1 |
< |
#include <cstring> |
1 |
> |
#define _FILE_OFFSET_BITS 64 |
2 |
> |
|
3 |
> |
#include <string.h> |
4 |
|
#include <iostream> |
5 |
|
#include <fstream> |
6 |
|
|
7 |
|
#ifdef IS_MPI |
8 |
|
#include <mpi.h> |
9 |
|
#include "mpiSimulation.hpp" |
10 |
< |
#define TAKE_THIS_TAG 0 |
10 |
> |
|
11 |
> |
namespace dWrite{ |
12 |
> |
void DieDieDie( void ); |
13 |
> |
} |
14 |
> |
|
15 |
> |
using namespace dWrite; |
16 |
|
#endif //is_mpi |
17 |
|
|
18 |
|
#include "ReadWrite.hpp" |
19 |
|
#include "simError.h" |
20 |
|
|
14 |
– |
|
15 |
– |
|
16 |
– |
|
17 |
– |
|
21 |
|
DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
22 |
|
|
23 |
|
entry_plug = the_entry_plug; |
25 |
|
#ifdef IS_MPI |
26 |
|
if(worldRank == 0 ){ |
27 |
|
#endif // is_mpi |
28 |
< |
|
26 |
< |
|
27 |
< |
|
28 |
> |
|
29 |
|
strcpy( outName, entry_plug->sampleName ); |
30 |
< |
|
30 |
> |
|
31 |
|
outFile.open(outName, ios::out | ios::trunc ); |
32 |
< |
|
32 |
> |
|
33 |
|
if( !outFile ){ |
34 |
< |
|
34 |
> |
|
35 |
|
sprintf( painCave.errMsg, |
36 |
|
"Could not open \"%s\" for dump output.\n", |
37 |
|
outName); |
38 |
|
painCave.isFatal = 1; |
39 |
|
simError(); |
40 |
|
} |
41 |
< |
|
41 |
> |
|
42 |
|
//outFile.setf( ios::scientific ); |
43 |
|
|
44 |
|
#ifdef IS_MPI |
64 |
|
} |
65 |
|
|
66 |
|
void DumpWriter::writeDump( double currentTime ){ |
67 |
< |
|
67 |
> |
|
68 |
|
const int BUFFERSIZE = 2000; |
69 |
+ |
const int MINIBUFFERSIZE = 100; |
70 |
+ |
|
71 |
|
char tempBuffer[BUFFERSIZE]; |
72 |
|
char writeLine[BUFFERSIZE]; |
73 |
|
|
74 |
|
int i; |
75 |
+ |
|
76 |
+ |
#ifdef IS_MPI |
77 |
+ |
|
78 |
+ |
int *potatoes; |
79 |
+ |
int myPotato; |
80 |
+ |
|
81 |
+ |
int nProc; |
82 |
+ |
int j, which_node, done, which_atom, local_index; |
83 |
+ |
double atomData6[6]; |
84 |
+ |
double atomData13[13]; |
85 |
+ |
int isDirectional; |
86 |
+ |
char* atomTypeString; |
87 |
+ |
char MPIatomTypeString[MINIBUFFERSIZE]; |
88 |
+ |
|
89 |
+ |
#else //is_mpi |
90 |
+ |
int nAtoms = entry_plug->n_atoms; |
91 |
+ |
#endif //is_mpi |
92 |
+ |
|
93 |
|
double q[4]; |
94 |
|
DirectionalAtom* dAtom; |
74 |
– |
int nAtoms = entry_plug->n_atoms; |
95 |
|
Atom** atoms = entry_plug->atoms; |
96 |
< |
|
96 |
> |
double pos[3], vel[3]; |
97 |
|
|
98 |
+ |
// write current frame to the eor file |
99 |
+ |
|
100 |
+ |
this->writeFinal( currentTime ); |
101 |
+ |
|
102 |
|
#ifndef IS_MPI |
103 |
< |
|
103 |
> |
|
104 |
|
outFile << nAtoms << "\n"; |
105 |
< |
|
106 |
< |
outFile << currentTime << "\t" |
107 |
< |
<< entry_plug->box_x << "\t" |
108 |
< |
<< entry_plug->box_y << "\t" |
109 |
< |
<< entry_plug->box_z << "\n"; |
110 |
< |
|
105 |
> |
|
106 |
> |
outFile << currentTime << ";\t" |
107 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
108 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
109 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
110 |
> |
|
111 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
112 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
113 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
114 |
> |
|
115 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
116 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
117 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
118 |
> |
//write out additional parameters, such as chi and eta |
119 |
> |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
120 |
> |
outFile << endl; |
121 |
> |
|
122 |
|
for( i=0; i<nAtoms; i++ ){ |
88 |
– |
|
123 |
|
|
124 |
+ |
atoms[i]->getPos(pos); |
125 |
+ |
atoms[i]->getVel(vel); |
126 |
+ |
|
127 |
|
sprintf( tempBuffer, |
128 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
129 |
|
atoms[i]->getType(), |
130 |
< |
atoms[i]->getX(), |
131 |
< |
atoms[i]->getY(), |
132 |
< |
atoms[i]->getZ(), |
133 |
< |
atoms[i]->get_vx(), |
134 |
< |
atoms[i]->get_vy(), |
135 |
< |
atoms[i]->get_vz()); |
130 |
> |
pos[0], |
131 |
> |
pos[1], |
132 |
> |
pos[2], |
133 |
> |
vel[0], |
134 |
> |
vel[1], |
135 |
> |
vel[2]); |
136 |
|
strcpy( writeLine, tempBuffer ); |
137 |
|
|
138 |
|
if( atoms[i]->isDirectional() ){ |
139 |
< |
|
139 |
> |
|
140 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
141 |
|
dAtom->getQ( q ); |
142 |
< |
|
142 |
> |
|
143 |
|
sprintf( tempBuffer, |
144 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
145 |
|
q[0], |
153 |
|
} |
154 |
|
else |
155 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
156 |
< |
|
156 |
> |
|
157 |
|
outFile << writeLine; |
158 |
|
} |
159 |
|
outFile.flush(); |
160 |
|
|
161 |
|
#else // is_mpi |
162 |
|
|
163 |
< |
int masterIndex; |
164 |
< |
int nodeAtomsStart; |
165 |
< |
int nodeAtomsEnd; |
166 |
< |
int mpiErr; |
167 |
< |
int sendError; |
168 |
< |
