaliablePhysMem = physMem - rssMem;
61	>
62
63	<	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
63	>	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
64
65	<	int bytesPerFrame = nStuntDoubles * bytesPerStuntDouble;
65	>	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
66
67	<	int frameCapacity = int (avalPhysMem / bytesPerFrame);
67	>	// total number of frames that can fit in memory
68	>	RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
69	>
70	>	// number of frames in each block given the need to hold multiple blocks
71	>	// in memory at the same time:
72	>	nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
73	>	reader_ = new DumpReader(info, filename);
74	>	nframes_ = reader_->getNFrames();
75	>	int nblocks = nframes_ / nSnapshotPerBlock_;
76	>	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
77	>	++nblocks;
78	>	}
79
80	<	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
80	>	for (int i = 0; i < nblocks; ++i) {
81	>	blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
82	>	}
83	>	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
84	>	blocks_.back().second = nframes_;
85
86	<	reader_ = new DumpReader(info, filename);
67	<	nframes_ = reader->getNFrames();
86	>	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
87
88	<	int nblocks = nframes / nSnapshotPerBlock_;
89	<	if (nframes % nSnapshotPerBlock != 0) {
90	<	++nblocks;
91	<	}
88	>	std::cout << "-----------------------------------------------------"<<std::endl;
89	>	std::cout << "BlockSnapshotManager memory report:" << std::endl;
90	>	std::cout << "\n";
91	>	std::cout << "  Physical Memory available:\t" << (unsigned long)physMem <<  " bytes" <<std::endl;
92	>	std::cout << "     Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
93	>	std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
94	>	std::cout << "      Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
95	>	std::cout << "            Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
96	>	std::cout << "             Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
97	>	std::cout << "       Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
98	>	std::cout << "        Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
99	>	std::cout << "     Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
100	>	std::cout << "-----------------------------------------------------"<<std::endl;
101
74	–	for (int i = 0; i < nblocks; ++i) {
75	–	blocks_.push_back(SnapshotBlock(i, (i+1)*nSnapshotPerBlock_);
102		}
77	–	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
78	–	blocks.back.second = nframes;
103
80	–	snapshots_.insert(snapshot_.begin(), nframes, NULL);
81	–
82	–	}
104
105	<
85	<	BlockSnapshotMananger::~BlockSnapshotMananger() {
105	>	BlockSnapshotManager::~BlockSnapshotManager() {
106		currentSnapshot_ = NULL;
107		previousSnapshot_ = NULL;
108
109		delete reader_;
90	–	std::for_each(activeBlocks_.begin(), activeBlocks_.end(), unloadBlock);
91	–	}
110
111	<	int BlockSnapshotManager::getNActiveBlocks() {
112	<	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::not);
113	<	}
111	>	std::vector<int>::iterator i;
112	>	for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
113	>	if (*i != -1) {
114	>	unloadBlock(*i);
115	>	}
116	>	}
117	>	}
118
119	<	bool BlockSnapshotManager::isBlockActive(int block) {
120	<	return std::find(activeBlocks_.begin(), activeBlocks_.end(), block) != activeBlocks_.end() ? true : false;
121	<	}
119	>	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
120	>	currentSnapshot_ = snapshots_[id];
121	>	return snapshots_[id];
122	>	}
123
124	<	bool BlockSnapshotManager::loadBlock(int block) {
124	>	int BlockSnapshotManager::getNActiveBlocks() {
125	>	#ifdef __RWSTD
126	>	int count = 0;
127	>	std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
128	>	return count;
129	>	#else
130	>	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
131	>	#endif
132	>	}
133	>
134	>
135	>
136	>	bool BlockSnapshotManager::loadBlock(int block) {
137	>	std::vector<int>::iterator i = findActiveBlock(block);
138		bool loadSuccess;
139	<	if (isBlockActive(block)) {
140	<	loadSuccess = true;
139	>	if (i != activeBlocks_.end()) {
140	>	//if block is already in memory, just increast the reference count
141	>	++activeRefCount_[i - activeBlocks_.begin()];
142	>	loadSuccess = true;
143		} else if (getNActiveBlocks() < blockCapacity_){
