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#define _FILE_OFFSET_BITS 64 |
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|
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#include <cstring> |
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#include <iostream> |
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#include <fstream> |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
7 |
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#include <mpi++.h> |
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#include "mpiSimulation.hpp" |
10 |
< |
#define TAKE_THIS_TAG 1 |
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> |
#define TAKE_THIS_TAG_CHAR 1 |
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> |
#define TAKE_THIS_TAG_INT 2 |
12 |
> |
|
13 |
> |
namespace dWrite{ |
14 |
> |
void nodeZeroError( void ); |
15 |
> |
void anonymousNodeDie( void ); |
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> |
} |
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|
18 |
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using namespace dWrite; |
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#endif //is_mpi |
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|
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#include "ReadWrite.hpp" |
29 |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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|
24 |
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|
32 |
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strcpy( outName, entry_plug->sampleName ); |
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|
34 |
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outFile.open(outName, ios::out | ios::trunc ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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|
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//outFile.setf( ios::scientific ); |
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|
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#ifdef IS_MPI |
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
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< |
int i, j, which_node, done, game_over, which_atom, local_index; |
75 |
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int i; |
76 |
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#ifdef IS_MPI |
77 |
> |
int j, which_node, done, which_atom, local_index; |
78 |
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#else //is_mpi |
79 |
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int nAtoms = entry_plug->n_atoms; |
80 |
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#endif //is_mpi |
81 |
> |
|
82 |
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double q[4]; |
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DirectionalAtom* dAtom; |
71 |
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int nAtoms = entry_plug->n_atoms; |
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Atom** atoms = entry_plug->atoms; |
85 |
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double pos[3], vel[3]; |
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|
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|
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// write current frame to the eor file |
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|
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this->writeFinal( currentTime ); |
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|
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#ifndef IS_MPI |
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|
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outFile << nAtoms << "\n"; |
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|
96 |
< |
outFile << currentTime << "\t" |
97 |
< |
<< entry_plug->box_x << "\t" |
98 |
< |
<< entry_plug->box_y << "\t" |
99 |
< |
<< entry_plug->box_z << "\n"; |
96 |
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outFile << currentTime << ";\t" |
97 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
101 |
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
104 |
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|
105 |
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<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
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<< entry_plug->Hmat[2][2] << ";\n"; |
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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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atoms[i]->getPos(pos); |