int procIndex; |
169 |
< |
|
170 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
163 |
> |
/* code to find maximum tag value */ |
164 |
> |
|
165 |
> |
int *tagub, flag, MAXTAG; |
166 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
167 |
> |
if (flag) { |
168 |
> |
MAXTAG = *tagub; |
169 |
> |
} else { |
170 |
> |
MAXTAG = 32767; |
171 |
> |
} |
172 |
|
|
173 |
< |
|
173 |
> |
int haveError; |
174 |
> |
|
175 |
> |
MPI_Status istatus; |
176 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
177 |
> |
|
178 |
|
// write out header and node 0's coordinates |
179 |
|
|
180 |
|
if( worldRank == 0 ){ |
139 |
– |
outFile << mpiSim->getTotAtoms() << "\n"; |
140 |
– |
|
141 |
– |
outFile << currentTime << "\t" |
142 |
– |
<< entry_plug->box_x << "\t" |
143 |
– |
<< entry_plug->box_y << "\t" |
144 |
– |
<< entry_plug->box_z << "\n"; |
181 |
|
|
182 |
< |
masterIndex = 0; |
147 |
< |
for( i=0; i<nAtoms; i++ ){ |
148 |
< |
|
149 |
< |
sprintf( tempBuffer, |
150 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
151 |
< |
atoms[i]->getType(), |
152 |
< |
atoms[i]->getX(), |
153 |
< |
atoms[i]->getY(), |
154 |
< |
atoms[i]->getZ(), |
155 |
< |
atoms[i]->get_vx(), |
156 |
< |
atoms[i]->get_vy(), |
157 |
< |
atoms[i]->get_vz()); |
158 |
< |
strcpy( writeLine, tempBuffer ); |
159 |
< |
|
160 |
< |
if( atoms[i]->isDirectional() ){ |
161 |
< |
|
162 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
163 |
< |
dAtom->getQ( q ); |
164 |
< |
|
165 |
< |
sprintf( tempBuffer, |
166 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
167 |
< |
q[0], |
168 |
< |
q[1], |
169 |
< |
q[2], |
170 |
< |
q[3], |
171 |
< |
dAtom->getJx(), |
172 |
< |
dAtom->getJy(), |
173 |
< |
dAtom->getJz()); |
174 |
< |
strcat( writeLine, tempBuffer ); |
175 |
< |
} |
176 |
< |
else |
177 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
178 |
< |
|
179 |
< |
outFile << writeLine; |
180 |
< |
masterIndex++; |
181 |
< |
} |
182 |
< |
outFile.flush(); |
183 |
< |
} |
182 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
183 |
|
|
184 |
< |
sprintf( checkPointMsg, |
185 |
< |
"Sucessfully wrote node 0's dump configuration.\n"); |
186 |
< |
MPIcheckPoint(); |
184 |
> |
nProc = mpiSim->getNumberProcessors(); |
185 |
> |
potatoes = new int[nProc]; |
186 |
> |
|
187 |
> |
for (i = 0; i < nProc; i++) |
188 |
> |
potatoes[i] = 0; |
189 |
|
|
190 |
< |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
190 |
< |
procIndex++){ |
190 |
> |
outFile << mpiSim->getTotAtoms() << "\n"; |
191 |
|
|
192 |
< |
if( worldRank == 0 ){ |
192 |
> |
outFile << currentTime << ";\t" |
193 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
194 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
195 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
196 |
> |
|
197 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
198 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
199 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
200 |
> |
|
201 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
202 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
203 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
204 |
> |
|
205 |
> |
outFile << entry_plug->the_integrator->getAdditionalParameters(); |
206 |
> |
outFile << endl; |
207 |
> |
outFile.flush(); |
208 |
> |
|
209 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
210 |
|
|
211 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
195 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
211 |
> |
// Get the Node number which has this atom; |
212 |
|
|
213 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
198 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
213 |
> |
which_node = AtomToProcMap[i]; |
214 |
|
|
215 |
< |
// Make sure where node 0 is writing to, matches where the |
201 |
< |
// receiving node expects it to be. |
202 |
< |
|
203 |
< |
if (masterIndex != nodeAtomsStart){ |
204 |
< |
sendError = 1; |
205 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
206 |
< |
MPI_COMM_WORLD); |
207 |
< |
sprintf(painCave.errMsg, |
208 |
< |
"DumpWriter error: atoms start index (%d) for " |
209 |
< |
"node %d not equal to master index (%d)", |
210 |
< |
nodeAtomsStart,procIndex,masterIndex ); |
211 |
< |
painCave.isFatal = 1; |
212 |
< |
simError(); |
213 |
< |
} |
214 |
< |
|
215 |
< |
sendError = 0; |
216 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
217 |
< |
MPI_COMM_WORLD); |
218 |
< |
|
219 |
< |
// recieve the nodes writeLines |
220 |
< |
|
221 |
< |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
222 |
< |
|
223 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
224 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
225 |
< |
|
226 |
< |
outFile << writeLine; |
