1 |
< |
#include <cstring> |
1 |
> |
#define _LARGEFILE_SOURCE64 |
2 |
> |
#define _FILE_OFFSET_BITS 64 |
3 |
> |
|
4 |
> |
#include <string.h> |
5 |
|
#include <iostream> |
6 |
|
#include <fstream> |
7 |
+ |
#include <algorithm> |
8 |
+ |
#include <utility> |
9 |
|
|
10 |
|
#ifdef IS_MPI |
11 |
|
#include <mpi.h> |
7 |
– |
#include <mpi++.h> |
12 |
|
#include "mpiSimulation.hpp" |
13 |
< |
#define TAKE_THIS_TAG 1 |
13 |
> |
|
14 |
> |
namespace dWrite{ |
15 |
> |
void DieDieDie( void ); |
16 |
> |
} |
17 |
> |
|
18 |
> |
using namespace dWrite; |
19 |
|
#endif //is_mpi |
20 |
|
|
21 |
|
#include "ReadWrite.hpp" |
28 |
|
#ifdef IS_MPI |
29 |
|
if(worldRank == 0 ){ |
30 |
|
#endif // is_mpi |
31 |
< |
|
32 |
< |
|
33 |
< |
|
34 |
< |
strcpy( outName, entry_plug->sampleName ); |
35 |
< |
|
27 |
< |
outFile.open(outName, ios::out | ios::trunc ); |
28 |
< |
|
29 |
< |
if( !outFile ){ |
30 |
< |
|
31 |
> |
|
32 |
> |
dumpFile.open(entry_plug->sampleName, ios::out | ios::trunc ); |
33 |
> |
|
34 |
> |
if( !dumpFile ){ |
35 |
> |
|
36 |
|
sprintf( painCave.errMsg, |
37 |
|
"Could not open \"%s\" for dump output.\n", |
38 |
< |
outName); |
38 |
> |
entry_plug->sampleName); |
39 |
|
painCave.isFatal = 1; |
40 |
|
simError(); |
41 |
|
} |
37 |
– |
|
38 |
– |
//outFile.setf( ios::scientific ); |
42 |
|
|
43 |
|
#ifdef IS_MPI |
44 |
|
} |
45 |
|
|
46 |
+ |
//sort the local atoms by global index |
47 |
+ |
sortByGlobalIndex(); |
48 |
+ |
|
49 |
|
sprintf( checkPointMsg, |
50 |
|
"Sucessfully opened output file for dumping.\n"); |
51 |
|
MPIcheckPoint(); |
58 |
|
if(worldRank == 0 ){ |
59 |
|
#endif // is_mpi |
60 |
|
|
61 |
< |
outFile.close(); |
61 |
> |
dumpFile.close(); |
62 |
|
|
63 |
|
#ifdef IS_MPI |
64 |
|
} |
65 |
|
#endif // is_mpi |
66 |
|
} |
67 |
|
|
68 |
< |
void DumpWriter::writeDump( double currentTime ){ |
68 |
> |
#ifdef IS_MPI |
69 |
> |
|
70 |
> |
/** |
71 |
> |
* A hook function to load balancing |
72 |
> |
*/ |
73 |
> |
|
74 |
> |
void DumpWriter::update(){ |
75 |
> |
sortByGlobalIndex(); |
76 |
> |
} |
77 |
|
|
78 |
< |
const int BUFFERSIZE = 2000; |
79 |
< |
char tempBuffer[BUFFERSIZE]; |
80 |
< |
char writeLine[BUFFERSIZE]; |
78 |
> |
/** |
79 |
> |
* Auxiliary sorting function |
80 |
> |
*/ |
81 |
> |
|
82 |
> |
bool indexSortingCriterion(const pair<int, int>& p1, const pair<int, int>& p2){ |
83 |
> |
return p1.second < p2.second; |
84 |
> |
} |
85 |
|
|
86 |
< |
int i, j, which_node, done, game_over, which_atom, local_index; |
87 |
< |
double q[4]; |
88 |
< |
DirectionalAtom* dAtom; |
89 |
< |
int nAtoms = entry_plug->n_atoms; |
90 |
< |
Atom** atoms = entry_plug->atoms; |
91 |
< |
|
86 |
> |
/** |
87 |
> |
* Sorting the local index by global index |
88 |
> |
*/ |
89 |
> |
|
90 |
> |
void DumpWriter::sortByGlobalIndex(){ |
91 |
> |
Molecule* mols = entry_plug->molecules; |
92 |
> |
indexArray.clear(); |
93 |
> |
|
94 |
> |
for(int i = 0; i < mpiSim->getMyNlocal();i++) |
95 |
> |
indexArray.push_back(make_pair(i, mols[i].getGlobalIndex())); |
96 |
> |
|
97 |
> |
sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
98 |
> |
} |
99 |
|
|
100 |
< |
#ifndef IS_MPI |
76 |
< |
|
77 |
< |
outFile << nAtoms << "\n"; |
78 |
< |
|
79 |
< |
outFile << currentTime << "\t" |
80 |
< |
<< entry_plug->box_x << "\t" |
81 |
< |
<< entry_plug->box_y << "\t" |
82 |
< |
<< entry_plug->box_z << "\n"; |
83 |
< |
|
84 |
< |
for( i=0; i<nAtoms; i++ ){ |
85 |
< |
|
100 |
> |
#endif |
101 |
|
|
102 |
< |
sprintf( tempBuffer, |
88 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
89 |
< |
atoms[i]->getType(), |
90 |
< |
atoms[i]->getX(), |
91 |
< |
atoms[i]->getY(), |
92 |
< |
atoms[i]->getZ(), |
93 |
< |
atoms[i]->get_vx(), |
94 |
< |
atoms[i]->get_vy(), |
95 |
< |
atoms[i]->get_vz()); |
96 |
< |
strcpy( writeLine, tempBuffer ); |
102 |
> |
void DumpWriter::writeDump(double currentTime){ |
103 |
|
|
104 |
< |
if( atoms[i]->isDirectional() ){ |
105 |
< |
|
106 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
107 |
< |
dAtom->getQ( q ); |
108 |
