# | Line 1 | Line 1 | |
---|---|---|
1 | < | #include <cstring> |
1 | > | #define _LARGEFILE_SOURCE64 |
2 | > | #define _FILE_OFFSET_BITS 64 |
3 | > | |
4 | > | #include <string.h> |
5 | #include <iostream> | |
6 | #include <fstream> | |
7 | + | #include <algorithm> |
8 | + | #include <utility> |
9 | ||
10 | #ifdef IS_MPI | |
11 | #include <mpi.h> | |
7 | – | #include <mpi++.h> |
12 | #include "mpiSimulation.hpp" | |
13 | < | #define TAKE_THIS_TAG 0 |
13 | > | |
14 | > | namespace dWrite{ |
15 | > | void DieDieDie( void ); |
16 | > | } |
17 | > | |
18 | > | using namespace dWrite; |
19 | #endif //is_mpi | |
20 | ||
21 | #include "ReadWrite.hpp" | |
# | Line 19 | Line 28 | DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ | |
28 | #ifdef IS_MPI | |
29 | if(worldRank == 0 ){ | |
30 | #endif // is_mpi | |
31 | < | |
32 | < | |
33 | < | |
34 | < | strcpy( outName, entry_plug->sampleName ); |
35 | < | |
27 | < | outFile.open(outName, ios::out | ios::trunc ); |
28 | < | |
29 | < | if( !outFile ){ |
30 | < | |
31 | > | |
32 | > | dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
33 | > | |
34 | > | if( !dumpFile ){ |
35 | > | |
36 | sprintf( painCave.errMsg, | |
37 | "Could not open \"%s\" for dump output.\n", | |
38 | < | outName); |
38 | > | entry_plug->sampleName); |
39 | painCave.isFatal = 1; | |
40 | simError(); | |
41 | } | |
37 | – | |
38 | – | //outFile.setf( ios::scientific ); |
42 | ||
43 | #ifdef IS_MPI | |
44 | } | |
45 | ||
46 | + | //sort the local atoms by global index |
47 | + | sortByGlobalIndex(); |
48 | + | |
49 | sprintf( checkPointMsg, | |
50 | "Sucessfully opened output file for dumping.\n"); | |
51 | MPIcheckPoint(); | |
# | Line 52 | Line 58 | DumpWriter::~DumpWriter( ){ | |
58 | if(worldRank == 0 ){ | |
59 | #endif // is_mpi | |
60 | ||
61 | < | outFile.close(); |
61 | > | dumpFile.close(); |
62 | ||
63 | #ifdef IS_MPI | |
64 | } | |
65 | #endif // is_mpi | |
66 | } | |
67 | ||
68 | < | void DumpWriter::writeDump( double currentTime ){ |
63 | < | |
64 | < | const int BUFFERSIZE = 2000; |
65 | < | char tempBuffer[BUFFERSIZE]; |
66 | < | char writeLine[BUFFERSIZE]; |
68 | > | #ifdef IS_MPI |
69 | ||
70 | < | int i, j, which_node, done, game_over, which_atom; |
71 | < | double q[4]; |
72 | < | DirectionalAtom* dAtom; |
71 | < | int nAtoms = entry_plug->n_atoms; |
72 | < | Atom** atoms = entry_plug->atoms; |
73 | < | |
70 | > | /** |
71 | > | * A hook function to load balancing |
72 | > | */ |
73 | ||
74 | < | #ifndef IS_MPI |
75 | < | |
76 | < | outFile << nAtoms << "\n"; |
77 | < | |
78 | < | outFile << currentTime << "\t" |
79 | < | << entry_plug->box_x << "\t" |
80 | < | << entry_plug->box_y << "\t" |
81 | < | << entry_plug->box_z << "\n"; |
82 | < | |
83 | < | for( i=0; i<nAtoms; i++ ){ |
84 | < | |
74 | > | void DumpWriter::update(){ |
75 | > | sortByGlobalIndex(); |
76 | > | } |
77 | > | |
78 | > | /** |
79 | > | * Auxiliary sorting function |
80 | > | */ |
81 | > | |
82 | > | bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
83 | > | return p1.second < p2.second; |
84 | > | } |
85 | ||
86 | < | sprintf( tempBuffer, |
87 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
88 | < | atoms[i]->getType(), |
89 | < | atoms[i]->getX(), |
90 | < | atoms[i]->getY(), |
91 | < | atoms[i]->getZ(), |
92 | < | atoms[i]->get_vx(), |
94 | < | atoms[i]->get_vy(), |
95 | < | atoms[i]->get_vz()); |
96 | < | strcpy( writeLine, tempBuffer ); |
97 | < | |
98 | < | if( atoms[i]->isDirectional() ){ |
99 | < | |
100 | < | dAtom = (DirectionalAtom *)atoms[i]; |
101 | < | dAtom->getQ( q ); |
102 | < | |
103 | < | sprintf( tempBuffer, |
104 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
105 | < | q[0], |
106 | < | q[1], |
107 | < | q[2], |
108 | < | q[3], |
109 | < | dAtom->getJx(), |
110 | < | dAtom->getJy(), |
111 | < | dAtom->getJz()); |
112 | < | strcat( writeLine, tempBuffer ); |
113 | < | } |
114 | < | else |
115 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
116 | < | |
117 | < | outFile << writeLine; |
