1 |
#define _FILE_OFFSET_BITS 64 |
2 |
|
3 |
#include <string.h> |
4 |
#include <iostream> |
5 |
#include <fstream> |
6 |
#include <algorithm> |
7 |
#include <utility> |
8 |
|
9 |
#ifdef IS_MPI |
10 |
#include <mpi.h> |
11 |
#include "mpiSimulation.hpp" |
12 |
|
13 |
namespace dWrite{ |
14 |
void DieDieDie( void ); |
15 |
} |
16 |
|
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using namespace dWrite; |
18 |
#endif //is_mpi |
19 |
|
20 |
#include "ReadWrite.hpp" |
21 |
#include "simError.h" |
22 |
|
23 |
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
24 |
|
25 |
entry_plug = the_entry_plug; |
26 |
|
27 |
#ifdef IS_MPI |
28 |
if(worldRank == 0 ){ |
29 |
#endif // is_mpi |
30 |
|
31 |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
32 |
|
33 |
if( !dumpFile ){ |
34 |
|
35 |
sprintf( painCave.errMsg, |
36 |
"Could not open \"%s\" for dump output.\n", |
37 |
entry_plug->sampleName); |
38 |
painCave.isFatal = 1; |
39 |
simError(); |
40 |
} |
41 |
|
42 |
#ifdef IS_MPI |
43 |
} |
44 |
|
45 |
//sort the local atoms by global index |
46 |
sortByGlobalIndex(); |
47 |
|
48 |
sprintf( checkPointMsg, |
49 |
"Sucessfully opened output file for dumping.\n"); |
50 |
MPIcheckPoint(); |
51 |
#endif // is_mpi |
52 |
} |
53 |
|
54 |
DumpWriter::~DumpWriter( ){ |
55 |
|
56 |
#ifdef IS_MPI |
57 |
if(worldRank == 0 ){ |
58 |
#endif // is_mpi |
59 |
|
60 |
dumpFile.close(); |
61 |
|
62 |
#ifdef IS_MPI |
63 |
} |
64 |
#endif // is_mpi |
65 |
} |
66 |
|
67 |
#ifdef IS_MPI |
68 |
|
69 |
/** |
70 |
* A hook function to load balancing |
71 |
*/ |
72 |
|
73 |
void DumpWriter::update(){ |
74 |
sortByGlobalIndex(); |
75 |
} |
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|
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/** |
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* Auxiliary sorting function |
79 |
*/ |
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|
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bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
82 |
return p1.second < p2.second; |
83 |
} |
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|
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/** |
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* Sorting the local index by global index |
87 |
*/ |
88 |
|
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void DumpWriter::sortByGlobalIndex(){ |
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Atom** atoms = entry_plug->atoms; |
91 |
|
92 |
indexArray.clear(); |
93 |
|
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for(int i = 0; i < mpiSim->getMyNlocal();i++) |
95 |
indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
96 |
|
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
98 |
|
99 |
//for (int i = 0; i < mpiSim->getMyNlocal(); i++) { |
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// printf("node %d has global %d at local %d\n", worldRank, indexArray[i].second, indexArray[i].first); |
101 |
//} |
102 |
|
103 |
} |
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|
105 |
#endif |
106 |
|
107 |
void DumpWriter::writeDump(double currentTime){ |
108 |
|
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ofstream finalOut; |
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vector<ofstream*> fileStreams; |
111 |
|
112 |
#ifdef IS_MPI |
113 |
if(worldRank == 0 ){ |
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#endif |
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finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
116 |
if( !finalOut ){ |
117 |
sprintf( painCave.errMsg, |
118 |
"Could not open \"%s\" for final dump output.\n", |
119 |
entry_plug->finalName ); |
120 |
painCave.isFatal = 1; |
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simError(); |
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} |
123 |
#ifdef IS_MPI |
124 |
} |
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#endif // is_mpi |
126 |
|
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fileStreams.push_back(&finalOut); |