< |
|
109 |
< |
sprintf( tempBuffer, |
110 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
111 |
< |
q[0], |
112 |
< |
q[1], |
113 |
< |
q[2], |
114 |
< |
q[3], |
115 |
< |
dAtom->getJx(), |
116 |
< |
dAtom->getJy(), |
111 |
< |
dAtom->getJz()); |
112 |
< |
strcat( writeLine, tempBuffer ); |
104 |
> |
ofstream finalOut; |
105 |
> |
vector<ofstream*> fileStreams; |
106 |
> |
|
107 |
> |
#ifdef IS_MPI |
108 |
> |
if(worldRank == 0 ){ |
109 |
> |
#endif |
110 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
111 |
> |
if( !finalOut ){ |
112 |
> |
sprintf( painCave.errMsg, |
113 |
> |
"Could not open \"%s\" for final dump output.\n", |
114 |
> |
entry_plug->finalName ); |
115 |
> |
painCave.isFatal = 1; |
116 |
> |
simError(); |
117 |
|
} |
118 |
< |
else |
115 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
116 |
< |
|
117 |
< |
outFile << writeLine; |
118 |
> |
#ifdef IS_MPI |
119 |
|
} |
120 |
< |
outFile.flush(); |
120 |
> |
#endif // is_mpi |
121 |
|
|
122 |
< |
#else // is_mpi |
122 |
> |
fileStreams.push_back(&finalOut); |
123 |
> |
fileStreams.push_back(&dumpFile); |
124 |
|
|
125 |
< |
MPI::Status istatus; |
124 |
< |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
125 |
< |
|
126 |
< |
// write out header and node 0's coordinates |
127 |
< |
|
128 |
< |
if( worldRank == 0 ){ |
129 |
< |
outFile << mpiSim->getTotAtoms() << "\n"; |
130 |
< |
|
131 |
< |
outFile << currentTime << "\t" |
132 |
< |
<< entry_plug->box_x << "\t" |
133 |
< |
<< entry_plug->box_y << "\t" |
134 |
< |
<< entry_plug->box_z << "\n"; |
135 |
< |
outFile.flush(); |
136 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
137 |
< |
// Get the Node number which has this atom; |
138 |
< |
|
139 |
< |
which_node = AtomToProcMap[i]; |
140 |
< |
|
141 |
< |
if (which_node == mpiSim->getMyNode()) { |
142 |
< |
sprintf( tempBuffer, |
143 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
144 |
< |
atoms[i]->getType(), |
145 |
< |
atoms[i]->getX(), |
146 |
< |
atoms[i]->getY(), |
147 |
< |
atoms[i]->getZ(), |
148 |
< |
atoms[i]->get_vx(), |
149 |
< |
atoms[i]->get_vy(), |
150 |
< |
atoms[i]->get_vz()); |
151 |
< |
strcpy( writeLine, tempBuffer ); |
152 |
< |
|
153 |
< |
if( atoms[i]->isDirectional() ){ |
154 |
< |
|
155 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
156 |
< |
dAtom->getQ( q ); |
157 |
< |
|
158 |
< |
sprintf( tempBuffer, |
159 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
160 |
< |
q[0], |
161 |
< |
q[1], |
162 |
< |
q[2], |
163 |
< |
q[3], |
164 |
< |
dAtom->getJx(), |
165 |
< |
dAtom->getJy(), |
166 |
< |
dAtom->getJz()); |
167 |
< |
strcat( writeLine, tempBuffer ); |
168 |
< |
} |
169 |
< |
else |
170 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
171 |
< |
|
172 |
< |
} else { |
173 |
< |
|
174 |
< |
std::cerr << "node 0: sending node " << which_node << " request for atom " << i << "\n"; |
175 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
176 |
< |
std::cerr << "node 0: sent!\n"; |
177 |
< |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
178 |
< |
TAKE_THIS_TAG, istatus); |
179 |
< |
std::cerr << "node 0: got this line: " << writeLine; |
180 |
< |
} |
181 |
< |
|
182 |
< |
outFile << writeLine; |
183 |
< |
outFile.flush(); |
184 |
< |
} |
185 |
< |
|
186 |
< |
// kill everyone off: |
187 |
< |
game_over = -1; |
188 |
< |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
189 |
< |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
190 |
< |
} |
125 |
> |
writeFrame(fileStreams, currentTime); |
126 |
|
|
127 |
< |
} else { |
128 |
< |
|
129 |
< |
done = 0; |
130 |
< |
while (!done) { |
196 |
< |
std::cerr << "node: " << mpiSim->getMyNode() << " Waiting for receive \n"; |
197 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
198 |
< |
TAKE_THIS_TAG, istatus); |
199 |
< |
std::cerr << "node: " << mpiSim->getMyNode() << " got request for atom " << which_atom << "\n"; |
200 |
< |
if (which_atom == -1) { |
201 |
< |
done=1; |
202 |
< |
continue; |
203 |
< |
} else { |
204 |
< |
local_index=-1; |
