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