118 | < | } |
119 | < | outFile.flush(); |
120 | < | |
121 | < | #else // is_mpi |
122 | < | |
123 | < | MPI::Status istatus; |
124 | < | int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
86 | > | /** |
87 | > | * Sorting the local index by global index |
88 | > | */ |
89 | > | |
90 | > | void DumpWriter::sortByGlobalIndex(){ |
91 | > | Molecule* mols = entry_plug->molecules; |
92 | > | indexArray.clear(); |
93 | ||
94 | < | // write out header and node 0's coordinates |
94 | > | for(int i = 0; i < entry_plug->n_mol;i++) |
95 | > | indexArray.push_back(make_pair(i, mols[i].getGlobalIndex())); |
96 | ||
97 | < | if( worldRank == 0 ){ |
98 | < | outFile << mpiSim->getTotAtoms() << "\n"; |
130 | < | |
131 | < | outFile << currentTime << "\t" |
132 | < | << entry_plug->box_x << "\t" |
133 | < | << entry_plug->box_y << "\t" |
134 | < | << entry_plug->box_z << "\n"; |
135 | < | |
136 | < | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
137 | < | // Get the Node number which has this molecule: |
138 | < | |
139 | < | which_node = AtomToProcMap[i]; |
140 | < | |
141 | < | if (which_node == mpiSim->getMyNode()) { |
142 | < | |
143 | < | sprintf( tempBuffer, |
144 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
145 | < | atoms[i]->getType(), |
146 | < | atoms[i]->getX(), |
147 | < | atoms[i]->getY(), |
148 | < | atoms[i]->getZ(), |
149 | < | atoms[i]->get_vx(), |
150 | < | atoms[i]->get_vy(), |
151 | < | atoms[i]->get_vz()); |
152 | < | strcpy( writeLine, tempBuffer ); |
153 | < | |
154 | < | if( atoms[i]->isDirectional() ){ |
155 | < | |
156 | < | dAtom = (DirectionalAtom *)atoms[i]; |
157 | < | dAtom->getQ( q ); |
158 | < | |
159 | < | sprintf( tempBuffer, |
160 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
161 | < | q[0], |
162 | < | q[1], |
163 | < | q[2], |
164 | < | q[3], |
165 | < | dAtom->getJx(), |
166 | < | dAtom->getJy(), |
167 | < | dAtom->getJz()); |
168 | < | strcat( writeLine, tempBuffer ); |
169 | < | } |
170 | < | else |
171 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
172 | < | |
173 | < | } else { |
174 | < | |
175 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
176 | < | MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
177 | < | TAKE_THIS_TAG, istatus); |
178 | < | } |
179 | < | |
180 | < | outFile << writeLine; |
181 | < | } |
182 | < | |
183 | < | // kill everyone off: |
184 | < | game_over = -1; |
185 | < | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
186 | < | MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
187 | < | } |
97 | > | sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
98 | > | } |
99 | ||
100 | < | } else { |
190 | < | |
191 | < | done = 0; |
192 | < | while (!done) { |
193 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
194 | < | TAKE_THIS_TAG, istatus); |
100 | > | #endif |
101 | ||
102 | < | if (which_atom == -1) { |
197 | < | done=1; |
198 | < | continue; |
199 | < | } else { |
102 | > | void DumpWriter::writeDump(double currentTime){ |
103 | ||
104 | < | //format the line |
105 | < | sprintf( tempBuffer, |
106 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
107 | < | atoms[which_atom]->getType(), |
108 | < | atoms[which_atom]->getX(), |
109 | < | atoms[which_atom]->getY(), |
110 | < | atoms[which_atom]->getZ(), |
111 | < | atoms[which_atom]->get_vx(), |
112 | < | atoms[which_atom]->get_vy(), |
113 | < | atoms[which_atom]->get_vz()); // check here. |
114 | < | strcpy( writeLine, tempBuffer ); |
115 | < | |
116 | < | if( atoms[which_atom]->isDirectional() ){ |
214 | < | |
215 | < | dAtom = (DirectionalAtom *)atoms[which_atom]; |
216 | < | dAtom->getQ( q ); |
217 | < | |
218 | < | sprintf( tempBuffer, |
219 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
220 | < | q[0], |
221 | < | q[1], |
222 | < | q[2], |
223 | < | q[3], |
224 | < | dAtom->getJx(), |
225 | < | dAtom->getJy(), |
226 | < | dAtom->getJz()); |
227 | < | strcat( writeLine, tempBuffer ); |
228 | < | } |
229 | < | else |