205 |
< |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
206 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
207 |
< |
} |
208 |
< |
if (local_index != -1) { |
209 |
< |
//format the line |
210 |
< |
sprintf( tempBuffer, |
211 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
212 |
< |
atoms[local_index]->getType(), |
213 |
< |
atoms[local_index]->getX(), |
214 |
< |
atoms[local_index]->getY(), |
215 |
< |
atoms[local_index]->getZ(), |
216 |
< |
atoms[local_index]->get_vx(), |
217 |
< |
atoms[local_index]->get_vy(), |
218 |
< |
atoms[local_index]->get_vz()); // check here. |
219 |
< |
strcpy( writeLine, tempBuffer ); |
220 |
< |
|
221 |
< |
if( atoms[local_index]->isDirectional() ){ |
222 |
< |
|
223 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
224 |
< |
dAtom->getQ( q ); |
225 |
< |
|
226 |
< |
sprintf( tempBuffer, |
227 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
228 |
< |
q[0], |
229 |
< |
q[1], |
230 |
< |
q[2], |
231 |
< |
q[3], |
232 |
< |
dAtom->getJx(), |
233 |
< |
dAtom->getJy(), |
234 |
< |
dAtom->getJz()); |
235 |
< |
strcat( writeLine, tempBuffer ); |
236 |
< |
} |
237 |
< |
else |
238 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
239 |
< |
std::cerr << "node: " << mpiSim->getMyNode() << " sending this line" << writeLine; |
240 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
241 |
< |
TAKE_THIS_TAG); |
242 |
< |
} else { |
243 |
< |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
244 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
245 |
< |
TAKE_THIS_TAG); |
246 |
< |
} |
247 |
< |
} |
248 |
< |
} |
249 |
< |
} |
250 |
< |
outFile.flush(); |
251 |
< |
sprintf( checkPointMsg, |
252 |
< |
"Sucessfully took a dump.\n"); |
253 |
< |
MPIcheckPoint(); |
254 |
< |
#endif // is_mpi |
127 |
> |
#ifdef IS_MPI |
128 |
> |
finalOut.close(); |
129 |
> |
#endif |
130 |
> |
|
131 |
|
} |
132 |
|
|
133 |
< |
void DumpWriter::writeFinal(){ |
133 |
> |
void DumpWriter::writeFinal(double currentTime){ |
134 |
|
|
259 |
– |
char finalName[500]; |
135 |
|
ofstream finalOut; |
136 |
+ |
vector<ofstream*> fileStreams; |
137 |
|
|
262 |
– |
const int BUFFERSIZE = 2000; |
263 |
– |
char tempBuffer[BUFFERSIZE]; |
264 |
– |
char writeLine[BUFFERSIZE]; |
265 |
– |
|
266 |
– |
double q[4]; |
267 |
– |
DirectionalAtom* dAtom; |
268 |
– |
int nAtoms = entry_plug->n_atoms; |
269 |
– |
Atom** atoms = entry_plug->atoms; |
270 |
– |
int i, j, which_node, done, game_over, which_atom, local_index; |
271 |
– |
|
272 |
– |
|
138 |
|
#ifdef IS_MPI |
139 |
|
if(worldRank == 0 ){ |
140 |
|
#endif // is_mpi |
141 |
< |
|
142 |
< |
strcpy( finalName, entry_plug->finalName ); |
143 |
< |
|
279 |
< |
finalOut.open( finalName, ios::out | ios::trunc ); |
141 |
> |
|
142 |
> |
finalOut.open( entry_plug->finalName, ios::out | ios::trunc ); |
143 |
> |
|
144 |
|
if( !finalOut ){ |
145 |
|
sprintf( painCave.errMsg, |
146 |
|
"Could not open \"%s\" for final dump output.\n", |
147 |
< |
finalName ); |
147 |
> |
entry_plug->finalName ); |
148 |
|
painCave.isFatal = 1; |
149 |
|
simError(); |
150 |
|
} |
151 |
< |
|
288 |
< |
// finalOut.setf( ios::scientific ); |
289 |
< |
|
151 |
> |
|
152 |
|
#ifdef IS_MPI |
153 |
|
} |
154 |
+ |
#endif // is_mpi |
155 |
|
|
156 |
< |
sprintf(checkPointMsg,"Opened file for final configuration\n"); |
157 |
< |
MPIcheckPoint(); |
156 |
> |
fileStreams.push_back(&finalOut); |
157 |
> |
writeFrame(fileStreams, currentTime); |
158 |
> |
|
159 |
> |
#ifdef IS_MPI |
160 |
> |
finalOut.close(); |
161 |
> |
#endif |
162 |
|
|
163 |
< |
#endif //is_mpi |
163 |
> |
} |
164 |
|
|
165 |
+ |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
166 |
+ |
|
167 |
+ |
const int BUFFERSIZE = 2000; |
168 |
+ |
const int MINIBUFFERSIZE = 100; |
169 |
+ |
|
170 |
+ |
char tempBuffer[BUFFERSIZE]; |
171 |
+ |
char writeLine[BUFFERSIZE]; |
172 |
+ |
|
173 |
+ |
int i, k; |
174 |
+ |
|
175 |
+ |
#ifdef IS_MPI |
176 |
|
|
177 |
+ |
/********************************************************************* |
