| 38 |
|
* University of Notre Dame has been advised of the possibility of |
| 39 |
|
* such damages. |
| 40 |
|
*/ |
| 41 |
– |
|
| 42 |
– |
#include <algorithm> |
| 43 |
– |
#include <iostream> |
| 44 |
– |
#include <map> |
| 41 |
|
|
| 46 |
– |
#include "primitives/Molecule.hpp" |
| 42 |
|
#include "io/RestWriter.hpp" |
| 43 |
+ |
#include "primitives/Molecule.hpp" |
| 44 |
|
#include "utils/simError.h" |
| 45 |
+ |
#include "io/basic_teebuf.hpp" |
| 46 |
|
|
| 47 |
+ |
#ifdef IS_MPI |
| 48 |
+ |
#include <mpi.h> |
| 49 |
+ |
#define TAKE_THIS_TAG_INT 1 |
| 50 |
+ |
#define TAKE_THIS_TAG_REAL 2 |
| 51 |
+ |
#endif //is_mpi |
| 52 |
|
|
| 53 |
|
namespace oopse { |
| 54 |
|
RestWriter::RestWriter(SimInfo* info) : |
| 55 |
< |
info_(info) { |
| 56 |
< |
|
| 57 |
< |
// only the master node writes to the disk |
| 55 |
> |
info_(info), outName_(info_->getRestFileName()) { |
| 56 |
> |
} |
| 57 |
> |
|
| 58 |
> |
RestWriter::~RestWriter() {} |
| 59 |
> |
|
| 60 |
> |
void RestWriter::writeZAngFile() { |
| 61 |
> |
std::ostream* zangStream; |
| 62 |
> |
|
| 63 |
|
#ifdef IS_MPI |
| 64 |
|
if (worldRank == 0) { |
| 65 |
|
#endif // is_mpi |
| 66 |
< |
|
| 67 |
< |
outName = info_->getRestFileName(); |
| 68 |
< |
|
| 66 |
> |
|
| 67 |
> |
zangStream = new std::ofstream(outName_.c_str()); |
| 68 |
> |
|
| 69 |
|
#ifdef IS_MPI |
| 70 |
|
} |
| 71 |
+ |
#endif // is_mpi |
| 72 |
+ |
|
| 73 |
+ |
writeZangle(*zangStream); |
| 74 |
+ |
|
| 75 |
+ |
#ifdef IS_MPI |
| 76 |
+ |
if (worldRank == 0) { |
| 77 |
|
#endif // is_mpi |
| 78 |
+ |
delete zangStream; |
| 79 |
+ |
|
| 80 |
+ |
#ifdef IS_MPI |
| 81 |
+ |
} |
| 82 |
+ |
#endif // is_mpi |
| 83 |
+ |
|
| 84 |
|
} |
| 85 |
< |
|
| 86 |
< |
RestWriter::~RestWriter() {} |
| 68 |
< |
|
| 69 |
< |
void RestWriter::writeZangle(){ |
| 85 |
> |
|
| 86 |
> |
void RestWriter::writeZangle(std::ostream& finalOut){ |
| 87 |
|
const int BUFFERSIZE = 2000; |
| 88 |
|
char tempBuffer[BUFFERSIZE]; |
| 89 |
|
char writeLine[BUFFERSIZE]; |
| 90 |
|
|
| 74 |
– |
std::ofstream finalOut; |
| 75 |
– |
|
| 91 |
|
Molecule* mol; |
| 92 |
|
StuntDouble* integrableObject; |
| 93 |
|
SimInfo::MoleculeIterator mi; |
| 94 |
|
Molecule::IntegrableObjectIterator ii; |
| 80 |
– |
|
| 81 |
– |
#ifdef IS_MPI |
| 82 |
– |
if(worldRank == 0 ){ |
| 83 |
– |
#endif |
| 84 |
– |
finalOut.open( outName.c_str(), std::ios::out | std::ios::trunc ); |
| 85 |
– |
if( !finalOut ){ |
| 86 |
– |
sprintf( painCave.errMsg, |
| 87 |
– |
"Could not open \"%s\" for zAngle output.\n", |
| 88 |
– |
outName.c_str() ); |
| 89 |
– |
painCave.isFatal = 1; |
| 90 |
– |
simError(); |
| 91 |
– |
} |
| 92 |
– |
#ifdef IS_MPI |
| 93 |
– |
} |
| 94 |
– |
#endif // is_mpi |
| 95 |
|
|
| 96 |
|
#ifndef IS_MPI |
| 97 |
|
// first we do output for the single processor version |