227 |
< |
masterIndex++; |
228 |
< |
} |
229 |
< |
} |
215 |
> |
if (which_node != 0) { |
216 |
|
|
217 |
< |
else if( worldRank == procIndex ){ |
217 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
218 |
> |
// The potato was going to exceed the maximum value, |
219 |
> |
// so wrap this processor potato back to 0: |
220 |
|
|
221 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
222 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
221 |
> |
potatoes[which_node] = 0; |
222 |
> |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
223 |
> |
|
224 |
> |
} |
225 |
|
|
226 |
< |
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
227 |
< |
MPI_COMM_WORLD); |
228 |
< |
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
229 |
< |
MPI_COMM_WORLD); |
226 |
> |
myPotato = potatoes[which_node]; |
227 |
> |
|
228 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
229 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
230 |
> |
|
231 |
> |
//strncpy(atomTypeString, MPIatomTypeString, MINIBUFFERSIZE); |
232 |
> |
|
233 |
> |
// Null terminate the atomTypeString just in case: |
234 |
> |
|
235 |
> |
//atomTypeString[strlen(atomTypeString) - 1] = '\0'; |
236 |
> |
atomTypeString = MPIatomTypeString; |
237 |
|
|
238 |
< |
sendError = -1; |
242 |
< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
243 |
< |
MPI_COMM_WORLD, istatus); |
238 |
> |
myPotato++; |
239 |
|
|
240 |
< |
if (sendError) MPIcheckPoint(); |
240 |
> |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
241 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
242 |
> |
|
243 |
> |
myPotato++; |
244 |
|
|
245 |
< |
// send current node's configuration line by line. |
245 |
> |
if (isDirectional) { |
246 |
> |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
247 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
248 |
> |
} else { |
249 |
> |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
250 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
251 |
> |
} |
252 |
> |
|
253 |
> |
myPotato++; |
254 |
> |
potatoes[which_node] = myPotato; |
255 |
|
|
256 |
< |
for( i=0; i<nAtoms; i++ ){ |
256 |
> |
} else { |
257 |
> |
|
258 |
> |
haveError = 0; |
259 |
> |
which_atom = i; |
260 |
> |
local_index=-1; |
261 |
> |
|
262 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
263 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
264 |
> |
} |
265 |
> |
|
266 |
> |
if (local_index != -1) { |
267 |
> |
|
268 |
> |
atomTypeString = atoms[local_index]->getType(); |
269 |
|
|
270 |
+ |
atoms[local_index]->getPos(pos); |
271 |
+ |
atoms[local_index]->getVel(vel); |
272 |
+ |
|
273 |
+ |
atomData6[0] = pos[0]; |
274 |
+ |
atomData6[1] = pos[1]; |
275 |
+ |
atomData6[2] = pos[2]; |
276 |
+ |
|
277 |
+ |
atomData6[3] = vel[0]; |
278 |
+ |
atomData6[4] = vel[1]; |
279 |
+ |
atomData6[5] = vel[2]; |
280 |
+ |
|
281 |
+ |
isDirectional = 0; |
282 |
+ |
|
283 |
+ |
if( atoms[local_index]->isDirectional() ){ |
284 |
+ |
|
285 |
+ |
isDirectional = 1; |
286 |
+ |
|
287 |
+ |
dAtom = (DirectionalAtom *)atoms[local_index]; |
288 |
+ |
dAtom->getQ( q ); |
289 |
+ |
|
290 |
+ |
for (int j = 0; j < 6 ; j++) |
291 |
+ |
atomData13[j] = atomData6[j]; |
292 |
+ |
|
293 |
+ |
atomData13[6] = q[0]; |
294 |
+ |
atomData13[7] = q[1]; |
295 |
+ |
atomData13[8] = q[2]; |
296 |
+ |
atomData13[9] = q[3]; |
297 |
+ |
|
298 |
+ |
atomData13[10] = dAtom->getJx(); |
299 |
+ |
atomData13[11] = dAtom->getJy(); |
300 |
+ |
atomData13[12] = dAtom->getJz(); |
301 |
+ |
} |
302 |
+ |
|
303 |
+ |
} else { |
304 |
+ |
sprintf(painCave.errMsg, |
305 |
+ |
"Atom %d not found on processor %d\n", |
306 |
+ |
i, worldRank ); |
307 |
+ |
haveError= 1; |
308 |
+ |
simError(); |
309 |
+ |
} |
310 |
+ |
|
311 |
+ |
if(haveError) DieDieDie(); |
312 |
+ |
|
313 |
+ |
} |
314 |
+ |
// If we've survived to here, format the line: |
315 |
+ |
|
316 |
+ |
if (!isDirectional) { |
317 |
+ |
|
318 |
|
sprintf( tempBuffer, |
319 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
320 |
< |
atoms[i]->getType(), |
321 |
< |
atoms[i]->getX(), |
322 |
< |
atoms[i]->getY(), |
323 |
< |
atoms[i]->getZ(), |
324 |
< |
atoms[i]->get_vx(), |
325 |
< |
atoms[i]->get_vy(), |
326 |
< |
atoms[i]->get_vz()); // check here. |
320 |
> |
atomTypeString, |
321 |
> |
atomData6[0], |
322 |
> |
atomData6[1], |
323 |
> |
atomData6[2], |
324 |
> |
atomData6[3], |
325 |
> |
atomData6[4], |
326 |
> |
atomData6[5]); |
327 |
> |
|
328 |
|
strcpy( writeLine, tempBuffer ); |
329 |
< |
|
330 |
< |
if( atoms[i]->isDirectional() ){ |
331 |
< |
|
332 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
333 |
< |
dAtom->getQ( q ); |
334 |
< |
|
335 |
< |
sprintf( tempBuffer, |
336 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