230 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
231 | < | |
232 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
233 | < | TAKE_THIS_TAG); |
234 | < | } |
104 | > | ofstream finalOut; |
105 | > | vector<ofstream*> fileStreams; |
106 | > | |
107 | > | #ifdef IS_MPI |
108 | > | if(worldRank == 0 ){ |
109 | > | #endif |
110 | > | finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
111 | > | if( !finalOut ){ |
112 | > | sprintf( painCave.errMsg, |
113 | > | "Could not open \"%s\" for final dump output.\n", |
114 | > | entry_plug->finalName ); |
115 | > | painCave.isFatal = 1; |
116 | > | simError(); |
117 | } | |
118 | < | } |
119 | < | outFile.flush(); |
238 | < | sprintf( checkPointMsg, |
239 | < | "Sucessfully took a dump.\n"); |
240 | < | MPIcheckPoint(); |
118 | > | #ifdef IS_MPI |
119 | > | } |
120 | #endif // is_mpi | |
121 | + | |
122 | + | fileStreams.push_back(&finalOut); |
123 | + | fileStreams.push_back(&dumpFile); |
124 | + | |
125 | + | writeFrame(fileStreams, currentTime); |
126 | + | |
127 | + | #ifdef IS_MPI |
128 | + | finalOut.close(); |
129 | + | #endif |
130 | + | |
131 | } | |
132 | ||
133 | < | void DumpWriter::writeFinal(){ |
133 | > | void DumpWriter::writeFinal(double currentTime){ |
134 | ||
246 | – | char finalName[500]; |
135 | ofstream finalOut; | |
136 | + | vector<ofstream*> fileStreams; |
137 | ||
249 | – | const int BUFFERSIZE = 2000; |
250 | – | char tempBuffer[BUFFERSIZE]; |
251 | – | char writeLine[BUFFERSIZE]; |
252 | – | |
253 | – | double q[4]; |
254 | – | DirectionalAtom* dAtom; |
255 | – | int nAtoms = entry_plug->n_atoms; |
256 | – | Atom** atoms = entry_plug->atoms; |
257 | – | int i, j, which_node, done, game_over, which_atom; |
258 | – | |
259 | – | |
138 | #ifdef IS_MPI | |
139 | if(worldRank == 0 ){ | |
140 | #endif // is_mpi | |
141 | < | |
142 | < | strcpy( finalName, entry_plug->finalName ); |
143 | < | |
266 | < | finalOut.open( finalName, ios::out | ios::trunc ); |
141 | > | |
142 | > | finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
143 | > | |
144 | if( !finalOut ){ | |
145 | sprintf( painCave.errMsg, | |
146 | "Could not open \"%s\" for final dump output.\n", | |
147 | < | finalName ); |
147 | > | entry_plug->finalName ); |
148 | painCave.isFatal = 1; | |
149 | simError(); | |
150 | } | |
151 | < | |
275 | < | // finalOut.setf( ios::scientific ); |
276 | < | |
151 | > | |
152 | #ifdef IS_MPI | |
153 | } | |
154 | + | #endif // is_mpi |
155 | ||
156 | < | sprintf(checkPointMsg,"Opened file for final configuration\n"); |
157 | < | MPIcheckPoint(); |
156 | > | fileStreams.push_back(&finalOut); |
157 | > | writeFrame(fileStreams, currentTime); |
158 | > | |
159 | > | #ifdef IS_MPI |
160 | > | finalOut.close(); |
161 | > | #endif |
162 | ||
163 | < | #endif //is_mpi |
163 | > | } |
164 | ||
165 | + | void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
166 | + | |
167 | + | const int BUFFERSIZE = 2000; |
168 | + | const int MINIBUFFERSIZE = 100; |
169 | + | |
170 | + | char tempBuffer[BUFFERSIZE]; |
171 | + | char writeLine[BUFFERSIZE]; |
172 | + | |
173 | + | int i, k; |
174 | + | |
175 | + | #ifdef IS_MPI |
176 | ||
177 | + | /********************************************************************* |
178 | + | * Documentation? You want DOCUMENTATION? |
179 | + | * |
180 | + | * Why all the potatoes below? |
181 | + | * |
182 | + | * To make a long story short, the original version of DumpWriter |
183 | + | * worked in the most inefficient way possible. Node 0 would |
184 | + | * poke each of the node for an individual atom's formatted data |
185 | + | * as node 0 worked its way down the global index. This was particularly |
186 | + | * inefficient since the method blocked all processors at every atom |
187 | + | * (and did it twice!). |
188 | + | * |
189 | + | * An intermediate version of DumpWriter could be described from Node |
190 | + | * zero's perspective as follows: |
191 | + | * |
192 | + | * 1) Have 100 of your friends stand in a circle. |