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atoms[i]->getVel(vel); |
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|
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sprintf( tempBuffer, |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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atoms[i]->getType(), |
117 |
< |
atoms[i]->getX(), |
118 |
< |
atoms[i]->getY(), |
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< |
atoms[i]->getZ(), |
120 |
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atoms[i]->get_vx(), |
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atoms[i]->get_vy(), |
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atoms[i]->get_vz()); |
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pos[0], |
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pos[1], |
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pos[2], |
120 |
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vel[0], |
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vel[1], |
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vel[2]); |
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strcpy( writeLine, tempBuffer ); |
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|
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if( atoms[i]->isDirectional() ){ |
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|
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#else // is_mpi |
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|
150 |
< |
MPI::Status istatus; |
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// first thing first, suspend fatalities. |
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painCave.isEventLoop = 1; |
152 |
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|
153 |
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int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
154 |
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int haveError; |
155 |
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|
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MPI_Status istatus; |
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int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
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|
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// write out header and node 0's coordinates |
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|
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if( worldRank == 0 ){ |
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outFile << mpiSim->getTotAtoms() << "\n"; |
163 |
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|
164 |
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outFile << currentTime << ";\t" |
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<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
168 |
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|
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
172 |
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|
173 |
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<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
175 |
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<< entry_plug->Hmat[2][2] << ";\n"; |
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|
131 |
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outFile << currentTime << "\t" |
132 |
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<< entry_plug->box_x << "\t" |
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<< entry_plug->box_y << "\t" |
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<< entry_plug->box_z << "\n"; |
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outFile.flush(); |
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for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
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// Get the Node number which has this atom; |
180 |
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|
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which_node = AtomToProcMap[i]; |
182 |
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|
183 |
< |
if (which_node == mpiSim->getMyNode()) { |
142 |
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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 ); |
183 |
> |
if (which_node == 0 ) { |
184 |
|
|
185 |
< |
if( atoms[i]->isDirectional() ){ |
186 |
< |
|
187 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
188 |
< |
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 |