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fileStreams.push_back(&dumpFile); |
129 |
|
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writeFrame(fileStreams, currentTime); |
131 |
|
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#ifdef IS_MPI |
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finalOut.close(); |
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#endif |
135 |
|
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} |
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|
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void DumpWriter::writeFinal(double currentTime){ |
139 |
|
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ofstream finalOut; |
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vector<ofstream*> fileStreams; |
142 |
|
143 |
#ifdef IS_MPI |
144 |
if(worldRank == 0 ){ |
145 |
#endif // is_mpi |
146 |
|
147 |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
148 |
|
149 |
if( !finalOut ){ |
150 |
sprintf( painCave.errMsg, |
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"Could not open \"%s\" for final dump output.\n", |
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entry_plug->finalName ); |
153 |
painCave.isFatal = 1; |
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simError(); |
155 |
} |
156 |
|
157 |
#ifdef IS_MPI |
158 |
} |
159 |
#endif // is_mpi |
160 |
|
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fileStreams.push_back(&finalOut); |
162 |
writeFrame(fileStreams, currentTime); |
163 |
|
164 |
#ifdef IS_MPI |
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finalOut.close(); |
166 |
#endif |
167 |
|
168 |
} |
169 |
|
170 |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
171 |
|
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const int BUFFERSIZE = 2000; |
173 |
const int MINIBUFFERSIZE = 100; |
174 |
|
175 |
char tempBuffer[BUFFERSIZE]; |
176 |
char writeLine[BUFFERSIZE]; |
177 |
|
178 |
int i, k; |
179 |
|
180 |
#ifdef IS_MPI |
181 |
|
182 |
/********************************************************************* |
183 |
* Documentation? You want DOCUMENTATION? |
184 |
* |
185 |
* Why all the potatoes below? |
186 |
* |
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* To make a long story short, the original version of DumpWriter |
188 |
* worked in the most inefficient way possible. Node 0 would |
189 |
* poke each of the node for an individual atom's formatted data |
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* as node 0 worked its way down the global index. This was particularly |
191 |
* inefficient since the method blocked all processors at every atom |
192 |
* (and did it twice!). |
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* |
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* An intermediate version of DumpWriter could be described from Node |
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* zero's perspective as follows: |
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* |
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* 1) Have 100 of your friends stand in a circle. |
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* 2) When you say go, have all of them start tossing potatoes at |
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* you (one at a time). |
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* 3) Catch the potatoes. |
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* |
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* It was an improvement, but MPI has buffers and caches that could |
203 |
* best be described in this analogy as "potato nets", so there's no |
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* need to block the processors atom-by-atom. |
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* |
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* This new and improved DumpWriter works in an even more efficient |
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* way: |
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* |
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* 1) Have 100 of your friend stand in a circle. |
