1 |
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#define _LARGEFILE_SOURCE64 |
2 |
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#define _FILE_OFFSET_BITS 64 |
3 |
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4 |
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#include <string.h> |
5 |
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#include <iostream> |
6 |
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#include <fstream> |
7 |
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#include <algorithm> |
8 |
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#include <utility> |
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|
10 |
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#ifdef IS_MPI |
11 |
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#include <mpi.h> |
29 |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
31 |
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|
32 |
< |
strcpy( outName, entry_plug->sampleName ); |
32 |
> |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
33 |
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|
34 |
< |
outFile.open(outName, ios::out | ios::trunc ); |
34 |
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if( !dumpFile ){ |
35 |
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|
33 |
– |
if( !outFile ){ |
34 |
– |
|
36 |
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sprintf( painCave.errMsg, |
37 |
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"Could not open \"%s\" for dump output.\n", |
38 |
< |
outName); |
38 |
> |
entry_plug->sampleName); |
39 |
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painCave.isFatal = 1; |
40 |
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simError(); |
41 |
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} |
42 |
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|
42 |
– |
//outFile.setf( ios::scientific ); |
43 |
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|
43 |
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#ifdef IS_MPI |
44 |
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} |
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|
46 |
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//sort the local atoms by global index |
47 |
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sortByGlobalIndex(); |
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|
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sprintf( checkPointMsg, |
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"Sucessfully opened output file for dumping.\n"); |
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MPIcheckPoint(); |
58 |
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if(worldRank == 0 ){ |
59 |
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#endif // is_mpi |
60 |
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|
61 |
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outFile.close(); |
61 |
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dumpFile.close(); |
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|
63 |
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#ifdef IS_MPI |
64 |
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} |
65 |
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#endif // is_mpi |
66 |
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} |
67 |
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|
68 |
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void DumpWriter::writeDump( double currentTime ){ |
68 |
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#ifdef IS_MPI |
69 |
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|
70 |
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const int BUFFERSIZE = 2000; |
71 |
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const int MINIBUFFERSIZE = 100; |
70 |
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/** |
71 |
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* A hook function to load balancing |
72 |