< |
} |
191 |
< |
|
192 |
< |
} else { |
193 |
< |
|
194 |
< |
done = 0; |
195 |
< |
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++) { |
185 |
> |
haveError = 0; |
186 |
> |
which_atom = i; |
187 |
> |
local_index=-1; |
188 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
189 |
|
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
190 |
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} |
191 |
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if (local_index != -1) { |
192 |
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//format the line |
193 |
+ |
|
194 |
+ |
atoms[local_index]->getPos(pos); |
195 |
+ |
atoms[local_index]->getVel(vel); |
196 |
+ |
|
197 |
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sprintf( tempBuffer, |
198 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
199 |
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atoms[local_index]->getType(), |
200 |
< |
atoms[local_index]->getX(), |
201 |
< |
atoms[local_index]->getY(), |
202 |
< |
atoms[local_index]->getZ(), |
203 |
< |
atoms[local_index]->get_vx(), |
204 |
< |
atoms[local_index]->get_vy(), |
205 |
< |
atoms[local_index]->get_vz()); // check here. |
200 |
> |
pos[0], |
201 |
> |
pos[1], |
202 |
> |
pos[2], |
203 |
> |
vel[0], |
204 |
> |
vel[1], |
205 |
> |
vel[2]); // check here. |
206 |
|
strcpy( writeLine, tempBuffer ); |
207 |
|
|
208 |
|
if( atoms[local_index]->isDirectional() ){ |
220 |
|
dAtom->getJy(), |
221 |
|
dAtom->getJz()); |
222 |
|
strcat( writeLine, tempBuffer ); |
223 |
< |
} |
224 |
< |
else |
225 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
226 |
< |
std::cerr << "node: " << mpiSim->getMyNode() << " sending this line" << writeLine; |
227 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
228 |
< |
TAKE_THIS_TAG); |
229 |
< |
} else { |
230 |
< |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
231 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
232 |
< |
TAKE_THIS_TAG); |
233 |
< |
} |
223 |
> |
|
224 |
> |
} |
225 |
> |
else |
226 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
227 |
> |
} |
228 |
> |
else { |
229 |
> |
sprintf(painCave.errMsg, |
230 |
> |
"Atom %d not found on processor %d\n", |
231 |
> |
i, worldRank ); |
232 |
> |
haveError= 1; |
233 |
> |
simError(); |
234 |
> |
} |
235 |
> |
|
236 |
> |
if(haveError) nodeZeroError(); |
237 |
> |
|
238 |
|
} |
239 |
+ |
else { |
240 |
+ |
myStatus = 1; |
241 |
+ |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
242 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
243 |
+ |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
244 |
+ |
MPI_COMM_WORLD); |
245 |
+ |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
246 |
+ |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
247 |
+ |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
248 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
249 |
+ |
|
250 |
+ |
if(!myStatus) nodeZeroError(); |
251 |
+ |
|
252 |
+ |
} |
253 |
+ |
|
254 |
+ |
outFile << writeLine; |
255 |
+ |
outFile.flush(); |
256 |
|
} |
257 |
+ |
|
258 |
+ |
// kill everyone off: |
259 |
+ |
myStatus = -1; |
260 |
+ |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
261 |
+ |
MPI_Send(&myStatus, 1, MPI_INT, j, |
262 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
263 |
+ |
} |
264 |
+ |
|
265 |
+ |
} else { |
266 |
+ |
|
267 |
+ |
done = 0; |
268 |
+ |
while (!done) { |
269 |
+ |
|
270 |
+ |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
271 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
272 |
+ |
|
273 |
+ |
if(!myStatus) anonymousNodeDie(); |
274 |
+ |
|
275 |
+ |
if(myStatus < 0) break; |
276 |
+ |
|
277 |
+ |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
278 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
279 |
+ |
|
280 |
+ |
myStatus = 1; |
281 |
+ |
local_index=-1; |
282 |
+ |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
283 |
+ |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
284 |
+ |
} |
285 |
+ |
if (local_index != -1) { |
286 |
+ |
//format the line |
287 |
+ |
|
288 |
+ |
atoms[local_index]->getPos(pos); |
289 |
+ |
atoms[local_index]->getVel(vel); |
290 |
+ |
|
291 |
+ |
sprintf( tempBuffer, |
292 |
+ |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
293 |
+ |
atoms[local_index]->getType(), |
294 |
+ |
pos[0], |
295 |
+ |
pos[1], |
296 |
+ |
pos[2], |
297 |
+ |
vel[0], |
298 |
+ |
vel[1], |
299 |
+ |
vel[2]); // check here. |
300 |
+ |
strcpy( writeLine, tempBuffer ); |
301 |
+ |
|
302 |
+ |
if( atoms[local_index]->isDirectional() ){ |