337 |
< |
q[0], |
338 |
< |
q[1], |
339 |
< |
q[2], |
340 |
< |
q[3], |
341 |
< |
dAtom->getJx(), |
342 |
< |
dAtom->getJy(), |
343 |
< |
dAtom->getJz()); |
344 |
< |
strcat( writeLine, tempBuffer ); |
345 |
< |
} |
346 |
< |
else |
347 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
348 |
< |
|
349 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
350 |
< |
MPI_COMM_WORLD); |
329 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
330 |
> |
|
331 |
> |
} else { |
332 |
> |
|
333 |
> |
sprintf( tempBuffer, |
334 |
> |
"%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", |
335 |
> |
atomTypeString, |
336 |
> |
atomData13[0], |
337 |
> |
atomData13[1], |
338 |
> |
atomData13[2], |
339 |
> |
atomData13[3], |
340 |
> |
atomData13[4], |
341 |
> |
atomData13[5], |
342 |
> |
atomData13[6], |
343 |
> |
atomData13[7], |
344 |
> |
atomData13[8], |
345 |
> |
atomData13[9], |
346 |
> |
atomData13[10], |
347 |
> |
atomData13[11], |
348 |
> |
atomData13[12]); |
349 |
> |
|
350 |
> |
strcat( writeLine, tempBuffer ); |
351 |
> |
|
352 |
|
} |
353 |
+ |
|
354 |
+ |
outFile << writeLine; |
355 |
+ |
outFile.flush(); |
356 |
|
} |
357 |
+ |
|
358 |
+ |
|
359 |
+ |
outFile.flush(); |
360 |
+ |
sprintf( checkPointMsg, |
361 |
+ |
"Sucessfully took a dump.\n"); |
362 |
+ |
MPIcheckPoint(); |
363 |
+ |
delete[] potatoes; |
364 |
+ |
} else { |
365 |
+ |
|
366 |
+ |
// worldRank != 0, so I'm a remote node. |
367 |
+ |
|
368 |
+ |
// Set my magic potato to 0: |
369 |
+ |
|
370 |
+ |
myPotato = 0; |
371 |
+ |
|
372 |
+ |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
373 |
|
|
374 |
< |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
375 |
< |
procIndex); |
376 |
< |
MPIcheckPoint(); |
377 |
< |
} |
374 |
> |
// Am I the node which has this atom? |
375 |
> |
|
376 |
> |
if (AtomToProcMap[i] == worldRank) { |
377 |
> |
|
378 |
> |
if (myPotato + 3 >= MAXTAG) { |
379 |
> |
|
380 |
> |
// The potato was going to exceed the maximum value, |
381 |
> |
// so wrap this processor potato back to 0 (and block until |
382 |
> |
// node 0 says we can go: |
383 |
> |
|
384 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
385 |
> |
|
386 |
> |
} |
387 |
> |
which_atom = i; |
388 |
> |
local_index=-1; |
389 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
390 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
391 |
> |
} |
392 |
> |
if (local_index != -1) { |
393 |
> |
|
394 |
> |
atomTypeString = atoms[local_index]->getType(); |
395 |
> |
|
396 |
> |
atoms[local_index]->getPos(pos); |
397 |
> |
atoms[local_index]->getVel(vel); |
398 |
> |
|
399 |
> |
atomData6[0] = pos[0]; |
400 |
> |
atomData6[1] = pos[1]; |
401 |
> |
atomData6[2] = pos[2]; |
402 |
> |
|
403 |
> |
atomData6[3] = vel[0]; |
404 |
> |
atomData6[4] = vel[1]; |
405 |
> |
atomData6[5] = vel[2]; |
406 |
> |
|
407 |
> |
isDirectional = 0; |
408 |
> |
|
409 |
> |
if( atoms[local_index]->isDirectional() ){ |
410 |
> |
|
411 |
> |
isDirectional = 1; |
412 |
> |
|
413 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
414 |
> |
dAtom->getQ( q ); |
415 |
> |
|
416 |
> |
for (int j = 0; j < 6 ; j++) |
417 |
> |
atomData13[j] = atomData6[j]; |
418 |
> |
|
419 |
> |
atomData13[6] = q[0]; |
420 |
> |
atomData13[7] = q[1]; |
421 |
> |
atomData13[8] = q[2]; |
422 |
> |
atomData13[9] = q[3]; |
423 |
> |
|
424 |
> |
atomData13[10] = dAtom->getJx(); |
425 |
> |
atomData13[11] = dAtom->getJy(); |
426 |
> |
atomData13[12] = dAtom->getJz(); |
427 |
> |
} |
428 |
> |
|
429 |
> |
} else { |
430 |
> |
sprintf(painCave.errMsg, |
431 |
> |
"Atom %d not found on processor %d\n", |
432 |
> |
i, worldRank ); |
433 |
> |
haveError= 1; |
434 |
> |
simError(); |
435 |
> |
} |
436 |
> |
|
437 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
438 |
> |
|
439 |
> |
// null terminate the string before sending (just in case): |
440 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
441 |
> |
|
442 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
443 |
> |
myPotato, MPI_COMM_WORLD); |
444 |
> |
|
445 |
> |
myPotato++; |
446 |
> |
|
447 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
448 |
> |
myPotato, MPI_COMM_WORLD); |
449 |
> |
|
450 |
> |
myPotato++; |
451 |
> |
|
452 |
> |
if (isDirectional) { |
453 |
> |
|
454 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
455 |
> |
myPotato, MPI_COMM_WORLD); |
456 |
> |
|
457 |
> |
} else { |
458 |
> |
|
459 |
> |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
460 |
> |
myPotato, MPI_COMM_WORLD); |
461 |
> |
} |
462 |
> |
|
463 |
> |
myPotato++; |
464 |
> |
} |
465 |
> |
} |
466 |
> |
|
467 |
> |
sprintf( checkPointMsg, |
468 |
> |
"Sucessfully took a dump.\n"); |
469 |
> |
MPIcheckPoint(); |
470 |
|
|