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*/ |
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|
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
74 |
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int i; |
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|
76 |
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#ifdef IS_MPI |
74 |
> |
void DumpWriter::update(){ |
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sortByGlobalIndex(); |
76 |
> |
} |
77 |
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|
78 |
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int *potatoes; |
79 |
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int myPotato; |
78 |
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/** |
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* Auxiliary sorting function |
80 |
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*/ |
81 |
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|
82 |
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bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
83 |
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return p1.second < p2.second; |
84 |
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} |
85 |
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|
86 |
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int nProc; |
87 |
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int j, which_node, done, which_atom, local_index; |
88 |
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double atomData6[6]; |
89 |
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double atomData13[13]; |
90 |
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int isDirectional; |
86 |
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char* atomTypeString; |
87 |
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char MPIatomTypeString[MINIBUFFERSIZE]; |
88 |
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|
89 |
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#else //is_mpi |
90 |
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int nAtoms = entry_plug->n_atoms; |
91 |
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#endif //is_mpi |
92 |
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|
93 |
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double q[4]; |
94 |
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DirectionalAtom* dAtom; |
86 |
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/** |
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* Sorting the local index by global index |
88 |
> |
*/ |
89 |
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|
90 |
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void DumpWriter::sortByGlobalIndex(){ |
91 |
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Atom** atoms = entry_plug->atoms; |
92 |
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double pos[3], vel[3]; |
92 |
> |
|
93 |
> |
indexArray.clear(); |
94 |
> |
|
95 |
> |
for(int i = 0; i < mpiSim->getMyNlocal();i++) |
96 |
> |
indexArray.push_back(make_pair(i, atoms[i]->getGlobalIndex())); |
97 |
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|
98 |
> |
sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
99 |
> |
} |
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|
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// write current frame to the eor file |
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#endif |
102 |
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|
103 |
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this->writeFinal( currentTime ); |
103 |
> |
void DumpWriter::writeDump(double currentTime){ |
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|
105 |
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#ifndef IS_MPI |
105 |
> |
ofstream finalOut; |
106 |
> |
vector<ofstream*> fileStreams; |
107 |
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|
108 |
< |
outFile << nAtoms << "\n"; |
109 |
< |
|
110 |
< |
outFile << currentTime << ";\t" |