303 |
+ |
|
304 |
+ |
dAtom = (DirectionalAtom *)atoms[local_index]; |
305 |
+ |
dAtom->getQ( q ); |
306 |
+ |
|
307 |
+ |
sprintf( tempBuffer, |
308 |
+ |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
309 |
+ |
q[0], |
310 |
+ |
q[1], |
311 |
+ |
q[2], |
312 |
+ |
q[3], |
313 |
+ |
dAtom->getJx(), |
314 |
+ |
dAtom->getJy(), |
315 |
+ |
dAtom->getJz()); |
316 |
+ |
strcat( writeLine, tempBuffer ); |
317 |
+ |
} |
318 |
+ |
else{ |
319 |
+ |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
320 |
+ |
} |
321 |
+ |
} |
322 |
+ |
else { |
323 |
+ |
sprintf(painCave.errMsg, |
324 |
+ |
"Atom %d not found on processor %d\n", |
325 |
+ |
which_atom, worldRank ); |
326 |
+ |
myStatus = 0; |
327 |
+ |
simError(); |
328 |
+ |
|
329 |
+ |
strcpy( writeLine, "Hello, I'm an error.\n"); |
330 |
+ |
} |
331 |
+ |
|
332 |
+ |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
333 |
+ |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
334 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
335 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
336 |
+ |
} |
337 |
|
} |
338 |
|
outFile.flush(); |
339 |
|
sprintf( checkPointMsg, |
340 |
|
"Sucessfully took a dump.\n"); |
341 |
|
MPIcheckPoint(); |
342 |
+ |
|
343 |
+ |
// last thing last, enable fatalities. |
344 |
+ |
painCave.isEventLoop = 0; |
345 |
+ |
|
346 |
|
#endif // is_mpi |
347 |
|
} |
348 |
|
|
349 |
< |
void DumpWriter::writeFinal(){ |
349 |
> |
void DumpWriter::writeFinal(double finalTime){ |
350 |
|
|
351 |
|
char finalName[500]; |
352 |
|
ofstream finalOut; |
357 |
|
|
358 |
|
double q[4]; |
359 |
|
DirectionalAtom* dAtom; |
268 |
– |
int nAtoms = entry_plug->n_atoms; |
360 |
|
Atom** atoms = entry_plug->atoms; |
361 |
< |
int i, j, which_node, done, game_over, which_atom, local_index; |
361 |
> |
int i; |
362 |
> |
#ifdef IS_MPI |
363 |
> |
int j, which_node, done, which_atom, local_index; |
364 |
> |
#else //is_mpi |
365 |
> |
int nAtoms = entry_plug->n_atoms; |
366 |
> |
#endif //is_mpi |
367 |
|
|
368 |
+ |
double pos[3], vel[3]; |
369 |
|
|
370 |
|
#ifdef IS_MPI |
371 |
|
if(worldRank == 0 ){ |
397 |
|
|
398 |
|
finalOut << nAtoms << "\n"; |
399 |
|
|
400 |
< |
finalOut << entry_plug->box_x << "\t" |
401 |
< |
<< entry_plug->box_y << "\t" |
402 |
< |
<< entry_plug->box_z << "\n"; |
400 |
> |
finalOut << finalTime << ";\t" |
401 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
402 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
403 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
404 |
> |
|
405 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
406 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
407 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
408 |
> |
|
409 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
410 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
411 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
412 |
|
|
413 |
|
for( i=0; i<nAtoms; i++ ){ |
414 |
|
|
415 |
+ |
atoms[i]->getPos(pos); |
416 |
+ |
atoms[i]->getVel(vel); |
417 |
+ |
|
418 |
|
sprintf( tempBuffer, |
419 |
|
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
420 |
|
atoms[i]->getType(), |
421 |
< |
atoms[i]->getX(), |
422 |
< |
atoms[i]->getY(), |
423 |
< |
atoms[i]->getZ(), |
424 |
< |
atoms[i]->get_vx(), |
425 |
< |
atoms[i]->get_vy(), |
426 |
< |
atoms[i]->get_vz()); |
421 |
> |
pos[0], |
422 |
> |
pos[1], |
423 |
> |
pos[2], |
424 |
> |
vel[0], |
425 |
> |
vel[1], |
426 |
> |
vel[2]); |
427 |
|
strcpy( writeLine, tempBuffer ); |
428 |
|
|
429 |
|
if( atoms[i]->isDirectional() ){ |
452 |
|
|
453 |
|
#else // is_mpi |
454 |
|
|
455 |
< |
MPI::Status istatus; |
455 |
> |
// first thing first, suspend fatalities. |
456 |
> |
painCave.isEventLoop = 1; |
457 |
> |
|
458 |
> |
int myStatus; // 1 = wakeup & success; 0 = error; -1 = AllDone |
459 |
> |
int haveError; |
460 |
> |
|
461 |
> |
MPI_Status istatus; |
462 |
|
int *AtomToProcMap = mpiSim->getAtomToProcMap(); |
463 |
|
|
464 |
|
// write out header and node 0's coordinates |
465 |
|
|
466 |
+ |
haveError = 0; |
467 |
|
if( worldRank == 0 ){ |
468 |
|
finalOut << mpiSim->getTotAtoms() << "\n"; |
469 |
|
|
470 |
< |
finalOut << entry_plug->box_x << "\t" |
471 |
< |
<< entry_plug->box_y << "\t" |
472 |
< |
<< entry_plug->box_z << "\n"; |
470 |
> |
finalOut << finalTime << ";\t" |
471 |
> |
<< entry_plug->Hmat[0][0] << "\t" |
472 |
> |
<< entry_plug->Hmat[1][0] << "\t" |
473 |
> |
<< entry_plug->Hmat[2][0] << ";\t" |
474 |
> |
|
475 |
> |
<< entry_plug->Hmat[0][1] << "\t" |
476 |
> |
<< entry_plug->Hmat[1][1] << "\t" |
477 |