193 | + | * 2) When you say go, have all of them start tossing potatoes at |
194 | + | * you (one at a time). |
195 | + | * 3) Catch the potatoes. |
196 | + | * |
197 | + | * It was an improvement, but MPI has buffers and caches that could |
198 | + | * best be described in this analogy as "potato nets", so there's no |
199 | + | * need to block the processors atom-by-atom. |
200 | + | * |
201 | + | * This new and improved DumpWriter works in an even more efficient |
202 | + | * way: |
203 | + | * |
204 | + | * 1) Have 100 of your friend stand in a circle. |
205 | + | * 2) When you say go, have them start tossing 5-pound bags of |
206 | + | * potatoes at you. |
207 | + | * 3) Once you've caught a friend's bag of potatoes, |
208 | + | * toss them a spud to let them know they can toss another bag. |
209 | + | * |
210 | + | * How's THAT for documentation? |
211 | + | * |
212 | + | *********************************************************************/ |
213 | + | |
214 | + | int *potatoes; |
215 | + | int myPotato; |
216 | + | |
217 | + | int nProc; |
218 | + | int j, which_node, done, which_atom, local_index, currentIndex; |
219 | + | double atomData[13]; |
220 | + | int isDirectional; |
221 | + | char* atomTypeString; |
222 | + | char MPIatomTypeString[MINIBUFFERSIZE]; |
223 | + | int nObjects; |
224 | + | int msgLen; // the length of message actually recieved at master nodes |
225 | + | #endif //is_mpi |
226 | + | |
227 | + | double q[4], ji[3]; |
228 | + | DirectionalAtom* dAtom; |
229 | + | double pos[3], vel[3]; |
230 | + | int nTotObjects; |
231 | + | StuntDouble* sd; |
232 | + | char* molName; |
233 | + | vector<StuntDouble*> integrableObjects; |
234 | + | vector<StuntDouble*>::iterator iter; |
235 | + | nTotObjects = entry_plug->getTotIntegrableObjects(); |
236 | #ifndef IS_MPI | |
287 | – | |
288 | – | finalOut << nAtoms << "\n"; |
289 | – | |
290 | – | finalOut << entry_plug->box_x << "\t" |
291 | – | << entry_plug->box_y << "\t" |
292 | – | << entry_plug->box_z << "\n"; |
237 | ||
238 | < | for( i=0; i<nAtoms; i++ ){ |
239 | < | |
296 | < | sprintf( tempBuffer, |
297 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
298 | < | atoms[i]->getType(), |
299 | < | atoms[i]->getX(), |
300 | < | atoms[i]->getY(), |
301 | < | atoms[i]->getZ(), |
302 | < | atoms[i]->get_vx(), |
303 | < | atoms[i]->get_vy(), |
304 | < | atoms[i]->get_vz()); |
305 | < | strcpy( writeLine, tempBuffer ); |
238 | > | for(k = 0; k < outFile.size(); k++){ |
239 | > | *outFile[k] << nTotObjects << "\n"; |
240 | ||
241 | < | if( atoms[i]->isDirectional() ){ |
242 | < | |
243 | < | dAtom = (DirectionalAtom *)atoms[i]; |
244 | < | dAtom->getQ( q ); |
245 | < | |
246 | < | sprintf( tempBuffer, |
247 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
248 | < | q[0], |
315 | < | q[1], |
316 | < | q[2], |
317 | < | q[3], |
318 | < | dAtom->getJx(), |
319 | < | dAtom->getJy(), |
320 | < | dAtom->getJz()); |
321 | < | strcat( writeLine, tempBuffer ); |
322 | < | } |
323 | < | else |
324 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
325 | < | |
326 | < | finalOut << writeLine; |
327 | < | } |
328 | < | finalOut.flush(); |
329 | < | finalOut.close(); |
241 | > | *outFile[k] << currentTime << ";\t" |
242 | > | << entry_plug->Hmat[0][0] << "\t" |
243 | > | << entry_plug->Hmat[1][0] << "\t" |
244 | > | << entry_plug->Hmat[2][0] << ";\t" |
245 | > | |
246 | > | << entry_plug->Hmat[0][1] << "\t" |
247 | > | << entry_plug->Hmat[1][1] << "\t" |
248 | > | << entry_plug->Hmat[2][1] << ";\t" |
249 | ||
250 | < | #else // is_mpi |
251 | < | |
252 | < | MPI::Status istatus; |
334 | < | int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
250 | > | << entry_plug->Hmat[0][2] << "\t" |
251 | > | << entry_plug->Hmat[1][2] << "\t" |
252 | > | << entry_plug->Hmat[2][2] << ";"; |
253 | ||
254 | < | // write out header and node 0's coordinates |
254 | > | //write out additional parameters, such as chi and eta |
255 | > | *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
256 | > | } |