111 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
112 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
113 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
114 |
< |
|
115 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
116 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
117 |
< |
<< 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++ ){ |
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 |
< |
pos[0], |
131 |
< |
pos[1], |
132 |
< |
pos[2], |
133 |
< |
vel[0], |
134 |
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vel[1], |
135 |
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vel[2]); |
136 |
< |
strcpy( writeLine, tempBuffer ); |
137 |
< |
|
138 |
< |
if( atoms[i]->isDirectional() ){ |
139 |
< |
|
140 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
141 |
< |
dAtom->getQ( q ); |
142 |
< |
|
143 |
< |
sprintf( tempBuffer, |
144 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
145 |
< |
q[0], |
146 |
< |
q[1], |
147 |
< |
q[2], |
148 |
< |
q[3], |
149 |
< |
dAtom->getJx(), |
150 |
< |
dAtom->getJy(), |
151 |
< |
dAtom->getJz()); |
152 |
< |
strcat( writeLine, tempBuffer ); |
108 |
> |
#ifdef IS_MPI |
109 |
> |
if(worldRank == 0 ){ |
110 |
> |
#endif |
111 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
112 |
> |
if( !finalOut ){ |
113 |
> |
sprintf( painCave.errMsg, |
114 |
> |
"Could not open \"%s\" for final dump output.\n", |
115 |
> |
entry_plug->finalName ); |
116 |
> |
painCave.isFatal = 1; |
117 |
> |
simError(); |
118 |
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} |
119 |
< |
else |
155 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
156 |
< |
|
157 |
< |
outFile << writeLine; |
119 |
> |
#ifdef IS_MPI |
120 |
|
} |
121 |
< |
outFile.flush(); |
121 |
> |
#endif // is_mpi |
122 |
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|
123 |
< |
#else // is_mpi |
123 |
> |
fileStreams.push_back(&finalOut); |
124 |
> |
fileStreams.push_back(&dumpFile); |
125 |
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|
126 |
< |
/* 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 |
< |
} |
126 |
> |
writeFrame(fileStreams, currentTime); |
127 |
|
|
128 |
< |
int haveError; |
128 |
> |
#ifdef IS_MPI |
129 |
> |
finalOut.close(); |
130 |
> |
#endif |
131 |
> |
|
132 |
> |
} |
133 |
|
|
134 |
< |
MPI_Status istatus; |
176 |
< |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
134 |
> |
void DumpWriter::writeFinal(double currentTime){ |
135 |
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|
136 |
< |
// write out header and node 0's coordinates |
136 |
> |
ofstream finalOut; |
137 |
> |
vector<ofstream*> fileStreams; |
138 |
|
|
139 |
< |
if( worldRank == 0 ){ |
139 |
> |
#ifdef IS_MPI |
140 |
> |
if(worldRank == 0 ){ |
141 |
> |
#endif // is_mpi |
142 |
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|
143 |
< |
// Node 0 needs a list of the magic potatoes for each processor; |
143 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
144 |
|
|
145 |
< |
nProc = mpiSim->getNumberProcessors(); |
146 |
< |
potatoes = new int[nProc]; |
147 |
< |
|
148 |
< |
for (i = 0; i < nProc; i++) |
149 |
< |
potatoes[i] = 0; |
150 |
< |
|
190 |
< |
outFile << mpiSim->getTotAtoms() << "\n"; |
191 |
< |
|
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 |
< |
// Get the Node number which has this atom; |
212 |
< |
|
213 |
< |
which_node = AtomToProcMap[i]; |
214 |
< |
|
215 |
< |
if (which_node != 0) { |
216 |
< |
|
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 |
< |
potatoes[which_node] = 0; |
222 |
< |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
223 |
< |
|
224 |
< |
} |
225 |
< |
|
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 |
< |
myPotato++; |
239 |
< |
|
240 |
< |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
241 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
242 |
< |
|
243 |
< |
myPotato++; |
244 |
< |
|
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 |
< |
} 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 |
< |
// If we've survived to here, format the line: |