178 |
+ |
* Documentation? You want DOCUMENTATION? |
179 |
+ |
* |
180 |
+ |
* Why all the potatoes below? |
181 |
+ |
* |
182 |
+ |
* To make a long story short, the original version of DumpWriter |
183 |
+ |
* worked in the most inefficient way possible. Node 0 would |
184 |
+ |
* poke each of the node for an individual atom's formatted data |
185 |
+ |
* as node 0 worked its way down the global index. This was particularly |
186 |
+ |
* inefficient since the method blocked all processors at every atom |
187 |
+ |
* (and did it twice!). |
188 |
+ |
* |
189 |
+ |
* An intermediate version of DumpWriter could be described from Node |
190 |
+ |
* zero's perspective as follows: |
191 |
+ |
* |
192 |
+ |
* 1) Have 100 of your friends stand in a circle. |
193 |
+ |
* 2) When you say go, have all of them start tossing potatoes at |
194 |
+ |
* you (one at a time). |
195 |
+ |
* 3) Catch the potatoes. |
196 |
+ |
* |
197 |
+ |
* It was an improvement, but MPI has buffers and caches that could |
198 |
+ |
* best be described in this analogy as "potato nets", so there's no |
199 |
+ |
* need to block the processors atom-by-atom. |
200 |
+ |
* |
201 |
+ |
* This new and improved DumpWriter works in an even more efficient |
202 |
+ |
* way: |
203 |
+ |
* |
204 |
+ |
* 1) Have 100 of your friend stand in a circle. |
205 |
+ |
* 2) When you say go, have them start tossing 5-pound bags of |
206 |
+ |
* potatoes at you. |
207 |
+ |
* 3) Once you've caught a friend's bag of potatoes, |
208 |
+ |
* toss them a spud to let them know they can toss another bag. |
209 |
+ |
* |
210 |
+ |
* How's THAT for documentation? |
211 |
+ |
* |
212 |
+ |
*********************************************************************/ |
213 |
+ |
|
214 |
+ |
int *potatoes; |
215 |
+ |
int myPotato; |
216 |
+ |
|
217 |
+ |
int nProc; |
218 |
+ |
int j, which_node, done, which_atom, local_index, currentIndex; |
219 |
+ |
double atomData6[6]; |
220 |
+ |
double atomData13[13]; |
221 |
+ |
int isDirectional; |
222 |
+ |
char* atomTypeString; |
223 |
+ |
char MPIatomTypeString[MINIBUFFERSIZE]; |
224 |
+ |
int nObjects; |
225 |
+ |
#endif //is_mpi |
226 |
+ |
|
227 |
+ |
double q[4], ji[3]; |
228 |
+ |
DirectionalAtom* dAtom; |
229 |
+ |
double pos[3], vel[3]; |
230 |
+ |
int nTotObjects; |
231 |
+ |
StuntDouble* sd; |
232 |
+ |
char* molName; |
233 |
+ |
vector<StuntDouble*> integrableObjects; |
234 |
+ |
vector<StuntDouble*>::iterator iter; |
235 |
+ |
nTotObjects = entry_plug->getTotIntegrableObjects(); |
236 |
|
#ifndef IS_MPI |
300 |
– |
|
301 |
– |
finalOut << nAtoms << "\n"; |
302 |
– |
|
303 |
– |
finalOut << entry_plug->box_x << "\t" |
304 |
– |
<< entry_plug->box_y << "\t" |
305 |
– |
<< entry_plug->box_z << "\n"; |
237 |
|
|
238 |
< |
for( i=0; i<nAtoms; i++ ){ |
239 |
< |
|
309 |
< |
sprintf( tempBuffer, |
310 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
311 |
< |
atoms[i]->getType(), |
312 |
< |
atoms[i]->getX(), |
313 |
< |
atoms[i]->getY(), |
314 |
< |
atoms[i]->getZ(), |
315 |
< |
atoms[i]->get_vx(), |
316 |
< |
atoms[i]->get_vy(), |
317 |
< |
atoms[i]->get_vz()); |
318 |
< |
strcpy( writeLine, tempBuffer ); |
238 |
> |
for(k = 0; k < outFile.size(); k++){ |
239 |
> |
*outFile[k] << nTotObjects << "\n"; |
240 |
|
|
241 |
< |
if( atoms[i]->isDirectional() ){ |
242 |
< |
|
243 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
244 |
< |
dAtom->getQ( q ); |
245 |
< |
|
241 |
> |
*outFile[k] << currentTime << ";\t" |
242 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
243 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
244 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
245 |
> |
|
246 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
247 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
248 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
249 |
> |
|
250 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
251 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
252 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
253 |