471 |
+ |
} |
472 |
+ |
|
473 |
|
#endif // is_mpi |
474 |
|
} |
475 |
|
|
476 |
+ |
void DumpWriter::writeFinal(double finalTime){ |
477 |
|
|
478 |
+ |
char finalName[500]; |
479 |
+ |
ofstream finalOut; |
480 |
|
|
296 |
– |
void DumpWriter::writeFinal(){ |
297 |
– |
|
298 |
– |
|
481 |
|
const int BUFFERSIZE = 2000; |
482 |
< |
char tempBuffer[500]; |
482 |
> |
const int MINIBUFFERSIZE = 100; |
483 |
> |
char tempBuffer[BUFFERSIZE]; |
484 |
|
char writeLine[BUFFERSIZE]; |
302 |
– |
|
303 |
– |
char finalName[500]; |
485 |
|
|
305 |
– |
int i; |
486 |
|
double q[4]; |
487 |
|
DirectionalAtom* dAtom; |
308 |
– |
int nAtoms = entry_plug->n_atoms; |
488 |
|
Atom** atoms = entry_plug->atoms; |
489 |
+ |
int i; |
490 |
+ |
#ifdef IS_MPI |
491 |
|
|
492 |
< |
ofstream finalOut; |
493 |
< |
|
492 |
> |
int *potatoes; |
493 |
> |
int myPotato; |
494 |
> |
|
495 |
> |
int nProc; |
496 |
> |
int j, which_node, done, which_atom, local_index; |
497 |
> |
double atomData6[6]; |
498 |
> |
double atomData13[13]; |
499 |
> |
int isDirectional; |
500 |
> |
char* atomTypeString; |
501 |
> |
char MPIatomTypeString[MINIBUFFERSIZE]; |
502 |
> |
|
503 |
> |
#else //is_mpi |
504 |
> |
int nAtoms = entry_plug->n_atoms; |
505 |
> |
#endif //is_mpi |
506 |
> |
|
507 |
> |
double pos[3], vel[3]; |
508 |
> |
|
509 |
|
#ifdef IS_MPI |
510 |
|
if(worldRank == 0 ){ |
511 |
|
#endif // is_mpi |
512 |
< |
|
512 |
> |
|
513 |
|
strcpy( finalName, entry_plug->finalName ); |
514 |
< |
|
514 |
> |
|
515 |
|
finalOut.open( finalName, ios::out | ios::trunc ); |
516 |
|
if( !finalOut ){ |
517 |
|
sprintf( painCave.errMsg, |
520 |
|
painCave.isFatal = 1; |
521 |
|
simError(); |
522 |
|
} |
523 |
< |
|
523 |
> |
|
524 |
|
// finalOut.setf( ios::scientific ); |
525 |
< |
|
525 |
> |
|
526 |
|
#ifdef IS_MPI |
527 |
|
} |
528 |
< |
|
528 |
> |
|
529 |
|
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
530 |
< |
MPIcheckPoint(); |
531 |
< |
|
530 |
> |
MPIcheckPoint(); |
531 |
> |
|
532 |
|
#endif //is_mpi |
533 |
|
|
338 |
– |
|
534 |
|
|
535 |
|
#ifndef IS_MPI |
536 |
< |
|
536 |
> |
|
537 |
|
finalOut << nAtoms << "\n"; |
538 |
< |
|
539 |
< |
finalOut << entry_plug->box_x << "\t" |
540 |
< |
<< entry_plug->box_y << "\t" |
541 |
< |
<< entry_plug->box_z << "\n"; |
542 |
< |
|
538 |
> |
|
539 |
> |
finalOut << finalTime << ";\t" |
540 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
541 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
542 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
543 |
> |
|
544 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
545 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
546 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
547 |
> |
|
548 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
549 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
550 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
551 |
> |
|
552 |
> |
//write out additional parameters, such as chi and eta |
553 |
> |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
554 |
> |
finalOut << endl; |
555 |
> |
|
556 |
|
for( i=0; i<nAtoms; i++ ){ |
557 |
< |
|
557 |
> |
|
558 |
> |
atoms[i]->getPos(pos); |
559 |
> |
atoms[i]->getVel(vel); |
560 |
> |
|
561 |
|
sprintf( tempBuffer, |
562 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
563 |
|
atoms[i]->getType(), |
564 |
< |
atoms[i]->getX(), |
565 |
< |
atoms[i]->getY(), |
566 |
< |
atoms[i]->getZ(), |
567 |
< |
atoms[i]->get_vx(), |
568 |
< |
atoms[i]->get_vy(), |
569 |
< |
atoms[i]->get_vz()); |
564 |
> |
pos[0], |
565 |
> |
pos[1], |
566 |
> |
pos[2], |
567 |
> |
vel[0], |
568 |
> |
vel[1], |
569 |
> |
vel[2]); |
570 |
|
strcpy( writeLine, tempBuffer ); |
571 |
|
|
572 |
|
if( atoms[i]->isDirectional() ){ |
573 |
< |
|
573 |
> |
|
574 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
575 |
|
dAtom->getQ( q ); |
576 |
< |
|
576 |
> |
|
577 |
|
sprintf( tempBuffer, |
578 |
|
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
579 |
|
q[0], |
587 |
|
} |
588 |
|
else |
589 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
590 |
< |
|
590 |
> |
|
591 |
|
finalOut << writeLine; |
592 |
|
} |
593 |
|
finalOut.flush(); |
594 |
+ |
finalOut.close(); |
595 |
|
|
596 |
|
#else // is_mpi |
597 |
|
|
598 |
< |
int masterIndex; |
599 |
< |
int nodeAtomsStart; |
600 |
< |
int nodeAtomsEnd; |
601 |
< |
int mpiErr; |
602 |
< |
int sendError; |
603 |
< |
int procIndex; |
604 |
< |
|
605 |
< |
MPI_Status istatus[MPI_STATUS_SIZE]; |
598 |
> |
/* code to find maximum tag value */ |
599 |
> |
int *tagub, flag, MAXTAG; |
600 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
601 |
> |
if (flag) { |
602 |
> |
MAXTAG = *tagub; |
603 |
> |
} else { |
604 |
> |
MAXTAG = 32767; |