314 |
< |
|
315 |
< |
if (!isDirectional) { |
316 |
< |
|
317 |
< |
sprintf( tempBuffer, |
318 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
319 |
< |
atomTypeString, |
320 |
< |
atomData6[0], |
321 |
< |
atomData6[1], |
322 |
< |
atomData6[2], |
323 |
< |
atomData6[3], |
324 |
< |
atomData6[4], |
325 |
< |
atomData6[5]); |
326 |
< |
|
327 |
< |
strcpy( writeLine, tempBuffer ); |
328 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
329 |
< |
|
330 |
< |
} else { |
331 |
< |
|
332 |
< |
sprintf( tempBuffer, |
333 |
< |
"%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", |
334 |
< |
atomTypeString, |
335 |
< |
atomData13[0], |
336 |
< |
atomData13[1], |
337 |
< |
atomData13[2], |
338 |
< |
atomData13[3], |
339 |
< |
atomData13[4], |
340 |
< |
atomData13[5], |
341 |
< |
atomData13[6], |
342 |
< |
atomData13[7], |
343 |
< |
atomData13[8], |
344 |
< |
atomData13[9], |
345 |
< |
atomData13[10], |
346 |
< |
atomData13[11], |
347 |
< |
atomData13[12]); |
348 |
< |
|
349 |
< |
strcat( writeLine, tempBuffer ); |
350 |
< |
|
351 |
< |
} |
352 |
< |
|
353 |
< |
outFile << writeLine; |
354 |
< |
outFile.flush(); |
355 |
< |
} |
145 |
> |
if( !finalOut ){ |
146 |
> |
sprintf( painCave.errMsg, |
147 |
> |
"Could not open \"%s\" for final dump output.\n", |
148 |
> |
entry_plug->finalName ); |
149 |
> |
painCave.isFatal = 1; |
150 |
> |
simError(); |
151 |
|
} |
152 |
|
|
153 |
< |
outFile.flush(); |
154 |
< |
sprintf( checkPointMsg, |
155 |
< |
"Sucessfully took a dump.\n"); |
156 |
< |
MPIcheckPoint(); |
157 |
< |
delete[] potatoes; |
158 |
< |
} else { |
364 |
< |
|
365 |
< |
// worldRank != 0, so I'm a remote node. |
366 |
< |
|
367 |
< |
// Set my magic potato to 0: |
368 |
< |
|
369 |
< |
myPotato = 0; |
370 |
< |
|
371 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
372 |
< |
|
373 |
< |
// Am I the node which has this atom? |
374 |
< |
|
375 |
< |
if (AtomToProcMap[i] == worldRank) { |
376 |
< |
|
377 |
< |
if (myPotato + 3 >= MAXTAG) { |
378 |
< |
|
379 |
< |
// The potato was going to exceed the maximum value, |
380 |
< |
// so wrap this processor potato back to 0 (and block until |
381 |
< |
// node 0 says we can go: |
382 |
< |
|
383 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
384 |
< |
|
385 |
< |
} |
386 |
< |
which_atom = i; |
387 |
< |
local_index=-1; |
388 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
389 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
390 |
< |
} |
391 |
< |
if (local_index != -1) { |
392 |
< |
|
393 |
< |
atomTypeString = atoms[local_index]->getType(); |
394 |
< |
|
395 |
< |
atoms[local_index]->getPos(pos); |
396 |
< |
atoms[local_index]->getVel(vel); |
397 |
< |
|
398 |
< |
atomData6[0] = pos[0]; |
399 |
< |
atomData6[1] = pos[1]; |
400 |
< |
atomData6[2] = pos[2]; |
401 |
< |
|
402 |
< |
atomData6[3] = vel[0]; |
403 |
< |
atomData6[4] = vel[1]; |
404 |
< |
atomData6[5] = vel[2]; |
405 |
< |
|
406 |
< |
isDirectional = 0; |
407 |
< |
|
408 |
< |
if( atoms[local_index]->isDirectional() ){ |
153 |
> |
#ifdef IS_MPI |
154 |
> |
} |
155 |
> |
#endif // is_mpi |
156 |
> |
|
157 |
> |
fileStreams.push_back(&finalOut); |
158 |
> |
writeFrame(fileStreams, currentTime); |
159 |
|
|
160 |
< |
isDirectional = 1; |
161 |
< |
|
162 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
413 |
< |
dAtom->getQ( q ); |
414 |
< |
|
415 |
< |
for (int j = 0; j < 6 ; j++) |
416 |
< |
atomData13[j] = atomData6[j]; |
417 |
< |
|
418 |
< |
atomData13[6] = q[0]; |
419 |
< |
atomData13[7] = q[1]; |
420 |
< |
atomData13[8] = q[2]; |
421 |
< |
atomData13[9] = q[3]; |
422 |
< |
|
423 |
< |
atomData13[10] = dAtom->getJx(); |
424 |
< |
atomData13[11] = dAtom->getJy(); |
425 |
< |
atomData13[12] = dAtom->getJz(); |
426 |
< |
} |
427 |
< |
|
428 |
< |
} else { |
429 |
< |
sprintf(painCave.errMsg, |
430 |
< |
"Atom %d not found on processor %d\n", |
431 |
< |
i, worldRank ); |
432 |
< |
haveError= 1; |
433 |
< |
simError(); |
434 |
< |
} |
435 |
< |
|
436 |
< |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