> |
<< entry_plug->Hmat[2][1] << ";\t" |
478 |
> |
|
479 |
> |
<< entry_plug->Hmat[0][2] << "\t" |
480 |
> |
<< entry_plug->Hmat[1][2] << "\t" |
481 |
> |
<< entry_plug->Hmat[2][2] << ";\n"; |
482 |
|
|
483 |
|
for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) { |
484 |
|
// Get the Node number which has this molecule: |
486 |
|
which_node = AtomToProcMap[i]; |
487 |
|
|
488 |
|
if (which_node == mpiSim->getMyNode()) { |
489 |
< |
|
490 |
< |
sprintf( tempBuffer, |
491 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
492 |
< |
atoms[i]->getType(), |
493 |
< |
atoms[i]->getX(), |
494 |
< |
atoms[i]->getY(), |
495 |
< |
atoms[i]->getZ(), |
496 |
< |
atoms[i]->get_vx(), |
497 |
< |
atoms[i]->get_vy(), |
498 |
< |
atoms[i]->get_vz()); |
374 |
< |
strcpy( writeLine, tempBuffer ); |
375 |
< |
|
376 |
< |
if( atoms[i]->isDirectional() ){ |
489 |
> |
|
490 |
> |
which_atom = i; |
491 |
> |
local_index=-1; |
492 |
> |
for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) { |
493 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
494 |
> |
} |
495 |
> |
if (local_index != -1) { |
496 |
> |
|
497 |
> |
atoms[local_index]->getPos(pos); |
498 |
> |
atoms[local_index]->getVel(vel); |
499 |
|
|
500 |
< |
dAtom = (DirectionalAtom *)atoms[i]; |
501 |
< |
dAtom->getQ( q ); |
500 |
> |
sprintf( tempBuffer, |
501 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
502 |
> |
atoms[local_index]->getType(), |
503 |
> |
pos[0], |
504 |
> |
pos[1], |
505 |
> |
pos[2], |
506 |
> |
vel[0], |
507 |
> |
vel[1], |
508 |
> |
vel[2]); |
509 |
> |
strcpy( writeLine, tempBuffer ); |
510 |
|
|
511 |
< |
sprintf( tempBuffer, |
512 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
513 |
< |
q[0], |
514 |
< |
q[1], |
515 |
< |
q[2], |
516 |
< |
q[3], |
517 |
< |
dAtom->getJx(), |
518 |
< |
dAtom->getJy(), |
519 |
< |
dAtom->getJz()); |
520 |
< |
strcat( writeLine, tempBuffer ); |
521 |
< |
} |
522 |
< |
else |
523 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
511 |
> |
if( atoms[local_index]->isDirectional() ){ |
512 |
> |
|
513 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
514 |
> |
dAtom->getQ( q ); |
515 |
> |
|
516 |
> |
sprintf( tempBuffer, |
517 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
518 |
> |
q[0], |
519 |
> |
q[1], |
520 |
> |
q[2], |
521 |
> |
q[3], |
522 |
> |
dAtom->getJx(), |
523 |
> |
dAtom->getJy(), |
524 |
> |
dAtom->getJz()); |
525 |
> |
strcat( writeLine, tempBuffer ); |
526 |
> |
} |
527 |
> |
else |
528 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
529 |
> |
} |
530 |
> |
else { |
531 |
> |
sprintf(painCave.errMsg, |
532 |
> |
"Atom %d not found on processor %d\n", |
533 |
> |
i, worldRank ); |
534 |
> |
haveError= 1; |
535 |
> |
simError(); |
536 |
> |
} |
537 |
> |
|
538 |
> |
if(haveError) nodeZeroError(); |
539 |
> |
|
540 |
> |
} |
541 |
> |
else { |
542 |
|
|
543 |
< |
} else { |
544 |
< |
|
545 |
< |
MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG); |
546 |
< |
MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
547 |
< |
TAKE_THIS_TAG, istatus); |
543 |
> |
myStatus = 1; |
544 |
> |
MPI_Send(&myStatus, 1, MPI_INT, which_node, |
545 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
546 |
> |
MPI_Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG_INT, |
547 |
> |
MPI_COMM_WORLD); |
548 |
> |
MPI_Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node, |
549 |
> |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD, &istatus); |
550 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, which_node, |
551 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
552 |
> |
|
553 |
> |
if(!myStatus) nodeZeroError(); |
554 |
|
} |
555 |
|
|
556 |
|
finalOut << writeLine; |
557 |
|
} |
558 |
|
|
559 |
|
// kill everyone off: |
560 |
< |
game_over = -1; |
561 |
< |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
562 |
< |
MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG); |
560 |
> |
myStatus = -1; |
561 |
> |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
562 |
> |
MPI_Send(&myStatus, 1, MPI_INT, j, |
563 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
564 |
|
} |
565 |
|
|
566 |
|
} else { |
567 |
|
|
568 |
|
done = 0; |
569 |
|
while (!done) { |
415 |
– |
MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, |
416 |
– |
TAKE_THIS_TAG, istatus); |
570 |
|
|
571 |
< |
if (which_atom == -1) { |
572 |
< |
done=1; |
573 |
< |
continue; |
574 |
< |
} else { |
571 |
> |
MPI_Recv(&myStatus, 1, MPI_INT, 0, |
572 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
573 |
> |
|
574 |
> |