605 |
> |
} |
606 |
|
|
607 |
< |
|
607 |
> |
int haveError; |
608 |
> |
|
609 |
> |
MPI_Status istatus; |
610 |
> |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
611 |
> |
|
612 |
|
// write out header and node 0's coordinates |
613 |
|
|
614 |
|
if( worldRank == 0 ){ |
615 |
< |
finalOut << mpiSim->getTotAtoms() << "\n"; |
616 |
< |
|
617 |
< |
finalOut << entry_plug->box_x << "\t" |
618 |
< |
<< entry_plug->box_y << "\t" |
619 |
< |
<< entry_plug->box_z << "\n"; |
615 |
> |
|
616 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
617 |
> |
|
618 |
> |
nProc = mpiSim->getNumberProcessors(); |
619 |
> |
potatoes = new int[nProc]; |
620 |
> |
|
621 |
> |
for (i = 0; i < nProc; i++) |
622 |
> |
potatoes[i] = 0; |
623 |
|
|
624 |
< |
masterIndex = 0; |
406 |
< |
|
407 |
< |
for( i=0; i<nAtoms; i++ ){ |
408 |
< |
|
409 |
< |
sprintf( tempBuffer, |
410 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
411 |
< |
atoms[i]->getType(), |
412 |
< |
atoms[i]->getX(), |
413 |
< |
atoms[i]->getY(), |
414 |
< |
atoms[i]->getZ(), |
415 |
< |
atoms[i]->get_vx(), |
416 |
< |
atoms[i]->get_vy(), |
417 |
< |
atoms[i]->get_vz()); |
418 |
< |
strcpy( writeLine, tempBuffer ); |
419 |
< |
|
420 |
< |
if( atoms[i]->isDirectional() ){ |
421 |
< |
|
422 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
423 |
< |
dAtom->getQ( q ); |
424 |
< |
|
425 |
< |
sprintf( tempBuffer, |
426 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
427 |
< |
q[0], |
428 |
< |
q[1], |
429 |
< |
q[2], |
430 |
< |
q[3], |
431 |
< |
dAtom->getJx(), |
432 |
< |
dAtom->getJy(), |
433 |
< |
dAtom->getJz()); |
434 |
< |
strcat( writeLine, tempBuffer ); |
435 |
< |
} |
436 |
< |
else |
437 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
438 |
< |
|
439 |
< |
finalOut << writeLine; |
440 |
< |
masterIndex++; |
441 |
< |
} |
442 |
< |
finalOut.flush(); |
443 |
< |
} |
444 |
< |
|
445 |
< |
for (procIndex = 1; procIndex < mpiSim->getNumberProcessors(); |
446 |
< |
procIndex++){ |
624 |
> |
finalOut << mpiSim->getTotAtoms() << "\n"; |
625 |
|
|
626 |
< |
if( worldRank == 0 ){ |
627 |
< |
|
628 |
< |
mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex, |
629 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus); |
626 |
> |
finalOut << finalTime << ";\t" |
627 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
628 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
629 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
630 |
|
|
631 |
< |
mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex, |
632 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD, istatus); |
633 |
< |
|
456 |
< |
// Make sure where node 0 is writing to, matches where the |
457 |
< |
// receiving node expects it to be. |
458 |
< |
|
459 |
< |
if (masterIndex != nodeAtomsStart){ |
460 |
< |
sendError = 1; |
461 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
462 |
< |
MPI_COMM_WORLD); |
463 |
< |
sprintf(painCave.errMsg, |
464 |
< |
"DumpWriter error: atoms start index (%d) for " |
465 |
< |
"node %d not equal to master index (%d)", |
466 |
< |
nodeAtomsStart,procIndex,masterIndex ); |
467 |
< |
painCave.isFatal = 1; |
468 |
< |
simError(); |
469 |
< |
} |
470 |
< |
|
471 |
< |
sendError = 0; |
472 |
< |
mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG, |
473 |
< |
MPI_COMM_WORLD); |
631 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
632 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
633 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
634 |
|
|
635 |
< |
// recieve the nodes writeLines |
635 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
636 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
637 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
638 |
|
|
639 |
< |
for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){ |
640 |
< |
|
641 |
< |
mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex, |
480 |
< |
TAKE_THIS_TAG,MPI_COMM_WORLD,istatus ); |
639 |
> |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
640 |
> |
finalOut << endl; |
641 |
> |
finalOut.flush(); |
642 |
|
|
643 |
< |
finalOut << writeLine; |
644 |
< |
masterIndex++; |
645 |
< |
} |
643 |
> |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
644 |
> |
|
645 |
> |
// Get the Node number which has this atom; |
646 |
> |
|
647 |
> |
which_node = AtomToProcMap[i]; |
648 |
> |
|
649 |
> |
if (which_node != 0) { |
650 |
|
|
651 |
< |
finalOut.flush(); |
652 |
< |
} |
651 |
> |
if (potatoes[which_node] + 3 >= MAXTAG) { |
652 |
> |
// The potato was going to exceed the maximum value, |
653 |
> |
// so wrap this processor potato back to 0: |
654 |
|
|
655 |
< |
else if( worldRank == procIndex ){ |
655 |
> |
potatoes[which_node] = 0; |
656 |