437 |
< |
|
438 |
< |
// null terminate the string before sending (just in case): |
439 |
< |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
440 |
< |
|
441 |
< |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
442 |
< |
myPotato, MPI_COMM_WORLD); |
443 |
< |
|
444 |
< |
myPotato++; |
445 |
< |
|
446 |
< |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
447 |
< |
myPotato, MPI_COMM_WORLD); |
448 |
< |
|
449 |
< |
myPotato++; |
450 |
< |
|
451 |
< |
if (isDirectional) { |
452 |
< |
|
453 |
< |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
454 |
< |
myPotato, MPI_COMM_WORLD); |
455 |
< |
|
456 |
< |
} else { |
457 |
< |
|
458 |
< |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
459 |
< |
myPotato, MPI_COMM_WORLD); |
460 |
< |
} |
461 |
< |
|
462 |
< |
myPotato++; |
463 |
< |
} |
464 |
< |
} |
465 |
< |
|
466 |
< |
sprintf( checkPointMsg, |
467 |
< |
"Sucessfully took a dump.\n"); |
468 |
< |
MPIcheckPoint(); |
469 |
< |
|
470 |
< |
} |
160 |
> |
#ifdef IS_MPI |
161 |
> |
finalOut.close(); |
162 |
> |
#endif |
163 |
|
|
472 |
– |
#endif // is_mpi |
164 |
|
} |
165 |
|
|
166 |
< |
void DumpWriter::writeFinal(double finalTime){ |
166 |
> |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
167 |
|
|
477 |
– |
char finalName[500]; |
478 |
– |
ofstream finalOut; |
479 |
– |
|
168 |
|
const int BUFFERSIZE = 2000; |
169 |
|
const int MINIBUFFERSIZE = 100; |
170 |
< |
char tempBuffer[BUFFERSIZE]; |
170 |
> |
|
171 |
> |
char tempBuffer[BUFFERSIZE]; |
172 |
|
char writeLine[BUFFERSIZE]; |
173 |
|
|
174 |
< |
double q[4]; |
175 |
< |
DirectionalAtom* dAtom; |
487 |
< |
Atom** atoms = entry_plug->atoms; |
488 |
< |
int i; |
174 |
> |
int i, k; |
175 |
> |
|
176 |
|
#ifdef IS_MPI |
177 |
|
|
178 |
+ |
/********************************************************************* |
179 |
+ |
* Documentation? You want DOCUMENTATION? |
180 |
+ |
* |
181 |
+ |
* Why all the potatoes below? |
182 |
+ |
* |
183 |
+ |
* To make a long story short, the original version of DumpWriter |
184 |
+ |
* worked in the most inefficient way possible. Node 0 would |
185 |
+ |
* poke each of the node for an individual atom's formatted data |
186 |
+ |
* as node 0 worked its way down the global index. This was particularly |
187 |
+ |
* inefficient since the method blocked all processors at every atom |
188 |
+ |
* (and did it twice!). |
189 |
+ |
* |
190 |
+ |
* An intermediate version of DumpWriter could be described from Node |
191 |
+ |
* zero's perspective as follows: |
192 |
+ |
* |
193 |
+ |
* 1) Have 100 of your friends stand in a circle. |
194 |
+ |
* 2) When you say go, have all of them start tossing potatoes at |
195 |
+ |
* you (one at a time). |
196 |
+ |
* 3) Catch the potatoes. |
197 |
+ |
* |
198 |
+ |
* It was an improvement, but MPI has buffers and caches that could |
199 |
+ |
* best be described in this analogy as "potato nets", so there's no |
200 |
+ |
* need to block the processors atom-by-atom. |
201 |
+ |
* |
202 |
+ |
* This new and improved DumpWriter works in an even more efficient |
203 |
+ |
* way: |
204 |
+ |
* |
205 |
+ |
* 1) Have 100 of your friend stand in a circle. |
206 |
+ |
* 2) When you say go, have them start tossing 5-pound bags of |
207 |
+ |
* potatoes at you. |
208 |
+ |
* 3) Once you've caught a friend's bag of potatoes, |
209 |
+ |
* toss them a spud to let them know they can toss another bag. |
210 |
+ |
* |
211 |
+ |
* How's THAT for documentation? |
212 |
+ |
* |
213 |
+ |
*********************************************************************/ |
214 |
+ |
|
215 |
|
int *potatoes; |
216 |
|
int myPotato; |
217 |
|
|
218 |
|
int nProc; |
219 |
< |
int j, which_node, done, which_atom, local_index; |
219 |
> |
int j, which_node, done, which_atom, local_index, currentIndex; |
220 |
|
double atomData6[6]; |
221 |
|
double atomData13[13]; |
222 |
|
int isDirectional; |
227 |
|
int nAtoms = entry_plug->n_atoms; |
228 |
|
#endif //is_mpi |
229 |
|
|
230 |
+ |
double q[4]; |
231 |
+ |
DirectionalAtom* dAtom; |
232 |
+ |
Atom** atoms = entry_plug->atoms; |
