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