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root/OpenMD/branches/development/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.
branches/development/src/brains/BlockSnapshotManager.cpp (file contents), Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 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 "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	<	BlockSnapshotMananger::BlockSnapshotMananger(SimInfo* info, const std::string& filename,
51	<	int storageLayout, int blockCapacity)
52	<	: SnapshotManager(storageLayout), info_(info), 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	>	nCutoffGroups_ = info->getNCutoffGroups();
58
59	<	double avalPhysMem = physmem_available();
59	>	RealType physMem = physmem_total();
60	>	RealType rssMem = residentMem();
61	>	RealType avaliablePhysMem = physMem - rssMem;
62	>
63
64	<	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
64	>	int bytesPerStuntDouble = DataStorage::getBytesPerStuntDouble(storageLayout);
65
66	<	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
66	>	int bytesPerFrame = (nRigidBodies_ + nAtoms_) * bytesPerStuntDouble;
67
68	<	int frameCapacity = int (avalPhysMem / bytesPerFrame);
68	>	// total number of frames that can fit in memory
69	>	RealType frameCapacity = avaliablePhysMem / bytesPerFrame;
70	>
71	>	// number of frames in each block given the need to hold multiple blocks
72	>	// in memory at the same time:
73	>	nSnapshotPerBlock_ = int(frameCapacity) / blockCapacity_;
74	>	reader_ = new DumpReader(info, filename);
75	>	nframes_ = reader_->getNFrames();
76	>	int nblocks = nframes_ / nSnapshotPerBlock_;
77	>	if (nframes_ % int(nSnapshotPerBlock_) != 0) {
78	>	++nblocks;
79	>	}
80
81	<	nSnapshotPerBlock_ = frameCapacity /blockCapacity_ ;
81	>	for (int i = 0; i < nblocks; ++i) {
82	>	blocks_.push_back(SnapshotBlock(i*nSnapshotPerBlock_, (i+1)*nSnapshotPerBlock_));
83	>	}
84	>	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
85	>	blocks_.back().second = nframes_;
86
87	<	reader_ = new DumpReader(info, filename);
66	<	nframes_ = reader_->getNFrames();
87	>	snapshots_.insert(snapshots_.begin(), nframes_, static_cast<Snapshot*>(NULL));
88
89	<	int nblocks = nframes_ / nSnapshotPerBlock_;
90	<	if (nframes_ % nSnapshotPerBlock_ != 0) {
91	<	++nblocks;
92	<	}
89	>	std::cout << "-----------------------------------------------------"<<std::endl;
90	>	std::cout << "BlockSnapshotManager memory report:" << std::endl;
91	>	std::cout << "\n";
92	>	std::cout << "  Physical Memory available:\t" << (unsigned long)physMem <<  " bytes" <<std::endl;
93	>	std::cout << "     Resident Memory in use:\t" << (unsigned long)rssMem << " bytes" <<std::endl;
94	>	std::cout << "Memory available for OpenMD:\t" << (unsigned long)avaliablePhysMem << " bytes" <<std::endl;
95	>	std::cout << "      Bytes per StuntDouble:\t" << (unsigned long)bytesPerStuntDouble <<std::endl;
96	>	std::cout << "            Bytes per Frame:\t" << (unsigned long)bytesPerFrame <<std::endl;
97	>	std::cout << "             Frame Capacity:\t" << (unsigned long)frameCapacity <<std::endl;
98	>	std::cout << "       Frames in trajectory:\t" << (unsigned long)nframes_ <<std::endl;
99	>	std::cout << "        Snapshots per Block:\t" << (unsigned long)nSnapshotPerBlock_ <<std::endl;
100	>	std::cout << "     Total number of Blocks:\t" << (unsigned long)nblocks << std::endl;