> |
|
254 |
> |
//write out additional parameters, such as chi and eta |
255 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
256 |
> |
} |
257 |
> |
|
258 |
> |
for( i=0; i< entry_plug->n_mol; i++ ){ |
259 |
> |
|
260 |
> |
integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); |
261 |
> |
molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); |
262 |
> |
|
263 |
> |
for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ |
264 |
> |
sd = *iter; |
265 |
> |
sd->getPos(pos); |
266 |
> |
sd->getVel(vel); |
267 |
> |
|
268 |
|
sprintf( tempBuffer, |
269 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
270 |
< |
q[0], |
271 |
< |
q[1], |
272 |
< |
q[2], |
273 |
< |
q[3], |
274 |
< |
dAtom->getJx(), |
275 |
< |
dAtom->getJy(), |
276 |
< |
dAtom->getJz()); |
277 |
< |
strcat( writeLine, tempBuffer ); |
269 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
270 |
> |
sd->getType(), |
271 |
> |
pos[0], |
272 |
> |
pos[1], |
273 |
> |
pos[2], |
274 |
> |
vel[0], |
275 |
> |
vel[1], |
276 |
> |
vel[2]); |
277 |
> |
strcpy( writeLine, tempBuffer ); |
278 |
> |
|
279 |
> |
if( sd->isDirectional() ){ |
280 |
> |
|
281 |
> |
sd->getQ( q ); |
282 |
> |
sd->getJ( ji ); |
283 |
> |
|
284 |
> |
sprintf( tempBuffer, |
285 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
286 |
> |
q[0], |
287 |
> |
q[1], |
288 |
> |
q[2], |
289 |
> |
q[3], |
290 |
> |
ji[0], |
291 |
> |
ji[1], |
292 |
> |
ji[2]); |
293 |
> |
strcat( writeLine, tempBuffer ); |
294 |
> |
} |
295 |
> |
else |
296 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
297 |
|
} |
336 |
– |
else |
337 |
– |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
338 |
– |
|
339 |
– |
finalOut << writeLine; |
340 |
– |
} |
341 |
– |
finalOut.flush(); |
342 |
– |
finalOut.close(); |
298 |
|
|
299 |
+ |
|
300 |
+ |
for(k = 0; k < outFile.size(); k++) |
301 |
+ |
*outFile[k] << writeLine; |
302 |
+ |
} |
303 |
+ |
|
304 |
|
#else // is_mpi |
305 |
+ |
|
306 |
+ |
/* code to find maximum tag value */ |
307 |
|
|
308 |
< |
MPI::Status istatus; |
309 |
< |
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
308 |
> |
int *tagub, flag, MAXTAG; |
309 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
310 |
> |
if (flag) { |
311 |
> |
MAXTAG = *tagub; |
312 |
> |
} else { |
313 |
> |
MAXTAG = 32767; |
314 |
> |
} |
315 |
|
|
316 |
+ |
int haveError; |
317 |
+ |
|
318 |
+ |
MPI_Status istatus; |
319 |
+ |
int nCurObj; |
320 |
+ |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
321 |
+ |
|
322 |
|
// write out header and node 0's coordinates |
323 |
< |
|
323 |
> |
|
324 |
|
if( worldRank == 0 ){ |
325 |
< |
finalOut << mpiSim->getTotAtoms() << "\n"; |
325 |
> |
|
326 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
327 |
> |
|
328 |
> |
nProc = mpiSim->getNumberProcessors(); |
329 |
> |
potatoes = new int[nProc]; |
330 |
> |
|
331 |
> |
//write out the comment lines |
332 |
> |
for (i = 0; i < nProc; i++) |
333 |
> |
potatoes[i] = 0; |
334 |
|
|
335 |
< |
finalOut << entry_plug->box_x << "\t" |
336 |
< |
<< entry_plug->box_y << "\t" |
337 |
< |
<< entry_plug->box_z << "\n"; |
338 |
< |
|
339 |
< |
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
340 |
< |
// Get the Node number which has this molecule: |
335 |
> |
for(k = 0; k < outFile.size(); k++){ |
336 |
> |
*outFile[k] << nTotObjects << "\n"; |
337 |
> |
|
338 |
> |
*outFile[k] << currentTime << ";\t" |
339 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
340 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
341 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
342 |
> |
|
343 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
344 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
345 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
346 |
> |
|
347 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
348 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
349 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
350 |
> |
|
351 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