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* 2) When you say go, have them start tossing 5-pound bags of |
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* potatoes at you. |
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* 3) Once you've caught a friend's bag of potatoes, |
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* toss them a spud to let them know they can toss another bag. |
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* |
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* How's THAT for documentation? |
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* |
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*********************************************************************/ |
218 |
|
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int *potatoes; |
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int myPotato; |
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|
222 |
int nProc; |
223 |
int j, which_node, done, which_atom, local_index, currentIndex; |
224 |
double atomData6[6]; |
225 |
double atomData13[13]; |
226 |
int isDirectional; |
227 |
char* atomTypeString; |
228 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
229 |
|
230 |
#else //is_mpi |
231 |
int nAtoms = entry_plug->n_atoms; |
232 |
#endif //is_mpi |
233 |
|
234 |
double q[4]; |
235 |
DirectionalAtom* dAtom; |
236 |
Atom** atoms = entry_plug->atoms; |
237 |
double pos[3], vel[3]; |
238 |
|
239 |
#ifndef IS_MPI |
240 |
|
241 |
for(k = 0; k < outFile.size(); k++){ |
242 |
*outFile[k] << nAtoms << "\n"; |
243 |
|
244 |
*outFile[k] << currentTime << ";\t" |
245 |
<< entry_plug->Hmat[0][0] << "\t" |
246 |
<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
248 |
|
249 |
<< entry_plug->Hmat[0][1] << "\t" |
250 |
<< entry_plug->Hmat[1][1] << "\t" |
251 |
<< entry_plug->Hmat[2][1] << ";\t" |
252 |
|
253 |
<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
255 |
<< entry_plug->Hmat[2][2] << ";"; |
256 |
|
257 |
//write out additional parameters, such as chi and eta |
258 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
259 |
} |
260 |
|
261 |
for( i=0; i<nAtoms; i++ ){ |
262 |
|
263 |
atoms[i]->getPos(pos); |
264 |
atoms[i]->getVel(vel); |
265 |
|
266 |
sprintf( tempBuffer, |
267 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
268 |
atoms[i]->getType(), |
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pos[0], |
270 |
pos[1], |
271 |
pos[2], |
272 |
vel[0], |
273 |
vel[1], |
274 |
vel[2]); |
275 |
strcpy( writeLine, tempBuffer ); |
276 |
|
277 |
if( atoms[i]->isDirectional() ){ |
278 |
|
279 |
dAtom = (DirectionalAtom *)atoms[i]; |
280 |
dAtom->getQ( q ); |
281 |
|
282 |
sprintf( tempBuffer, |
283 |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
284 |
q[0], |
285 |
q[1], |
286 |
q[2], |
287 |
q[3], |
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dAtom->getJx(), |
289 |
dAtom->getJy(), |
290 |
dAtom->getJz()); |
291 |
strcat( writeLine, tempBuffer ); |
292 |
} |
293 |
else |
294 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
295 |
|
296 |
for(k = 0; k < outFile.size(); k++) |
297 |
*outFile[k] << writeLine; |
298 |
} |
299 |
|
300 |
#else // is_mpi |
301 |
|
302 |
/* code to find maximum tag value */ |
303 |
|
304 |
int *tagub, flag, MAXTAG; |
305 |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
306 |
if (flag) { |
307 |
MAXTAG = *tagub; |
308 |
} else { |
309 |
MAXTAG = 32767; |
310 |
} |
311 |
|
312 |
int haveError; |
313 |
|
314 |
MPI_Status istatus; |
315 |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
316 |
|
317 |
// write out header and node 0's coordinates |
318 |
|
319 |
if( worldRank == 0 ){ |
320 |
|
321 |
// Node 0 needs a list of the magic potatoes for each processor; |
322 |
|
323 |
nProc = mpiSim->getNumberProcessors(); |
324 |
potatoes = new int[nProc]; |
325 |
|
326 |
//write out the comment lines |
327 |
for (i = 0; i < nProc; i++) |
328 |
potatoes[i] = 0; |
329 |
|
330 |
for(k = 0; k < outFile.size(); k++){ |