144	<
145	<	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
146	<	snapshots_[i] = loadFrame(i);
147	<	}
148	<
149	<	std::vector<int>::iterator j;
150	<	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
151	<	assert(j != activeBlocks_.end());
152	<	*j = block;
153	<	loadSuccess = true;
154	<	}else {
155	<	loadSuccess = false;
144	>	//if number of active blocks is less than the block capacity, just load it
145	>	internalLoad(block);
146	>	loadSuccess = true;
147	>	} else if (hasZeroRefBlock() > 0) {
148	>	//if already reach the block capacity, need to unload a block with 0 reference
149	>	int zeroRefBlock = getFirstZeroRefBlock();
150	>	assert(zeroRefBlock != -1);
151	>	internalUnload(zeroRefBlock);
152	>	internalLoad(block);
153	>	} else {
154	>	//reach the capacity and all blocks in memory are not zero reference
155	>	loadSuccess = false;
156		}
157	<
157	>
158		return loadSuccess;
159	<	}
159	>	}
160
161	<	bool BlockSnapshotManager::unloadBlock(int block) {
161	>	bool BlockSnapshotManager::unloadBlock(int block) {
162		bool unloadSuccess;
163	<	if (!isBlockActive(block)){
164	<	unloadSuccess = false;
163	>	std::vector<int>::iterator i = findActiveBlock(block);
164	>
165	>	if (i != activeBlocks_.end()){
166	>	--activeRefCount_[i - activeBlocks_.begin()];
167	>	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
168	>	//in case, unloadBlock called multiple times
169	>	activeRefCount_[i - activeBlocks_.begin()]  = 0;
170	>	}
171	>
172	>	unloadSuccess = true;
173		} else {
174	<	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
129	<	delete snapshots_[i];
130	<	snapshots_[i] = NULL;
131	<	}
132	<	std::vector<int>::iterator j;
133	<	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
134	<	assert(j != activeBlocks_.end());
135	<	*j = -1;
174	>	unloadSuccess = false;
175		}
137	–	}
176
177	<	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
177	>	return unloadSuccess;
178	>	}
179	>
180	>	void BlockSnapshotManager::internalLoad(int block) {
181	>
182	>	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
183	>	snapshots_[i] = loadFrame(i);
184	>	}
185	>
186	>	std::vector<int>::iterator j;
187	>	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
188	>	assert(j != activeBlocks_.end());
189	>	*j = block;
190	>	++activeRefCount_[j - activeBlocks_.begin()];
191	>	}
192	>
193	>	void BlockSnapshotManager::internalUnload(int block) {
194	>	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
195	>	delete snapshots_[i];
196	>	snapshots_[i] = NULL;
197	>	}
198	>	std::vector<int>::iterator j;
199	>	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
200	>	assert(j != activeBlocks_.end());
201	>	*j = -1;
202	>	}
203	>
204	>	bool BlockSnapshotManager::hasZeroRefBlock(){
205	>	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ?  true : false;
206	>	}
207	>
208	>	int BlockSnapshotManager::getFirstZeroRefBlock(){
209	>	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
210	>	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
211	>	}
212	>
213	>	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
214		std::vector<int> result;
215	<	std::copy_if(activeBlocks_.begin(), activeBlocks_.end());
216	<	}
215	>	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
216	>	std::bind2nd(std::not_equal_to<int>(), -1));
217	>	return result;
218	>	}
219
220	<	Snapshot* BlockSnapshotManager::loadFrame(int frame){
220	>	Snapshot* BlockSnapshotManager::loadFrame(int frame){
221		Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
222		snapshot->setID(frame);
223	<	setCurrentSnapshot(snapshot);   /** @todo fixed me */
223	>
224	>	/** @todo fixed me */
225	>	Snapshot* oldSnapshot = currentSnapshot_;
226	>	currentSnapshot_ = snapshot;
227		reader_->readFrame(frame);
228	+
229	+	// What was this for?  It doesn't make sense!
230	+	//currentSnapshot_ = oldSnapshot;
231	+
232		return snapshot;
233	<	}
233	>	}
234
235	+	int BlockSnapshotManager::getNFrames() {
236	+	return reader_->getNFrames();
237	+	}
238	+
239	+	void BlockSnapshotManager::needCOMprops(bool ncp) {
240	+	reader_->setNeedCOMprops(ncp);
241	+	}
242	+
243		}

Comparing:
trunk/src/brains/BlockSnapshotManager.cpp (property svn:keywords), Revision 318 by tim, Sun Feb 13 06:57:48 2005 UTC vs.
branches/development/src/brains/BlockSnapshotManager.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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