if(!myStatus) anonymousNodeDie(); |
575 |
> |
|
576 |
> |
if(myStatus < 0) break; |
577 |
> |
|
578 |
> |
MPI_Recv(&which_atom, 1, MPI_INT, 0, |
579 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus); |
580 |
> |
|
581 |
> |
myStatus = 1; |
582 |
> |
local_index=-1; |
583 |
> |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
584 |
> |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
585 |
> |
} |
586 |
> |
if (local_index != -1) { |
587 |
|
|
588 |
< |
local_index=-1; |
589 |
< |
for (j=0; j < mpiSim->getMyNlocal(); j++) { |
425 |
< |
if (atoms[j]->getGlobalIndex() == which_atom) local_index = j; |
426 |
< |
} |
427 |
< |
if (local_index != -1) { |
588 |
> |
atoms[local_index]->getPos(pos); |
589 |
> |
atoms[local_index]->getVel(vel); |
590 |
|
|
591 |
< |
//format the line |
592 |
< |
sprintf( tempBuffer, |
593 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
594 |
< |
atoms[local_index]->getType(), |
595 |
< |
atoms[local_index]->getX(), |
596 |
< |
atoms[local_index]->getY(), |
597 |
< |
atoms[local_index]->getZ(), |
598 |
< |
atoms[local_index]->get_vx(), |
599 |
< |
atoms[local_index]->get_vy(), |
600 |
< |
atoms[local_index]->get_vz()); // check here. |
601 |
< |
strcpy( writeLine, tempBuffer ); |
591 |
> |
//format the line |
592 |
> |
sprintf( tempBuffer, |
593 |
> |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
594 |
> |
atoms[local_index]->getType(), |
595 |
> |
pos[0], |
596 |
> |
pos[1], |
597 |
> |
pos[2], |
598 |
> |
vel[0], |
599 |
> |
vel[1], |
600 |
> |
vel[2]); // check here. |
601 |
> |
strcpy( writeLine, tempBuffer ); |
602 |
> |
|
603 |
> |
if( atoms[local_index]->isDirectional() ){ |
604 |
|
|
605 |
< |
if( atoms[local_index]->isDirectional() ){ |
606 |
< |
|
607 |
< |
dAtom = (DirectionalAtom *)atoms[local_index]; |
608 |
< |
dAtom->getQ( q ); |
609 |
< |
|
610 |
< |
sprintf( tempBuffer, |
611 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
612 |
< |
q[0], |
613 |
< |
q[1], |
614 |
< |
q[2], |
615 |
< |
q[3], |
616 |
< |
dAtom->getJx(), |
617 |
< |
dAtom->getJy(), |
618 |
< |
dAtom->getJz()); |
619 |
< |
strcat( writeLine, tempBuffer ); |
620 |
< |
} |
621 |
< |
else |
622 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
623 |
< |
|
624 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
625 |
< |
TAKE_THIS_TAG); |
626 |
< |
} else { |
627 |
< |
strcpy( writeLine, "ATOM NOT FOUND ON THIS PROCESSOR"); |
628 |
< |
MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
629 |
< |
TAKE_THIS_TAG); |
630 |
< |
} |
605 |
> |
dAtom = (DirectionalAtom *)atoms[local_index]; |
606 |
> |
dAtom->getQ( q ); |
607 |
> |
|
608 |
> |
sprintf( tempBuffer, |
609 |
> |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
610 |
> |
q[0], |
611 |
> |
q[1], |
612 |
> |
q[2], |
613 |
> |
q[3], |
614 |
> |
dAtom->getJx(), |
615 |
> |
dAtom->getJy(), |
616 |
> |
dAtom->getJz()); |
617 |
> |
strcat( writeLine, tempBuffer ); |
618 |
> |
} |
619 |
> |
else{ |
620 |
> |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
621 |
> |
} |
622 |
> |
} |
623 |
> |
else { |
624 |
> |
sprintf(painCave.errMsg, |
625 |
> |
"Atom %d not found on processor %d\n", |
626 |
> |
which_atom, worldRank ); |
627 |
> |
myStatus = 0; |
628 |
> |
simError(); |
629 |
> |
|
630 |
> |
strcpy( writeLine, "Hello, I'm an error.\n"); |
631 |
|
} |
632 |
+ |
|
633 |
+ |
MPI_Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, |
634 |
+ |
TAKE_THIS_TAG_CHAR, MPI_COMM_WORLD); |
635 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, 0, |
636 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
637 |
|
} |
638 |
|
} |
639 |
|
finalOut.flush(); |
640 |
|
sprintf( checkPointMsg, |
641 |
|
"Sucessfully took a dump.\n"); |
642 |
|
MPIcheckPoint(); |
643 |
< |
|
643 |
> |
|
644 |
|
if( worldRank == 0 ) finalOut.close(); |
645 |
|
#endif // is_mpi |
646 |
|
} |
647 |
+ |
|
648 |
+ |
|
649 |
+ |
|
650 |
+ |
#ifdef IS_MPI |
651 |
+ |
|
652 |
+ |
// a couple of functions to let us escape the write loop |
653 |
+ |
|
654 |
+ |
void dWrite::nodeZeroError( void ){ |
655 |
+ |
int j, myStatus; |
656 |
+ |
|
657 |
+ |
myStatus = 0; |
658 |
+ |
for (j = 0; j < mpiSim->getNumberProcessors(); j++) { |
659 |
+ |
MPI_Send( &myStatus, 1, MPI_INT, j, |
660 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
661 |
+ |
} |
662 |
+ |
|
663 |
+ |
|
664 |
+ |
MPI_Finalize(); |
665 |
+ |
exit (0); |
666 |
+ |
|
667 |
+ |
} |
668 |
+ |
|
669 |
+ |
void dWrite::anonymousNodeDie( void ){ |
670 |
+ |
|
671 |
+ |
MPI_Finalize(); |
672 |
+ |
exit (0); |
673 |
+ |
} |
674 |
+ |
|
675 |
+ |
#endif //is_mpi |