331 |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
332 |
|
333 |
*outFile[k] << currentTime << ";\t" |
334 |
<< entry_plug->Hmat[0][0] << "\t" |
335 |
<< entry_plug->Hmat[1][0] << "\t" |
336 |
<< entry_plug->Hmat[2][0] << ";\t" |
337 |
|
338 |
<< entry_plug->Hmat[0][1] << "\t" |
339 |
<< entry_plug->Hmat[1][1] << "\t" |
340 |
<< entry_plug->Hmat[2][1] << ";\t" |
341 |
|
342 |
<< entry_plug->Hmat[0][2] << "\t" |
343 |
<< entry_plug->Hmat[1][2] << "\t" |
344 |
<< entry_plug->Hmat[2][2] << ";"; |
345 |
|
346 |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
347 |
} |
348 |
|
349 |
currentIndex = 0; |
350 |
|
351 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
352 |
|
353 |
// Get the Node number which has this atom; |
354 |
|
355 |
which_node = AtomToProcMap[i]; |
356 |
|
357 |
if (which_node != 0) { |
358 |
|
359 |
if (potatoes[which_node] + 3 >= MAXTAG) { |
360 |
// The potato was going to exceed the maximum value, |
361 |
// so wrap this processor potato back to 0: |
362 |
|
363 |
potatoes[which_node] = 0; |
364 |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
365 |
|
366 |
} |
367 |
|
368 |
myPotato = potatoes[which_node]; |
369 |
|
370 |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
371 |
myPotato, MPI_COMM_WORLD, &istatus); |
372 |
|
373 |
atomTypeString = MPIatomTypeString; |
374 |
|
375 |
myPotato++; |
376 |
|
377 |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
378 |
myPotato, MPI_COMM_WORLD, &istatus); |
379 |
|
380 |
myPotato++; |
381 |
|
382 |
if (isDirectional) { |
383 |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
384 |
myPotato, MPI_COMM_WORLD, &istatus); |
385 |
} else { |
386 |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
387 |
myPotato, MPI_COMM_WORLD, &istatus); |
388 |
} |
389 |
|
390 |
myPotato++; |
391 |
potatoes[which_node] = myPotato; |
392 |
|
393 |
} else { |
394 |
|
395 |
haveError = 0; |
396 |
which_atom = i; |
397 |
|
398 |
//local_index = -1; |
399 |
|
400 |
//for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
401 |
// if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
402 |
//} |
403 |
|
404 |
//if (local_index != -1) { |
405 |
|
406 |
local_index = indexArray[currentIndex].first; |
407 |
|
408 |
if (which_atom == indexArray[currentIndex].second) { |
409 |
|
410 |
atomTypeString = atoms[local_index]->getType(); |
411 |
|
412 |
atoms[local_index]->getPos(pos); |
413 |
atoms[local_index]->getVel(vel); |
414 |
|
415 |
atomData6[0] = pos[0]; |
416 |
atomData6[1] = pos[1]; |
417 |
atomData6[2] = pos[2]; |
418 |
|
419 |
atomData6[3] = vel[0]; |
420 |
atomData6[4] = vel[1]; |
421 |
atomData6[5] = vel[2]; |
422 |
|
423 |
isDirectional = 0; |
424 |
|
425 |
if( atoms[local_index]->isDirectional() ){ |
426 |
|
427 |
isDirectional = 1; |
428 |
|
429 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
430 |
dAtom->getQ( q ); |
431 |
|
432 |
for (int j = 0; j < 6 ; j++) |
433 |
atomData13[j] = atomData6[j]; |
434 |
|
435 |
atomData13[6] = q[0]; |
436 |
atomData13[7] = q[1]; |
437 |
atomData13[8] = q[2]; |
438 |
atomData13[9] = q[3]; |
439 |
|
440 |
atomData13[10] = dAtom->getJx(); |
441 |
atomData13[11] = dAtom->getJy(); |
442 |
atomData13[12] = dAtom->getJz(); |
443 |
} |
444 |
|
445 |
} else { |
446 |
sprintf(painCave.errMsg, |
447 |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
448 |
which_atom, worldRank, currentIndex, local_index ); |
449 |
haveError= 1; |
450 |
simError(); |
451 |
} |
452 |
|
453 |
if(haveError) DieDieDie(); |
454 |
|
455 |
currentIndex++; |
456 |
} |
457 |
// If we've survived to here, format the line: |
458 |
|
459 |
if (!isDirectional) { |
460 |
|
461 |
sprintf( writeLine, |
462 |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
463 |
atomTypeString, |
464 |
atomData6[0], |
465 |
atomData6[1], |
466 |
atomData6[2], |
467 |
atomData6[3], |
468 |
atomData6[4], |
469 |
atomData6[5]); |
470 |
|
471 |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
472 |
|
473 |
} else { |
474 |
|
475 |
sprintf( writeLine, |
476 |
"%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", |
477 |
atomTypeString, |