257 | ||
258 | < | if( worldRank == 0 ){ |
259 | < | finalOut << mpiSim->getTotAtoms() << "\n"; |
258 | > | for( i=0; i< entry_plug->n_mol; i++ ){ |
259 | > | |
260 | > | integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); |
261 | > | molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); |
262 | ||
263 | < | finalOut << entry_plug->box_x << "\t" |
264 | < | << entry_plug->box_y << "\t" |
265 | < | << entry_plug->box_z << "\n"; |
266 | < | |
267 | < | for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
268 | < | // Get the Node number which has this molecule: |
269 | < | |
270 | < | which_node = AtomToProcMap[i]; |
271 | < | |
272 | < | if (which_node == mpiSim->getMyNode()) { |
273 | < | |
274 | < | sprintf( tempBuffer, |
275 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
276 | < | atoms[i]->getType(), |
277 | < | atoms[i]->getX(), |
278 | < | atoms[i]->getY(), |
279 | < | atoms[i]->getZ(), |
280 | < | atoms[i]->get_vx(), |
281 | < | atoms[i]->get_vy(), |
282 | < | atoms[i]->get_vz()); |
283 | < | strcpy( writeLine, tempBuffer ); |
284 | < | |
285 | < | if( atoms[i]->isDirectional() ){ |
286 | < | |
287 | < | dAtom = (DirectionalAtom *)atoms[i]; |
288 | < | dAtom->getQ( q ); |
289 | < | |
290 | < | sprintf( tempBuffer, |
291 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
292 | < | q[0], |
293 | < | q[1], |
372 | < | q[2], |
373 | < | q[3], |
374 | < | dAtom->getJx(), |
375 | < | dAtom->getJy(), |
376 | < | dAtom->getJz()); |
377 | < | strcat( writeLine, tempBuffer ); |
378 | < | } |
379 | < | else |
380 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
381 | < | |
382 | < | } else { |
383 | < | |
384 | < | MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
385 | < | MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
386 | < | TAKE_THIS_TAG, istatus); |
263 | > | for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ |
264 | > | sd = *iter; |
265 | > | sd->getPos(pos); |
266 | > | sd->getVel(vel); |
267 | > | |
268 | > | sprintf( tempBuffer, |
269 | > | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
270 | > | sd->getType(), |
271 | > | pos[0], |
272 | > | pos[1], |
273 | > | pos[2], |
274 | > | vel[0], |
275 | > | vel[1], |
276 | > | vel[2]); |
277 | > | strcpy( writeLine, tempBuffer ); |
278 | > | |
279 | > | if( sd->isDirectional() ){ |
280 | > | |
281 | > | sd->getQ( q ); |
282 | > | sd->getJ( ji ); |
283 | > | |
284 | > | sprintf( tempBuffer, |
285 | > | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
286 | > | q[0], |
287 | > | q[1], |
288 | > | q[2], |
289 | > | q[3], |
290 | > | ji[0], |
291 | > | ji[1], |
292 | > | ji[2]); |
293 | > | strcat( writeLine, tempBuffer ); |
294 | } | |
295 | < | |
296 | < | finalOut << writeLine; |
295 | > | else |
296 | > | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
297 | > | |
298 | > | for(k = 0; k < outFile.size(); k++) |
299 | > | *outFile[k] << writeLine; |
300 | } | |
301 | + | |
302 | + | } |
303 | + | |
304 | + | #else // is_mpi |
305 | + | |
306 | + | /* code to find maximum tag value */ |
307 | + | |
308 | + | int *tagub, flag, MAXTAG; |
309 | + | MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
310 | + | if (flag) { |
311 | + | MAXTAG = *tagub; |
312 | + | } else { |
313 | + | MAXTAG = 32767; |
314 | + | } |
315 | + | |
316 | + | int haveError; |
317 | + | |
318 | + | MPI_Status istatus; |
319 | + | int nCurObj; |
320 | + | int *MolToProcMap = mpiSim->getMolToProcMap(); |
321 | + | |
322 | + | // write out header and node 0's coordinates |
323 | + | |
324 | + | if( worldRank == 0 ){ |
325 | + | |
326 | + | // Node 0 needs a list of the magic potatoes for each processor; |
327 | + | |
328 | + | nProc = mpiSim->getNProcessors(); |
329 | + | potatoes = new int[nProc]; |
330 | + | |
331 | + | //write out the comment lines |
332 | + | for (i = 0; i < nProc; i++) |
333 | + | potatoes[i] = 0; |
334 | ||
335 | < | // kill everyone off: |
336 | < | game_over = -1; |
337 | < | for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