233 |
|
double pos[3], vel[3]; |
234 |
|
|
508 |
– |
#ifdef IS_MPI |
509 |
– |
if(worldRank == 0 ){ |
510 |
– |
#endif // is_mpi |
511 |
– |
|
512 |
– |
strcpy( finalName, entry_plug->finalName ); |
513 |
– |
|
514 |
– |
finalOut.open( finalName, ios::out | ios::trunc ); |
515 |
– |
if( !finalOut ){ |
516 |
– |
sprintf( painCave.errMsg, |
517 |
– |
"Could not open \"%s\" for final dump output.\n", |
518 |
– |
finalName ); |
519 |
– |
painCave.isFatal = 1; |
520 |
– |
simError(); |
521 |
– |
} |
522 |
– |
|
523 |
– |
// finalOut.setf( ios::scientific ); |
524 |
– |
|
525 |
– |
#ifdef IS_MPI |
526 |
– |
} |
527 |
– |
|
528 |
– |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
529 |
– |
MPIcheckPoint(); |
530 |
– |
|
531 |
– |
#endif //is_mpi |
532 |
– |
|
533 |
– |
|
235 |
|
#ifndef IS_MPI |
236 |
+ |
|
237 |
+ |
for(k = 0; k < outFile.size(); k++){ |
238 |
+ |
*outFile[k] << nAtoms << "\n"; |
239 |
|
|
240 |
< |
finalOut << nAtoms << "\n"; |
240 |
> |
*outFile[k] << currentTime << ";\t" |
241 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
242 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
243 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
244 |
> |
|
245 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
246 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
247 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
248 |
|
|
249 |
< |
finalOut << finalTime << ";\t" |
250 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
251 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
541 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
249 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
250 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
251 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
252 |
|
|
253 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
254 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
255 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
256 |
< |
|
547 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
548 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
549 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
550 |
< |
|
551 |
< |
//write out additional parameters, such as chi and eta |
552 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
553 |
< |
finalOut << endl; |
554 |
< |
|
253 |
> |
//write out additional parameters, such as chi and eta |
254 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
255 |
> |
} |
256 |
> |
|
257 |
|
for( i=0; i<nAtoms; i++ ){ |
258 |
|
|
259 |
|
atoms[i]->getPos(pos); |
289 |
|
else |
290 |
|
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
291 |
|
|
292 |
< |
finalOut << writeLine; |
292 |
> |
for(k = 0; k < outFile.size(); k++) |
293 |
> |
*outFile[k] << writeLine; |
294 |
|
} |
592 |
– |
finalOut.flush(); |
593 |
– |
finalOut.close(); |
295 |
|
|
296 |
|
#else // is_mpi |
297 |
|
|
298 |
|
/* code to find maximum tag value */ |
299 |
+ |
|
300 |
|
int *tagub, flag, MAXTAG; |
301 |
|
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
302 |
|
if (flag) { |
319 |
|
nProc = mpiSim->getNumberProcessors(); |
320 |
|
potatoes = new int[nProc]; |
321 |
|
|
322 |
+ |
//write out the comment lines |
323 |
|
for (i = 0; i < nProc; i++) |
324 |
|
potatoes[i] = 0; |
325 |
|
|
326 |
< |
finalOut << mpiSim->getTotAtoms() << "\n"; |
326 |
> |
for(k = 0; k < outFile.size(); k++){ |
327 |
> |
*outFile[k] << mpiSim->getTotAtoms() << "\n"; |
328 |
|
|
329 |
< |
finalOut << finalTime << ";\t" |
330 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
331 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
332 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
329 |
> |
*outFile[k] << currentTime << ";\t" |
330 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
331 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
332 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
333 |
|
|
334 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
335 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