> |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
657 |
> |
|
658 |
> |
} |
659 |
|
|
660 |
< |
nodeAtomsStart = mpiSim->getMyAtomStart(); |
661 |
< |
nodeAtomsEnd = mpiSim->getMyAtomEnd(); |
662 |
< |
|
663 |
< |
mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG, |
664 |
< |
MPI_COMM_WORLD); |
665 |
< |
mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG, |
666 |
< |
MPI_COMM_WORLD); |
667 |
< |
|
499 |
< |
mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG, |
500 |
< |
MPI_COMM_WORLD, istatus); |
501 |
< |
if (sendError) MPIcheckPoint(); |
660 |
> |
myPotato = potatoes[which_node]; |
661 |
> |
|
662 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
663 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
664 |
> |
|
665 |
> |
atomTypeString = MPIatomTypeString; |
666 |
> |
|
667 |
> |
myPotato++; |
668 |
|
|
669 |
< |
// send current node's configuration line by line. |
669 |
> |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
670 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
671 |
> |
|
672 |
> |
myPotato++; |
673 |
|
|
674 |
< |
for( i=0; i<nAtoms; i++ ){ |
675 |
< |
|
674 |
> |
if (isDirectional) { |
675 |
> |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
676 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
677 |
> |
} else { |
678 |
> |
printf("inside \n"); |
679 |
> |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
680 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
681 |
> |
} |
682 |
> |
|
683 |
> |
myPotato++; |
684 |
> |
potatoes[which_node] = myPotato; |
685 |
> |
|
686 |
> |
} else { |
687 |
> |
|
688 |
> |
haveError = 0; |
689 |
> |
which_atom = i; |
690 |
> |
local_index=-1; |
691 |
> |
|
692 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
693 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
694 |
> |
} |
695 |
> |
|
696 |
> |
if (local_index != -1) { |
697 |
> |
|
698 |
> |
atomTypeString = atoms[local_index]->getType(); |
699 |
> |
|
700 |
> |
atoms[local_index]->getPos(pos); |
701 |
> |
atoms[local_index]->getVel(vel); |
702 |
> |
|
703 |
> |
atomData6[0] = pos[0]; |
704 |
> |
atomData6[1] = pos[1]; |
705 |
> |
atomData6[2] = pos[2]; |
706 |
> |
|
707 |
> |
atomData6[3] = vel[0]; |
708 |
> |
atomData6[4] = vel[1]; |
709 |
> |
atomData6[5] = vel[2]; |
710 |
> |
|
711 |
> |
isDirectional = 0; |
712 |
> |
|
713 |
> |
if( atoms[local_index]->isDirectional() ){ |
714 |
> |
|
715 |
> |
isDirectional = 1; |
716 |
> |
|
717 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
718 |
> |
dAtom->getQ( q ); |
719 |
> |
|
720 |
> |
for (int j = 0; j < 6 ; j++) |
721 |
> |
atomData13[j] = atomData6[j]; |
722 |
> |
|
723 |
> |
atomData13[6] = q[0]; |
724 |
> |
atomData13[7] = q[1]; |
725 |
> |
atomData13[8] = q[2]; |
726 |
> |
atomData13[9] = q[3]; |
727 |
> |
|
728 |
> |
atomData13[10] = dAtom->getJx(); |
729 |
> |
atomData13[11] = dAtom->getJy(); |
730 |
> |
atomData13[12] = dAtom->getJz(); |
731 |
> |
} |
732 |
> |
|
733 |
> |
} else { |
734 |
> |
sprintf(painCave.errMsg, |
735 |
> |
"Atom %d not found on processor %d\n", |
736 |
> |
i, worldRank ); |
737 |
> |
haveError= 1; |
738 |
> |
simError(); |
739 |
> |
} |
740 |
> |
|
741 |
> |
if(haveError) DieDieDie(); |
742 |
> |
|
743 |
> |
} |
744 |
> |
|
745 |
> |
|
746 |
> |
// If we've survived to here, format the line: |
747 |
> |
|
748 |
> |
if (!isDirectional) { |
749 |
> |
|
750 |
|
sprintf( tempBuffer, |
751 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
752 |
< |
atoms[i]->getType(), |
753 |
< |
atoms[i]->getX(), |
754 |
< |
atoms[i]->getY(), |
755 |
< |
atoms[i]->getZ(), |
756 |
< |
atoms[i]->get_vx(), |
757 |
< |
atoms[i]->get_vy(), |
758 |
< |
atoms[i]->get_vz()); |
752 |
> |
atomTypeString, |
753 |
> |
atomData6[0], |
754 |
> |
atomData6[1], |
755 |
> |
atomData6[2], |
756 |
> |
atomData6[3], |
757 |
> |
atomData6[4], |
758 |
> |
atomData6[5]); |
759 |
> |
|
760 |
|
strcpy( writeLine, tempBuffer ); |
761 |
< |
|
762 |
< |
if( atoms[i]->isDirectional() ){ |
763 |
< |
|
764 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
765 |
< |
dAtom->getQ( q ); |
766 |
< |
|
767 |
< |
sprintf( tempBuffer, |
768 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
769 |
< |
q[0], |
770 |
< |
q[1], |
771 |
< |
q[2], |
772 |
< |
q[3], |
773 |
< |
dAtom->getJx(), |
774 |
< |
dAtom->getJy(), |
775 |
< |
dAtom->getJz()); |
776 |
< |
strcat( writeLine, tempBuffer ); |
777 |
< |
} |
778 |
< |
else |
779 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
780 |
< |
|
781 |
< |
mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG, |
782 |
< |
MPI_COMM_WORLD); |
761 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
762 |
> |
|
763 |
> |
} else { |
764 |
> |
|
765 |
> |
sprintf( tempBuffer, |