478 |
atomData13[0], |
479 |
atomData13[1], |
480 |
atomData13[2], |
481 |
atomData13[3], |
482 |
atomData13[4], |
483 |
atomData13[5], |
484 |
atomData13[6], |
485 |
atomData13[7], |
486 |
atomData13[8], |
487 |
atomData13[9], |
488 |
atomData13[10], |
489 |
atomData13[11], |
490 |
atomData13[12]); |
491 |
|
492 |
} |
493 |
|
494 |
for(k = 0; k < outFile.size(); k++) |
495 |
*outFile[k] << writeLine; |
496 |
} |
497 |
|
498 |
for(k = 0; k < outFile.size(); k++) |
499 |
outFile[k]->flush(); |
500 |
|
501 |
sprintf( checkPointMsg, |
502 |
"Sucessfully took a dump.\n"); |
503 |
|
504 |
MPIcheckPoint(); |
505 |
|
506 |
delete[] potatoes; |
507 |
|
508 |
} else { |
509 |
|
510 |
// worldRank != 0, so I'm a remote node. |
511 |
|
512 |
// Set my magic potato to 0: |
513 |
|
514 |
myPotato = 0; |
515 |
currentIndex = 0; |
516 |
|
517 |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
518 |
|
519 |
// Am I the node which has this atom? |
520 |
|
521 |
if (AtomToProcMap[i] == worldRank) { |
522 |
|
523 |
if (myPotato + 3 >= MAXTAG) { |
524 |
|
525 |
// The potato was going to exceed the maximum value, |
526 |
// so wrap this processor potato back to 0 (and block until |
527 |
// node 0 says we can go: |
528 |
|
529 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
530 |
|
531 |
} |
532 |
which_atom = i; |
533 |
|
534 |
//local_index = -1; |
535 |
|
536 |
//for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
537 |
// if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
538 |
//} |
539 |
|
540 |
//if (local_index != -1) { |
541 |
|
542 |
local_index = indexArray[currentIndex].first; |
543 |
|
544 |
if (which_atom == indexArray[currentIndex].second) { |
545 |
|
546 |
atomTypeString = atoms[local_index]->getType(); |
547 |
|
548 |
atoms[local_index]->getPos(pos); |
549 |
atoms[local_index]->getVel(vel); |
550 |
|
551 |
atomData6[0] = pos[0]; |
552 |
atomData6[1] = pos[1]; |
553 |
atomData6[2] = pos[2]; |
554 |
|
555 |
atomData6[3] = vel[0]; |
556 |
atomData6[4] = vel[1]; |
557 |
atomData6[5] = vel[2]; |
558 |
|
559 |
isDirectional = 0; |
560 |
|
561 |
if( atoms[local_index]->isDirectional() ){ |
562 |
|
563 |
isDirectional = 1; |
564 |
|
565 |
dAtom = (DirectionalAtom *)atoms[local_index]; |
566 |
dAtom->getQ( q ); |
567 |
|
568 |
for (int j = 0; j < 6 ; j++) |
569 |
atomData13[j] = atomData6[j]; |
570 |
|
571 |
atomData13[6] = q[0]; |
572 |
atomData13[7] = q[1]; |
573 |
atomData13[8] = q[2]; |
574 |
atomData13[9] = q[3]; |
575 |
|
576 |
atomData13[10] = dAtom->getJx(); |
577 |
atomData13[11] = dAtom->getJy(); |
578 |
atomData13[12] = dAtom->getJz(); |
579 |
} |
580 |
|
581 |
} else { |
582 |
sprintf(painCave.errMsg, |
583 |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
584 |
which_atom, worldRank, currentIndex, local_index ); |
585 |
haveError= 1; |
586 |
simError(); |
587 |
} |
588 |
|
589 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
590 |
|
591 |
// null terminate the string before sending (just in case): |
592 |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
593 |
|
594 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
595 |
myPotato, MPI_COMM_WORLD); |
596 |
|
597 |
myPotato++; |
598 |
|
599 |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
600 |
myPotato, MPI_COMM_WORLD); |
601 |
|
602 |
myPotato++; |
603 |
|
604 |
if (isDirectional) { |
605 |
|
606 |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
607 |
myPotato, MPI_COMM_WORLD); |
608 |
|
609 |
} else { |
610 |
|
611 |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
612 |
myPotato, MPI_COMM_WORLD); |
613 |
} |
614 |
|
615 |
myPotato++; |
616 |
currentIndex++; |
617 |
} |
618 |
} |
619 |
|
620 |
sprintf( checkPointMsg, |
621 |
"Sucessfully took a dump.\n"); |
622 |
MPIcheckPoint(); |
623 |
|
624 |
} |
625 |
|
626 |
#endif // is_mpi |
627 |
} |
628 |
|
629 |
#ifdef IS_MPI |
630 |
|
631 |
// a couple of functions to let us escape the write loop |
632 |
|
633 |
void dWrite::DieDieDie( void ){ |
634 |
|
635 |
MPI_Finalize(); |
636 |
exit (0); |
637 |
} |
638 |
|
639 |
#endif //is_mpi |