336 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
334 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
335 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
336 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
337 |
|
|
338 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
339 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
340 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
338 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
339 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
340 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
341 |
> |
|
342 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
343 |
> |
} |
344 |
|
|
345 |
< |
finalOut << entry_plug->the_integrator->getAdditionalParameters(); |
639 |
< |
finalOut << endl; |
640 |
< |
finalOut.flush(); |
345 |
> |
currentIndex = 0; |
346 |
|
|
347 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
348 |
|
|
367 |
|
myPotato, MPI_COMM_WORLD, &istatus); |
368 |
|
|
369 |
|
atomTypeString = MPIatomTypeString; |
370 |
< |
|
370 |
> |
|
371 |
|
myPotato++; |
372 |
|
|
373 |
|
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
388 |
|
|
389 |
|
} else { |
390 |
|
|
391 |
< |
haveError = 0; |
391 |
> |
haveError = 0; |
392 |
|
which_atom = i; |
688 |
– |
local_index=-1; |
393 |
|
|
394 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
691 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
692 |
< |
} |
693 |
< |
|
694 |
< |
if (local_index != -1) { |
394 |
> |
local_index = indexArray[currentIndex].first; |
395 |
|
|
396 |
< |
atomTypeString = atoms[local_index]->getType(); |
397 |
< |
|
396 |
> |
if (which_atom == indexArray[currentIndex].second) { |
397 |
> |
|
398 |
> |
atomTypeString = atoms[local_index]->getType(); |
399 |
> |
|
400 |
|
atoms[local_index]->getPos(pos); |
401 |
|
atoms[local_index]->getVel(vel); |
402 |
< |
|
402 |
> |
|
403 |
|
atomData6[0] = pos[0]; |
404 |
|
atomData6[1] = pos[1]; |
405 |
|
atomData6[2] = pos[2]; |
432 |
|
|
433 |
|
} else { |
434 |
|
sprintf(painCave.errMsg, |
435 |
< |
"Atom %d not found on processor %d\n", |
436 |
< |
i, worldRank ); |
435 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
436 |
> |
which_atom, worldRank, currentIndex, local_index ); |
437 |
|
haveError= 1; |
438 |
|
simError(); |
439 |
|
} |
440 |
|
|
441 |
< |
if(haveError) DieDieDie(); |
441 |
> |
if(haveError) DieDieDie(); |
442 |
|
|
443 |
< |
// If we've survived to here, format the line: |
444 |
< |
|
445 |
< |
if (!isDirectional) { |
446 |
< |
|
447 |
< |
sprintf( tempBuffer, |
448 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
449 |
< |
atomTypeString, |
450 |
< |
atomData6[0], |
451 |
< |
atomData6[1], |
452 |
< |
atomData6[2], |
453 |
< |
atomData6[3], |
454 |
< |
atomData6[4], |
455 |
< |
atomData6[5]); |
456 |
< |
|
457 |
< |
strcpy( writeLine, tempBuffer ); |
458 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
459 |
< |
|
460 |
< |
} else { |
461 |
< |
|
462 |
< |
sprintf( tempBuffer, |
463 |
< |
"%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", |
464 |
< |
atomTypeString, |
465 |
< |
atomData13[0], |
466 |
< |
atomData13[1], |
467 |
< |
atomData13[2], |
468 |
< |
atomData13[3], |
469 |
< |
atomData13[4], |
470 |
< |
atomData13[5], |
471 |
< |
atomData13[6], |
472 |
< |
atomData13[7], |
473 |
< |
atomData13[8], |
474 |
< |
atomData13[9], |
475 |
< |
atomData13[10], |
476 |
< |
atomData13[11], |
477 |
< |
atomData13[12]); |
478 |
< |
|
777 |
< |
strcat( writeLine, tempBuffer ); |
778 |
< |
|
779 |
< |
} |
443 |
> |
currentIndex++; |
444 |
> |
} |
445 |
> |
// If we've survived to here, format the line: |
446 |
> |
|
447 |
> |
if (!isDirectional) { |
448 |
> |
|
449 |
> |
sprintf( writeLine, |
450 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
451 |
> |
atomTypeString, |
452 |
> |
atomData6[0], |
453 |
> |
atomData6[1], |
454 |
> |
atomData6[2], |
455 |
> |
atomData6[3], |
456 |
> |
atomData6[4], |
457 |
> |
atomData6[5]); |
458 |
> |
|
459 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
460 |
> |
|
461 |
> |
} else { |