766 |
> |
"%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", |
767 |
> |
atomTypeString, |
768 |
> |
atomData13[0], |
769 |
> |
atomData13[1], |
770 |
> |
atomData13[2], |
771 |
> |
atomData13[3], |
772 |
> |
atomData13[4], |
773 |
> |
atomData13[5], |
774 |
> |
atomData13[6], |
775 |
> |
atomData13[7], |
776 |
> |
atomData13[8], |
777 |
> |
atomData13[9], |
778 |
> |
atomData13[10], |
779 |
> |
atomData13[11], |
780 |
> |
atomData13[12]); |
781 |
> |
|
782 |
> |
strcat( writeLine, tempBuffer ); |
783 |
> |
|
784 |
|
} |
785 |
+ |
|
786 |
+ |
finalOut << writeLine; |
787 |
+ |
finalOut.flush(); |
788 |
|
} |
789 |
+ |
|
790 |
+ |
finalOut.flush(); |
791 |
+ |
sprintf( checkPointMsg, |
792 |
+ |
"Sucessfully took a dump.\n"); |
793 |
+ |
delete[] potatoes; |
794 |
+ |
|
795 |
+ |
MPIcheckPoint(); |
796 |
+ |
|
797 |
+ |
} else { |
798 |
+ |
|
799 |
+ |
// worldRank != 0, so I'm a remote node. |
800 |
+ |
|
801 |
+ |
// Set my magic potato to 0: |
802 |
+ |
|
803 |
+ |
myPotato = 0; |
804 |
+ |
|
805 |
+ |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
806 |
|
|
807 |
< |
sprintf(checkPointMsg,"Node %d sent dump configuration.", |
808 |
< |
procIndex); |
809 |
< |
MPIcheckPoint(); |
545 |
< |
} |
807 |
> |
// Am I the node which has this atom? |
808 |
> |
|
809 |
> |
if (AtomToProcMap[i] == worldRank) { |
810 |
|
|
811 |
< |
if( worldRank == 0 ) finalOut.close(); |
811 |
> |
if (myPotato + 3 >= MAXTAG) { |
812 |
|
|
813 |
+ |
// The potato was going to exceed the maximum value, |
814 |
+ |
// so wrap this processor potato back to 0 (and block until |
815 |
+ |
// node 0 says we can go: |
816 |
+ |
|
817 |
+ |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
818 |
+ |
|
819 |
+ |
} |
820 |
+ |
which_atom = i; |
821 |
+ |
local_index=-1; |
822 |
+ |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
823 |
+ |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
824 |
+ |
} |
825 |
+ |
if (local_index != -1) { |
826 |
+ |
|
827 |
+ |
atomTypeString = atoms[local_index]->getType(); |
828 |
+ |
|
829 |
+ |
atoms[local_index]->getPos(pos); |
830 |
+ |
atoms[local_index]->getVel(vel); |
831 |
+ |
|
832 |
+ |
atomData6[0] = pos[0]; |
833 |
+ |
atomData6[1] = pos[1]; |
834 |
+ |
atomData6[2] = pos[2]; |
835 |
+ |
|
836 |
+ |
atomData6[3] = vel[0]; |
837 |
+ |
atomData6[4] = vel[1]; |
838 |
+ |
atomData6[5] = vel[2]; |
839 |
+ |
|
840 |
+ |
isDirectional = 0; |
841 |
+ |
|
842 |
+ |
if( atoms[local_index]->isDirectional() ){ |
843 |
+ |
|
844 |
+ |
isDirectional = 1; |
845 |
+ |
|
846 |
+ |
dAtom = (DirectionalAtom *)atoms[local_index]; |
847 |
+ |
dAtom->getQ( q ); |
848 |
+ |
|
849 |
+ |
for (int j = 0; j < 6 ; j++) |
850 |
+ |
atomData13[j] = atomData6[j]; |
851 |
+ |
|
852 |
+ |
atomData13[6] = q[0]; |
853 |
+ |
atomData13[7] = q[1]; |
854 |
+ |
atomData13[8] = q[2]; |
855 |
+ |
atomData13[9] = q[3]; |
856 |
+ |
|
857 |
+ |
atomData13[10] = dAtom->getJx(); |
858 |
+ |
atomData13[11] = dAtom->getJy(); |
859 |
+ |
atomData13[12] = dAtom->getJz(); |
860 |
+ |
} |
861 |
+ |
|
862 |
+ |
} else { |
863 |
+ |
sprintf(painCave.errMsg, |
864 |
+ |
"Atom %d not found on processor %d\n", |
865 |
+ |
i, worldRank ); |
866 |
+ |
haveError= 1; |
867 |
+ |
simError(); |
868 |
+ |
} |
869 |
+ |
|
870 |
+ |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
871 |
+ |
|
872 |
+ |
// null terminate the string before sending (just in case): |
873 |
+ |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
874 |
+ |
|
875 |
+ |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
876 |
+ |
myPotato, MPI_COMM_WORLD); |
877 |
+ |
|
878 |
+ |
myPotato++; |
879 |
+ |
|
880 |
+ |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
881 |
+ |
myPotato, MPI_COMM_WORLD); |
882 |
+ |
|
883 |
+ |
myPotato++; |
884 |
+ |
|
885 |
+ |
if (isDirectional) { |
886 |
+ |
|
887 |
+ |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
888 |
+ |
myPotato, MPI_COMM_WORLD); |
889 |
+ |
|
890 |
+ |
} else { |
891 |
+ |
|
892 |
+ |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
893 |
+ |
myPotato, MPI_COMM_WORLD); |
894 |
+ |
} |
895 |
+ |
|
896 |
+ |
myPotato++; |
897 |
+ |
} |
898 |
+ |
} |
899 |
+ |
|
900 |
+ |
sprintf( checkPointMsg, |
901 |
+ |
"Sucessfully took a dump.\n"); |
902 |
+ |
MPIcheckPoint(); |
903 |
|
|
904 |
+ |
} |
905 |
+ |
|
906 |
+ |
if( worldRank == 0 ) finalOut.close(); |
907 |
|
#endif // is_mpi |
908 |
|
} |
909 |
+ |
|
910 |
+ |
|
911 |
+ |
|
912 |
+ |
#ifdef IS_MPI |
913 |
+ |
|
914 |
+ |
// a couple of functions to let us escape the write loop |
915 |
+ |
|
916 |
+ |
void dWrite::DieDieDie( void ){ |
917 |
+ |
|
918 |
+ |
MPI_Finalize(); |
919 |
+ |
exit (0); |
920 |
+ |
} |
921 |
+ |
|
922 |
+ |
#endif //is_mpi |