338 | < | MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
335 | > | for(k = 0; k < outFile.size(); k++){ |
336 | > | *outFile[k] << nTotObjects << "\n"; |
337 | > | |
338 | > | *outFile[k] << currentTime << ";\t" |
339 | > | << entry_plug->Hmat[0][0] << "\t" |
340 | > | << entry_plug->Hmat[1][0] << "\t" |
341 | > | << entry_plug->Hmat[2][0] << ";\t" |
342 | > | |
343 | > | << entry_plug->Hmat[0][1] << "\t" |
344 | > | << entry_plug->Hmat[1][1] << "\t" |
345 | > | << entry_plug->Hmat[2][1] << ";\t" |
346 | > | |
347 | > | << entry_plug->Hmat[0][2] << "\t" |
348 | > | << entry_plug->Hmat[1][2] << "\t" |
349 | > | << entry_plug->Hmat[2][2] << ";"; |
350 | > | |
351 | > | *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
352 | } | |
353 | ||
354 | + | currentIndex = 0; |
355 | + | |
356 | + | for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { |
357 | + | |
358 | + | // Get the Node number which has this atom; |
359 | + | |
360 | + | which_node = MolToProcMap[i]; |
361 | + | |
362 | + | if (which_node != 0) { |
363 | + | |
364 | + | if (potatoes[which_node] + 1 >= MAXTAG) { |
365 | + | // The potato was going to exceed the maximum value, |
366 | + | // so wrap this processor potato back to 0: |
367 | + | |
368 | + | potatoes[which_node] = 0; |
369 | + | MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
370 | + | |
371 | + | } |
372 | + | |
373 | + | myPotato = potatoes[which_node]; |
374 | + | |
375 | + | //recieve the number of integrableObject in current molecule |
376 | + | MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
377 | + | myPotato, MPI_COMM_WORLD, &istatus); |
378 | + | myPotato++; |
379 | + | |
380 | + | for(int l = 0; l < nCurObj; l++){ |
381 | + | |
382 | + | if (potatoes[which_node] + 2 >= MAXTAG) { |
383 | + | // The potato was going to exceed the maximum value, |
384 | + | // so wrap this processor potato back to 0: |
385 | + | |
386 | + | potatoes[which_node] = 0; |
387 | + | MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
388 | + | |
389 | + | } |
390 | + | |
391 | + | MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
392 | + | myPotato, MPI_COMM_WORLD, &istatus); |
393 | + | |
394 | + | atomTypeString = MPIatomTypeString; |
395 | + | |
396 | + | myPotato++; |
397 | + | |
398 | + | MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus); |
399 | + | myPotato++; |
400 | + | |
401 | + | MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
402 | + | |
403 | + | if(msgLen == 13) |
404 | + | isDirectional = 1; |
405 | + | else |
406 | + | isDirectional = 0; |
407 | + | |
408 | + | // If we've survived to here, format the line: |
409 | + | |
410 | + | if (!isDirectional) { |
411 | + | |
412 | + | sprintf( writeLine, |
413 | + | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
414 | + | atomTypeString, |
415 | + | atomData[0], |
416 | + | atomData[1], |
417 | + | atomData[2], |
418 | + | atomData[3], |
419 | + | atomData[4], |
420 | + | atomData[5]); |
421 | + | |
422 | + | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
423 | + | |
424 | + | } |
425 | + | else { |
426 | + | |
427 | + | sprintf( writeLine, |
428 | + | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
429 | + | atomTypeString, |
430 | + | atomData[0], |
431 | + | atomData[1], |
432 | + | atomData[2], |
433 | + | atomData[3], |
434 | + | atomData[4], |
435 | + | atomData[5], |
436 | + | atomData[6], |
437 | + | atomData[7], |
438 | + | atomData[8], |
439 | + | atomData[9], |
440 | + | atomData[10], |
441 | + | atomData[11], |
442 | + | atomData[12]); |
443 | + | |
444 | + | } |
445 | + | |
446 | + | for(k = 0; k < outFile.size(); k++) |
447 | + | *outFile[k] << writeLine; |
448 | + | |
449 | + | }// end for(int l =0) |
450 | + | potatoes[which_node] = myPotato; |
451 | + | |
452 | + | } |
453 | + | else { |
454 | + | |
455 | + | haveError = 0; |
456 | + | |
457 | + | local_index = indexArray[currentIndex].first; |
458 | + | |
459 | + | integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); |