462 |
> |
|
463 |
> |
sprintf( writeLine, |
464 |
> |
"%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", |
465 |
> |
atomTypeString, |
466 |
> |
atomData13[0], |
467 |
> |
atomData13[1], |
468 |
> |
atomData13[2], |
469 |
> |
atomData13[3], |
470 |
> |
atomData13[4], |
471 |
> |
atomData13[5], |
472 |
> |
atomData13[6], |
473 |
> |
atomData13[7], |
474 |
> |
atomData13[8], |
475 |
> |
atomData13[9], |
476 |
> |
atomData13[10], |
477 |
> |
atomData13[11], |
478 |
> |
atomData13[12]); |
479 |
|
|
781 |
– |
finalOut << writeLine; |
782 |
– |
finalOut.flush(); |
480 |
|
} |
481 |
+ |
|
482 |
+ |
for(k = 0; k < outFile.size(); k++) |
483 |
+ |
*outFile[k] << writeLine; |
484 |
|
} |
485 |
< |
|
486 |
< |
finalOut.flush(); |
485 |
> |
|
486 |
> |
for(k = 0; k < outFile.size(); k++) |
487 |
> |
outFile[k]->flush(); |
488 |
> |
|
489 |
|
sprintf( checkPointMsg, |
490 |
|
"Sucessfully took a dump.\n"); |
491 |
< |
delete[] potatoes; |
790 |
< |
|
491 |
> |
|
492 |
|
MPIcheckPoint(); |
493 |
|
|
494 |
+ |
delete[] potatoes; |
495 |
+ |
|
496 |
|
} else { |
497 |
|
|
498 |
|
// worldRank != 0, so I'm a remote node. |
500 |
|
// Set my magic potato to 0: |
501 |
|
|
502 |
|
myPotato = 0; |
503 |
+ |
currentIndex = 0; |
504 |
|
|
505 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
506 |
|
|
509 |
|
if (AtomToProcMap[i] == worldRank) { |
510 |
|
|
511 |
|
if (myPotato + 3 >= MAXTAG) { |
512 |
< |
|
512 |
> |
|
513 |
|
// The potato was going to exceed the maximum value, |
514 |
|
// so wrap this processor potato back to 0 (and block until |
515 |
|
// node 0 says we can go: |
516 |
< |
|
516 |
> |
|
517 |
|
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
518 |
|
|
519 |
|
} |
520 |
< |
which_atom = i; |
521 |
< |
local_index=-1; |
522 |
< |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
523 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
524 |
< |
} |
821 |
< |
if (local_index != -1) { |
520 |
> |
which_atom = i; |
521 |
> |
|
522 |
> |
local_index = indexArray[currentIndex].first; |
523 |
> |
|
524 |
> |
if (which_atom == indexArray[currentIndex].second) { |
525 |
|
|
526 |
|
atomTypeString = atoms[local_index]->getType(); |
527 |
< |
|
527 |
> |
|
528 |
|
atoms[local_index]->getPos(pos); |
529 |
|
atoms[local_index]->getVel(vel); |
530 |
< |
|
530 |
> |
|
531 |
|
atomData6[0] = pos[0]; |
532 |
|
atomData6[1] = pos[1]; |
533 |
|
atomData6[2] = pos[2]; |
552 |
|
atomData13[7] = q[1]; |
553 |
|
atomData13[8] = q[2]; |
554 |
|
atomData13[9] = q[3]; |
555 |
< |
|
555 |
> |
|
556 |
|
atomData13[10] = dAtom->getJx(); |
557 |
|
atomData13[11] = dAtom->getJy(); |
558 |
|
atomData13[12] = dAtom->getJz(); |
560 |
|
|
561 |
|
} else { |
562 |
|
sprintf(painCave.errMsg, |
563 |
< |
"Atom %d not found on processor %d\n", |
564 |
< |
i, worldRank ); |
563 |
> |
"Atom %d not found on processor %d, currentIndex = %d, local_index = %d\n", |
564 |
> |
which_atom, worldRank, currentIndex, local_index ); |
565 |
|
haveError= 1; |
566 |
|
simError(); |
567 |
|
} |
568 |
< |
|
568 |
> |
|
569 |
|
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
570 |
|
|
571 |
|
// null terminate the string before sending (just in case): |
572 |
|
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
573 |
|
|
574 |
|
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
575 |
< |
myPotato, MPI_COMM_WORLD); |
575 |
> |
myPotato, MPI_COMM_WORLD); |
576 |
|
|
577 |
|
myPotato++; |
578 |
|
|
579 |
|
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
580 |
< |
myPotato, MPI_COMM_WORLD); |
580 |
> |
myPotato, MPI_COMM_WORLD); |
581 |
|
|
582 |
|
myPotato++; |
583 |
|
|
592 |
|
myPotato, MPI_COMM_WORLD); |
593 |
|
} |
594 |
|
|
595 |
< |
myPotato++; |
595 |
> |
myPotato++; |
596 |
> |
currentIndex++; |
597 |
|
} |
598 |
|
} |
599 |
|
|
603 |
|
|
604 |
|
} |
605 |
|
|
902 |
– |
if( worldRank == 0 ) finalOut.close(); |
606 |
|
#endif // is_mpi |
607 |
|
} |
608 |
|
|
906 |
– |
|
907 |
– |
|
609 |
|
#ifdef IS_MPI |
610 |
|
|
611 |
|
// a couple of functions to let us escape the write loop |