101	>	std::cout << "-----------------------------------------------------"<<std::endl;
102
73	–	for (int i = 0; i < nblocks; ++i) {
74	–	blocks_.push_back(SnapshotBlock(i, (i+1)*nSnapshotPerBlock_);
103		}
76	–	//the last block may not have nSnapshotPerBlock frames, we need to consider this special situation
77	–	blocks_.back.second = nframes_;
104
79	–	snapshots_.insert(snapshots_.begin(), nframes_, NULL);
80	–
81	–	}
105
106	<
84	<	BlockSnapshotMananger::~BlockSnapshotMananger() {
106	>	BlockSnapshotManager::~BlockSnapshotManager() {
107		currentSnapshot_ = NULL;
108		previousSnapshot_ = NULL;
109
110		delete reader_;
89	–	std::for_each(activeBlocks_.begin(), activeBlocks_.end(), unloadBlock);
90	–	}
111
112	<	int BlockSnapshotManager::getNActiveBlocks() {
113	<	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::not);
114	<	}
112	>	std::vector<int>::iterator i;
113	>	for (i = activeBlocks_.begin(); i != activeBlocks_.end(); ++i) {
114	>	if (*i != -1) {
115	>	unloadBlock(*i);
116	>	}
117	>	}
118	>	}
119
120	<	bool BlockSnapshotManager::isBlockActive(int block) {
121	<	return std::find(activeBlocks_.begin(), activeBlocks_.end(), block) != activeBlocks_.end() ? true : false;
122	<	}
120	>	Snapshot* BlockSnapshotManager::getSnapshot(int id) {
121	>	currentSnapshot_ = snapshots_[id];
122	>	return snapshots_[id];
123	>	}
124
125	<	bool BlockSnapshotManager::loadBlock(int block) {
125	>	int BlockSnapshotManager::getNActiveBlocks() {
126	>	#ifdef __RWSTD
127	>	int count = 0;
128	>	std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1), count);
129	>	return count;
130	>	#else
131	>	return std::count_if(activeBlocks_.begin(), activeBlocks_.end(), std::bind2nd(std::not_equal_to<int>(), -1));
132	>	#endif
133	>	}
134	>
135	>
136	>
137	>	bool BlockSnapshotManager::loadBlock(int block) {
138	>	std::vector<int>::iterator i = findActiveBlock(block);
139		bool loadSuccess;
140	<	if (isBlockActive(block)) {
141	<	loadSuccess = true;
140	>	if (i != activeBlocks_.end()) {
141	>	//if block is already in memory, just increast the reference count
142	>	++activeRefCount_[i - activeBlocks_.begin()];
143	>	loadSuccess = true;
144		} else if (getNActiveBlocks() < blockCapacity_){
145	<
146	<	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
147	<	snapshots_[i] = loadFrame(i);
148	<	}
149	<
150	<	std::vector<int>::iterator j;
151	<	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
152	<	assert(j != activeBlocks_.end());
153	<	*j = block;
154	<	loadSuccess = true;
155	<	}else {
156	<	loadSuccess = false;
145	>	//if number of active blocks is less than the block capacity, just load it
146	>	internalLoad(block);
147	>	loadSuccess = true;
148	>	} else if (hasZeroRefBlock() > 0) {
149	>	//if already reach the block capacity, need to unload a block with 0 reference
150	>	int zeroRefBlock = getFirstZeroRefBlock();
151	>	assert(zeroRefBlock != -1);
152	>	internalUnload(zeroRefBlock);
153	>	internalLoad(block);
154	>	} else {
155	>	//reach the capacity and all blocks in memory are not zero reference
156	>	loadSuccess = false;
157		}
158	<
158	>
159		return loadSuccess;
160	<	}
160	>	}
161
162	<	bool BlockSnapshotManager::unloadBlock(int block) {
162	>	bool BlockSnapshotManager::unloadBlock(int block) {
163		bool unloadSuccess;
164	<	if (!isBlockActive(block)){
165	<	unloadSuccess = false;
164	>	std::vector<int>::iterator i = findActiveBlock(block);