460 | + | |
461 | + | for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){ |
462 | + | sd = *iter; |
463 | + | atomTypeString = sd->getType(); |
464 | + | |
465 | + | sd->getPos(pos); |
466 | + | sd->getVel(vel); |
467 | + | |
468 | + | atomData[0] = pos[0]; |
469 | + | atomData[1] = pos[1]; |
470 | + | atomData[2] = pos[2]; |
471 | + | |
472 | + | atomData[3] = vel[0]; |
473 | + | atomData[4] = vel[1]; |
474 | + | atomData[5] = vel[2]; |
475 | + | |
476 | + | isDirectional = 0; |
477 | + | |
478 | + | if( sd->isDirectional() ){ |
479 | + | |
480 | + | isDirectional = 1; |
481 | + | |
482 | + | sd->getQ( q ); |
483 | + | sd->getJ( ji ); |
484 | + | |
485 | + | for (int j = 0; j < 6 ; j++) |
486 | + | atomData[j] = atomData[j]; |
487 | + | |
488 | + | atomData[6] = q[0]; |
489 | + | atomData[7] = q[1]; |
490 | + | atomData[8] = q[2]; |
491 | + | atomData[9] = q[3]; |
492 | + | |
493 | + | atomData[10] = ji[0]; |
494 | + | atomData[11] = ji[1]; |
495 | + | atomData[12] = ji[2]; |
496 | + | } |
497 | + | |
498 | + | // If we've survived to here, format the line: |
499 | + | |
500 | + | if (!isDirectional) { |
501 | + | |
502 | + | sprintf( writeLine, |
503 | + | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
504 | + | atomTypeString, |
505 | + | atomData[0], |
506 | + | atomData[1], |
507 | + | atomData[2], |
508 | + | atomData[3], |
509 | + | atomData[4], |
510 | + | atomData[5]); |
511 | + | |
512 | + | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
513 | + | |
514 | + | } |
515 | + | else { |
516 | + | |
517 | + | sprintf( writeLine, |
518 | + | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
519 | + | atomTypeString, |
520 | + | atomData[0], |
521 | + | atomData[1], |
522 | + | atomData[2], |
523 | + | atomData[3], |
524 | + | atomData[4], |
525 | + | atomData[5], |
526 | + | atomData[6], |
527 | + | atomData[7], |
528 | + | atomData[8], |
529 | + | atomData[9], |
530 | + | atomData[10], |
531 | + | atomData[11], |
532 | + | atomData[12]); |
533 | + | |
534 | + | } |
535 | + | |
536 | + | for(k = 0; k < outFile.size(); k++) |
537 | + | *outFile[k] << writeLine; |
538 | + | |
539 | + | |
540 | + | }//end for(iter = integrableObject.begin()) |
541 | + | |
542 | + | currentIndex++; |
543 | + | } |
544 | + | |
545 | + | }//end for(i = 0; i < mpiSim->getNmol()) |
546 | + | |
547 | + | for(k = 0; k < outFile.size(); k++) |
548 | + | outFile[k]->flush(); |
549 | + | |
550 | + | sprintf( checkPointMsg, |
551 | + | "Sucessfully took a dump.\n"); |
552 | + | |
553 | + | MPIcheckPoint(); |
554 | + | |
555 | + | delete[] potatoes; |
556 | + | |
557 | } else { | |
558 | + | |
559 | + | // worldRank != 0, so I'm a remote node. |
560 | + | |
561 | + | // Set my magic potato to 0: |
562 | + | |
563 | + | myPotato = 0; |
564 | + | currentIndex = 0; |
565 | ||
566 | < | done = 0; |
567 | < | while (!done) { |
568 | < | MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
569 | < | TAKE_THIS_TAG, istatus); |
566 | > | for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { |
567 | > | |
568 | > | // Am I the node which has this integrableObject? |
569 | > | |
570 | > | if (MolToProcMap[i] == worldRank) { |
571 | ||
405 | – | if (which_atom == -1) { |
406 | – | done=1; |
407 | – | continue; |
408 | – | } else { |
572 | ||
573 | < | //format the line |
411 | < | sprintf( tempBuffer, |
412 | < | "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
413 | < | atoms[which_atom]->getType(), |
414 | < | atoms[which_atom]->getX(), |
415 | < | atoms[which_atom]->getY(), |
416 | < | atoms[which_atom]->getZ(), |
417 | < | atoms[which_atom]->get_vx(), |
418 | < | atoms[which_atom]->get_vy(), |
419 | < | atoms[which_atom]->get_vz()); // check here. |
420 | < | strcpy( writeLine, tempBuffer ); |
573 | > | if (myPotato + 1 >= MAXTAG) { |
574 | ||
575 | < | if( atoms[which_atom]->isDirectional() ){ |
576 | < | |
577 | < | dAtom = (DirectionalAtom *)atoms[which_atom]; |
578 | < | dAtom->getQ( q ); |
579 | < | |