352 |
> |
} |
353 |
> |
|
354 |
> |
currentIndex = 0; |
355 |
> |
|
356 |
> |
for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) { |
357 |
|
|
358 |
< |
which_node = AtomToProcMap[i]; |
358 |
> |
// Get the Node number which has this atom; |
359 |
|
|
360 |
< |
if (which_node == mpiSim->getMyNode()) { |
360 |
> |
which_node = MolToProcMap[i]; |
361 |
> |
|
362 |
> |
if (which_node != 0) { |
363 |
|
|
364 |
< |
sprintf( tempBuffer, |
365 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
366 |
< |
atoms[i]->getType(), |
367 |
< |
atoms[i]->getX(), |
368 |
< |
atoms[i]->getY(), |
369 |
< |
atoms[i]->getZ(), |
370 |
< |
atoms[i]->get_vx(), |
372 |
< |
atoms[i]->get_vy(), |
373 |
< |
atoms[i]->get_vz()); |
374 |
< |
strcpy( writeLine, tempBuffer ); |
375 |
< |
|
376 |
< |
if( atoms[i]->isDirectional() ){ |
377 |
< |
|
378 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
379 |
< |
dAtom->getQ( q ); |
380 |
< |
|
381 |
< |
sprintf( tempBuffer, |
382 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
383 |
< |
q[0], |
384 |
< |
q[1], |
385 |
< |
q[2], |
386 |
< |
q[3], |
387 |
< |
dAtom->getJx(), |
388 |
< |
dAtom->getJy(), |
389 |
< |
dAtom->getJz()); |
390 |
< |
strcat( writeLine, tempBuffer ); |
364 |
> |
if (potatoes[which_node] + 1 >= MAXTAG) { |
365 |
> |
// The potato was going to exceed the maximum value, |
366 |
> |
// so wrap this processor potato back to 0: |
367 |
> |
|
368 |
> |
potatoes[which_node] = 0; |
369 |
> |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
370 |
> |
|
371 |
|
} |
372 |
< |
else |
373 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
372 |
> |
|
373 |
> |
myPotato = potatoes[which_node]; |
374 |
> |
|
375 |
> |
//recieve the number of integrableObject in current molecule |
376 |
> |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
377 |
> |
myPotato, MPI_COMM_WORLD, &istatus); |
378 |
|
|
379 |
+ |
for(int l = 0; l < nCurObj; l++){ |
380 |
+ |
|
381 |
+ |
if (potatoes[which_node] + 3 >= MAXTAG) { |
382 |
+ |
// The potato was going to exceed the maximum value, |
383 |
+ |
// so wrap this processor potato back to 0: |
384 |
+ |
|
385 |
+ |
potatoes[which_node] = 0; |
386 |
+ |
MPI_Send(0, 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
387 |
+ |
|
388 |
+ |
} |
389 |
+ |
|
390 |
+ |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
391 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
392 |
+ |
|
393 |
+ |
atomTypeString = MPIatomTypeString; |
394 |
+ |
|
395 |
+ |
myPotato++; |
396 |
+ |
|
397 |
+ |
MPI_Recv(&isDirectional, 1, MPI_INT, which_node, |
398 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
399 |
+ |
|
400 |
+ |
myPotato++; |
401 |
+ |
|
402 |
+ |
if (isDirectional) { |
403 |
+ |
MPI_Recv(atomData13, 13, MPI_DOUBLE, which_node, |
404 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
405 |
+ |
} else { |
406 |
+ |
MPI_Recv(atomData6, 6, MPI_DOUBLE, which_node, |
407 |
+ |
myPotato, MPI_COMM_WORLD, &istatus); |
408 |
+ |
} |
409 |
+ |
|
410 |
+ |
myPotato++; |
411 |
+ |
} |
412 |
+ |
potatoes[which_node] = myPotato; |
413 |
+ |
|
414 |
|
} else { |
415 |
|
|
416 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
417 |
< |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
418 |
< |
TAKE_THIS_TAG, istatus); |
416 |
> |
haveError = 0; |
417 |
> |
|
418 |
> |
local_index = indexArray[currentIndex].first; |
419 |
> |
|
420 |
> |
integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); |
421 |
> |
|
422 |
> |
for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){ |
423 |
> |
sd = *iter; |
424 |
> |
atomTypeString = sd->getType(); |
425 |
> |
|
426 |
> |
sd->getPos(pos); |
427 |
> |
sd->getVel(vel); |
428 |
> |
|
429 |
> |
atomData6[0] = pos[0]; |
430 |
> |
atomData6[1] = pos[1]; |
431 |
> |
atomData6[2] = pos[2]; |
432 |
> |
|
433 |
> |
atomData6[3] = vel[0]; |
434 |
> |
atomData6[4] = vel[1]; |
435 |
> |
atomData6[5] = vel[2]; |
436 |
> |
|
437 |
> |
isDirectional = 0; |
438 |
> |
|
439 |
> |
if( sd->isDirectional() ){ |
440 |
> |
|
441 |