165	>
166	>	if (i != activeBlocks_.end()){
167	>	--activeRefCount_[i - activeBlocks_.begin()];
168	>	if (activeRefCount_[i - activeBlocks_.begin()] < 0) {
169	>	//in case, unloadBlock called multiple times
170	>	activeRefCount_[i - activeBlocks_.begin()]  = 0;
171	>	}
172	>
173	>	unloadSuccess = true;
174		} else {
175	<	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;
175	>	unloadSuccess = false;
176		}
136	–	}
177
178	<	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
178	>	return unloadSuccess;
179	>	}
180	>
181	>	void BlockSnapshotManager::internalLoad(int block) {
182	>
183	>	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
184	>	snapshots_[i] = loadFrame(i);
185	>	}
186	>
187	>	std::vector<int>::iterator j;
188	>	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), -1);
189	>	assert(j != activeBlocks_.end());
190	>	*j = block;
191	>	++activeRefCount_[j - activeBlocks_.begin()];
192	>	}
193	>
194	>	void BlockSnapshotManager::internalUnload(int block) {
195	>	for (int i = blocks_[block].first; i < blocks_[block].second; ++i) {
196	>	delete snapshots_[i];
197	>	snapshots_[i] = NULL;
198	>	}
199	>	std::vector<int>::iterator j;
200	>	j = std::find(activeBlocks_.begin(), activeBlocks_.end(), block);
201	>	assert(j != activeBlocks_.end());
202	>	*j = -1;
203	>	}
204	>
205	>	bool BlockSnapshotManager::hasZeroRefBlock(){
206	>	return std::find(activeRefCount_.begin(), activeRefCount_.end(), 0) != activeRefCount_.end() ?  true : false;
207	>	}
208	>
209	>	int BlockSnapshotManager::getFirstZeroRefBlock(){
210	>	std::vector<int>::iterator i = std::find(activeRefCount_.begin(), activeRefCount_.end(), 0);
211	>	return i != activeRefCount_.end() ? activeBlocks_[i - activeRefCount_.begin()] : -1;
212	>	}
213	>
214	>	std::vector<int> BlockSnapshotManager::getActiveBlocks() {
215		std::vector<int> result;
216	<	std::copy_if(activeBlocks_.begin(), activeBlocks_.end());
217	<	}
216	>	OpenMD::copy_if(activeBlocks_.begin(), activeBlocks_.end(), std::back_inserter(result),
217	>	std::bind2nd(std::not_equal_to<int>(), -1));
218	>	return result;
219	>	}
220
221	<	Snapshot* BlockSnapshotManager::loadFrame(int frame){
222	<	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, getStorageLayout());
221	>	Snapshot* BlockSnapshotManager::loadFrame(int frame){
222	>	Snapshot* snapshot = new Snapshot(nAtoms_, nRigidBodies_, nCutoffGroups_, getStorageLayout());
223		snapshot->setID(frame);
224	<	setCurrentSnapshot(snapshot);   /** @todo fixed me */
224	>
225	>	/** @todo fixed me */
226	>	Snapshot* oldSnapshot = currentSnapshot_;
227	>	currentSnapshot_ = snapshot;
228		reader_->readFrame(frame);
229	+
230	+	// What was this for?  It doesn't make sense!
231	+	//currentSnapshot_ = oldSnapshot;
232	+
233		return snapshot;
234	<	}
234	>	}
235
236	<	int BlockSnapshotManager::getNFrames() {
236	>	int BlockSnapshotManager::getNFrames() {
237		return reader_->getNFrames();
238	<	}
238	>	}
239
240	+	void BlockSnapshotManager::needCOMprops(bool ncp) {
241	+	reader_->setNeedCOMprops(ncp);
242	+	}
243	+
244		}

Comparing:
trunk/src/brains/BlockSnapshotManager.cpp (property svn:keywords), Revision 323 by tim, Sun Feb 13 15:56:10 2005 UTC vs.
branches/development/src/brains/BlockSnapshotManager.cpp (property svn:keywords), Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC

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