580 | < | sprintf( tempBuffer, |
581 | < | "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
582 | < | q[0], |
583 | < | q[1], |
584 | < | q[2], |
585 | < | q[3], |
586 | < | dAtom->getJx(), |
587 | < | dAtom->getJy(), |
588 | < | dAtom->getJz()); |
589 | < | strcat( writeLine, tempBuffer ); |
590 | < | } |
591 | < | else |
592 | < | strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
593 | < | |
594 | < | MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
595 | < | TAKE_THIS_TAG); |
575 | > | // The potato was going to exceed the maximum value, |
576 | > | // so wrap this processor potato back to 0 (and block until |
577 | > | // node 0 says we can go: |
578 | > | |
579 | > | MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
580 | > | |
581 | > | } |
582 | > | |
583 | > | local_index = indexArray[currentIndex].first; |
584 | > | integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects(); |
585 | > | |
586 | > | nCurObj = integrableObjects.size(); |
587 | > | |
588 | > | MPI_Send(&nCurObj, 1, MPI_INT, 0, |
589 | > | myPotato, MPI_COMM_WORLD); |
590 | > | myPotato++; |
591 | > | |
592 | > | for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ |
593 | > | |
594 | > | if (myPotato + 2 >= MAXTAG) { |
595 | > | |
596 | > | // The potato was going to exceed the maximum value, |
597 | > | // so wrap this processor potato back to 0 (and block until |
598 | > | // node 0 says we can go: |
599 | > | |
600 | > | MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
601 | > | |
602 | > | } |
603 | > | |
604 | > | sd = *iter; |
605 | > | |
606 | > | atomTypeString = sd->getType(); |
607 | > | |
608 | > | sd->getPos(pos); |
609 | > | sd->getVel(vel); |
610 | > | |
611 | > | atomData[0] = pos[0]; |
612 | > | atomData[1] = pos[1]; |
613 | > | atomData[2] = pos[2]; |
614 | > | |
615 | > | atomData[3] = vel[0]; |
616 | > | atomData[4] = vel[1]; |
617 | > | atomData[5] = vel[2]; |
618 | > | |
619 | > | isDirectional = 0; |
620 | > | |
621 | > | if( sd->isDirectional() ){ |
622 | > | |
623 | > | isDirectional = 1; |
624 | > | |
625 | > | sd->getQ( q ); |
626 | > | sd->getJ( ji ); |
627 | > | |
628 | > | |
629 | > | atomData[6] = q[0]; |
630 | > | atomData[7] = q[1]; |
631 | > | atomData[8] = q[2]; |
632 | > | atomData[9] = q[3]; |
633 | > | |
634 | > | atomData[10] = ji[0]; |
635 | > | atomData[11] = ji[1]; |
636 | > | atomData[12] = ji[2]; |
637 | > | } |
638 | > | |
639 | > | |
640 | > | strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
641 | > | |
642 | > | // null terminate the string before sending (just in case): |
643 | > | MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
644 | > | |
645 | > | MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
646 | > | myPotato, MPI_COMM_WORLD); |
647 | > | |
648 | > | myPotato++; |
649 | > | |
650 | > | if (isDirectional) { |
651 | > | |
652 | > | MPI_Send(atomData, 13, MPI_DOUBLE, 0, |
653 | > | myPotato, MPI_COMM_WORLD); |
654 | > | |
655 | > | } else { |
656 | > | |
657 | > | MPI_Send(atomData, 6, MPI_DOUBLE, 0, |
658 | > | myPotato, MPI_COMM_WORLD); |
659 | > | } |
660 | > | |
661 | > | myPotato++; |
662 | > | |
663 | > | } |
664 | > | |
665 | > | currentIndex++; |
666 | > | |
667 | > | } |
668 | > | |
669 | } | |
670 | + | |
671 | + | sprintf( checkPointMsg, |
672 | + | "Sucessfully took a dump.\n"); |
673 | + | MPIcheckPoint(); |
674 | + | |
675 | } | |
445 | – | } |
446 | – | finalOut.flush(); |
447 | – | sprintf( checkPointMsg, |
448 | – | "Sucessfully took a dump.\n"); |
449 | – | MPIcheckPoint(); |
676 | ||
677 | < | if( worldRank == 0 ) finalOut.close(); |
677 | > | |
678 | > | |
679 | #endif // is_mpi | |
680 | } | |
681 | + | |
682 | + | #ifdef IS_MPI |
683 | + | |
684 | + | // a couple of functions to let us escape the write loop |
685 | + | |
686 | + | void dWrite::DieDieDie( void ){ |
687 | + | |
688 | + | MPI_Finalize(); |
689 | + | exit (0); |
690 | + | } |
691 | + | |
692 | + | #endif //is_mpi |
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