> |
isDirectional = 1; |
442 |
> |
|
443 |
> |
sd->getQ( q ); |
444 |
> |
sd->getJ( ji ); |
445 |
> |
|
446 |
> |
for (int j = 0; j < 6 ; j++) |
447 |
> |
atomData13[j] = atomData6[j]; |
448 |
> |
|
449 |
> |
atomData13[6] = q[0]; |
450 |
> |
atomData13[7] = q[1]; |
451 |
> |
atomData13[8] = q[2]; |
452 |
> |
atomData13[9] = q[3]; |
453 |
> |
|
454 |
> |
atomData13[10] = ji[0]; |
455 |
> |
atomData13[11] = ji[1]; |
456 |
> |
atomData13[12] = ji[2]; |
457 |
> |
} |
458 |
> |
|
459 |
> |
} |
460 |
> |
|
461 |
> |
currentIndex++; |
462 |
|
} |
463 |
+ |
// If we've survived to here, format the line: |
464 |
|
|
465 |
< |
finalOut << writeLine; |
465 |
> |
if (!isDirectional) { |
466 |
> |
|
467 |
> |
sprintf( writeLine, |
468 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
469 |
> |
atomTypeString, |
470 |
> |
atomData6[0], |
471 |
> |
atomData6[1], |
472 |
> |
atomData6[2], |
473 |
> |
atomData6[3], |
474 |
> |
atomData6[4], |
475 |
> |
atomData6[5]); |
476 |
> |
|
477 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
478 |
> |
|
479 |
> |
} else { |
480 |
> |
|
481 |
> |
sprintf( writeLine, |
482 |
> |
"%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", |
483 |
> |
atomTypeString, |
484 |
> |
atomData13[0], |
485 |
> |
atomData13[1], |
486 |
> |
atomData13[2], |
487 |
> |
atomData13[3], |
488 |
> |
atomData13[4], |
489 |
> |
atomData13[5], |
490 |
> |
atomData13[6], |
491 |
> |
atomData13[7], |
492 |
> |
atomData13[8], |
493 |
> |
atomData13[9], |
494 |
> |
atomData13[10], |
495 |
> |
atomData13[11], |
496 |
> |
atomData13[12]); |
497 |
> |
|
498 |
> |
} |
499 |
> |
|
500 |
> |
for(k = 0; k < outFile.size(); k++) |
501 |
> |
*outFile[k] << writeLine; |
502 |
|
} |
503 |
|
|
504 |
< |
// kill everyone off: |
505 |
< |
game_over = -1; |
506 |
< |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
507 |
< |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
508 |
< |
} |
509 |
< |
|
504 |
> |
for(k = 0; k < outFile.size(); k++) |
505 |
> |
outFile[k]->flush(); |
506 |
> |
|
507 |
> |
sprintf( checkPointMsg, |
508 |
> |
"Sucessfully took a dump.\n"); |
509 |
> |
|
510 |
> |
MPIcheckPoint(); |
511 |
> |
|
512 |
> |
delete[] potatoes; |
513 |
> |
|
514 |
|
} else { |
515 |
+ |
|
516 |
+ |
// worldRank != 0, so I'm a remote node. |
517 |
+ |
|
518 |
+ |
// Set my magic potato to 0: |
519 |
+ |
|
520 |
+ |
myPotato = 0; |
521 |
+ |
currentIndex = 0; |
522 |
|
|
523 |
< |
done = 0; |
524 |
< |
while (!done) { |
525 |
< |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
526 |
< |
TAKE_THIS_TAG, istatus); |
523 |
> |
for (i = 0 ; i < mpiSim->getTotNmol(); i++ ) { |
524 |
> |
|
525 |
> |
// Am I the node which has this integrableObject? |
526 |
> |
|
527 |
> |
if (MolToProcMap[i] == worldRank) { |
528 |
|
|
418 |
– |
if (which_atom == -1) { |
419 |
– |
done=1; |
420 |
– |
continue; |
421 |
– |
} else { |
529 |
|
|
530 |
< |
local_index=-1; |
531 |
< |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
532 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
530 |
> |
if (myPotato + 1 >= MAXTAG) { |
531 |
> |
|
532 |
> |
// The potato was going to exceed the maximum value, |
533 |
> |
// so wrap this processor potato back to 0 (and block until |
534 |
> |
// node 0 says we can go: |
535 |
> |
|
536 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
537 |
> |
|
538 |
|
} |
427 |
– |
if (local_index != -1) { |
539 |
|
|
540 |
< |
//format the line |
541 |
< |
sprintf( tempBuffer, |
542 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
543 |
< |
atoms[local_index]->getType(), |
544 |
< |
atoms[local_index]->getX(), |
545 |
< |
atoms[local_index]->getY(), |
546 |
< |
atoms[local_index]->getZ(), |
547 |
< |
atoms[local_index]->get_vx(), |
548 |
< |
atoms[local_index]->get_vy(), |
549 |
< |
atoms[local_index]->get_vz()); // check here. |
550 |
< |
strcpy( writeLine, tempBuffer ); |
551 |
< |
|
552 |
< |
if( atoms[local_index]->isDirectional() ){ |
540 |
> |
local_index = indexArray[currentIndex].first; |
541 |
> |
integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects(); |
542 |
> |
|
543 |
> |
nCurObj = integrableObjects.size(); |
544 |
> |
|
545 |
> |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
546 |
> |
myPotato, MPI_COMM_WORLD); |
547 |
> |
|
548 |
> |
for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ |
549 |
> |
|
550 |
> |
if (myPotato + 3 >= MAXTAG) { |
551 |
> |
|
552 |
> |
// The potato was going to exceed the maximum value, |
553 |
> |
// so wrap this processor potato back to 0 (and block until |
554 |
> |
// node 0 says we can go: |
555 |
> |
|
556 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
557 |
> |
|
558 |
> |
} |
559 |
|
|
560 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
561 |
< |
dAtom->getQ( q ); |
562 |
< |
|
563 |
< |
sprintf( tempBuffer, |
564 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
565 |
< |
q[0], |
566 |
< |
q[1], |
567 |
< |
q[2], |
568 |
< |
q[3], |
569 |
< |
dAtom->getJx(), |
570 |
< |
dAtom->getJy(), |
571 |
< |
dAtom->getJz()); |
572 |
< |
strcat( writeLine, tempBuffer ); |
560 |
> |
sd = *iter; |
561 |
> |
|
562 |
> |
atomTypeString = sd->getType(); |
563 |
> |
|
564 |
> |
sd->getPos(pos); |
565 |
> |
sd->getVel(vel); |
566 |
> |
|
567 |
> |
atomData6[0] = pos[0]; |
568 |
> |
atomData6[1] = pos[1]; |
569 |
> |
atomData6[2] = pos[2]; |
570 |
> |
|
571 |
> |
atomData6[3] = vel[0]; |
572 |
> |
atomData6[4] = vel[1]; |
573 |
> |
atomData6[5] = vel[2]; |
574 |
> |
|
575 |
> |
isDirectional = 0; |
576 |
> |
|
577 |
> |
if( sd->isDirectional() ){ |
578 |
> |
|
579 |
> |
isDirectional = 1; |
580 |
> |
|
581 |
> |
sd->getQ( q ); |
582 |
> |
sd->getJ( ji ); |
583 |
> |
|
584 |
> |
for (int j = 0; j < 6 ; j++) |
585 |
> |
atomData13[j] = atomData6[j]; |
586 |
> |
|
587 |
> |
atomData13[6] = q[0]; |
588 |
> |
atomData13[7] = q[1]; |
589 |
> |
atomData13[8] = q[2]; |
590 |
> |
atomData13[9] = q[3]; |
591 |
> |
|
592 |
> |
atomData13[10] = ji[0]; |
593 |
> |
atomData13[11] = ji[1]; |
594 |
> |
atomData13[12] = ji[2]; |
595 |
> |
} |
596 |
> |
|
597 |
> |
|
598 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
599 |
> |
|
600 |
> |
// null terminate the string before sending (just in case): |
601 |
> |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
602 |
> |
|
603 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
604 |
> |
myPotato, MPI_COMM_WORLD); |
605 |
> |
|
606 |
> |
myPotato++; |
607 |
> |
|
608 |
> |
MPI_Send(&isDirectional, 1, MPI_INT, 0, |
609 |
> |
myPotato, MPI_COMM_WORLD); |
610 |
> |
|
611 |
> |
myPotato++; |
612 |
> |
|
613 |
> |
if (isDirectional) { |
614 |
> |
|
615 |
> |
MPI_Send(atomData13, 13, MPI_DOUBLE, 0, |
616 |
> |
myPotato, MPI_COMM_WORLD); |
617 |
> |
|
618 |
> |
} else { |
619 |
> |
|
620 |
> |
MPI_Send(atomData6, 6, MPI_DOUBLE, 0, |
621 |
> |
myPotato, MPI_COMM_WORLD); |
622 |
> |
} |
623 |
> |
|
624 |
> |
myPotato++; |
625 |
> |
|
626 |
|
} |
627 |
< |
else |
628 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
627 |
> |
|
628 |
> |
currentIndex++; |
629 |
|
|
460 |
– |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
461 |
– |
TAKE_THIS_TAG); |
462 |
– |
} else { |
463 |
– |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
464 |
– |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
465 |
– |
TAKE_THIS_TAG); |
630 |
|
} |
631 |
+ |
|
632 |
|
} |
633 |
+ |
|
634 |
|
} |
469 |
– |
} |
470 |
– |
finalOut.flush(); |
471 |
– |
sprintf( checkPointMsg, |
472 |
– |
"Sucessfully took a dump.\n"); |
473 |
– |
MPIcheckPoint(); |
635 |
|
|
636 |
< |
if( worldRank == 0 ) finalOut.close(); |
636 |
> |
sprintf( checkPointMsg, |
637 |
> |
"Sucessfully took a dump.\n"); |
638 |
> |
MPIcheckPoint(); |
639 |
> |
|
640 |
> |
|
641 |
|
#endif // is_mpi |
642 |
|
} |
643 |
+ |
|
644 |
+ |
#ifdef IS_MPI |
645 |
+ |
|
646 |
+ |
// a couple of functions to let us escape the write loop |
647 |
+ |
|
648 |
+ |
void dWrite::DieDieDie( void ){ |
649 |
+ |
|
650 |
+ |
MPI_Finalize(); |
651 |
+ |
exit (0); |
652 |
+ |
} |
653 |
+ |
|
654 |
+ |
#endif //is_mpi |