| 109 |
|
sprintf( tempBuffer, |
| 110 |
|
"%14.10lf\n", |
| 111 |
|
integrableObject->getZangle()); |
| 112 |
< |
strcpy( writeLine, tempBuffer ); |
| 113 |
< |
|
| 114 |
< |
finalOut << writeLine; |
| 112 |
> |
strcpy( writeLine, tempBuffer ); |
| 113 |
> |
|
| 114 |
> |
finalOut << writeLine; |
| 115 |
> |
|
| 116 |
|
} |
| 116 |
– |
|
| 117 |
|
} |
| 118 |
|
|
| 119 |
|
#else |
| 120 |
|
int nproc; |
| 121 |
|
MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
| 122 |
|
const int masterNode = 0; |
| 123 |
– |
int myNode = worldRank; |
| 124 |
– |
std::vector<int> tmpNIntObjects(nproc, 0); |
| 125 |
– |
std::vector<int> nIntObjectsInProc(nproc, 0); |
| 126 |
– |
tmpNIntObjects[myNode] = info_->getNGlobalIntegrableObjects(); |
| 123 |
|
|
| 128 |
– |
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
| 129 |
– |
MPI_Allreduce(&tmpNIntObjects[0], &nIntObjectsInProc[0], nproc, MPI_INT, |
| 130 |
– |
MPI_SUM, MPI_COMM_WORLD); |
| 131 |
– |
|
| 124 |
|
MPI_Status ierr; |
| 125 |
|
int intObIndex; |
| 126 |
+ |
int vecLength; |
| 127 |
|
RealType zAngle; |
| 128 |
< |
|
| 128 |
> |
std::vector<int> gIndex; |
| 129 |
> |
std::vector<RealType> zValues; |
| 130 |
> |
|
| 131 |
|
if (worldRank == masterNode) { |
| 132 |
|
std::map<int, RealType> zAngData; |
| 133 |
|
for(int i = 0 ; i < nproc; ++i) { |
| 146 |
|
} |
| 147 |
|
} |
| 148 |
|
} else { |
| 149 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 150 |
< |
mol = info_->nextMolecule(mi)) { |
| 151 |
< |
|
| 152 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); |
| 153 |
< |
integrableObject != NULL; |
| 154 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 155 |
< |
|
| 156 |
< |
MPI_Recv(&intObIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr); |
| 157 |
< |
MPI_Recv(&zAngle, 1, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr); |
| 158 |
< |
zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle)); |
| 159 |
< |
} |
| 149 |
> |
MPI_Recv(&vecLength, 1, MPI_INT, i, |
| 150 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &ierr); |
| 151 |
> |
// make sure the vectors are the right size for the incoming data |
| 152 |
> |
gIndex.resize(vecLength); |
| 153 |
> |
zValues.resize(vecLength); |
| 154 |
> |
|
| 155 |
> |
MPI_Recv(&gIndex[0], vecLength, MPI_INT, i, |
| 156 |
> |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &ierr); |
| 157 |
> |
MPI_Recv(&zValues[0], vecLength, MPI_REALTYPE, i, |
| 158 |
> |
TAKE_THIS_TAG_REAL, MPI_COMM_WORLD, &ierr); |
| 159 |
> |
|
| 160 |
> |
for (int k = 0; k < vecLength; k++){ |
| 161 |
> |
zAngData.insert(std::pair<int, RealType>(gIndex[k], zValues[k])); |
| 162 |
|
} |
| 163 |
+ |
gIndex.clear(); |
| 164 |
+ |
zValues.clear(); |
| 165 |
|
} |
| 166 |
|
} |
| 167 |
|
|
| 168 |
< |
finalOut |
| 169 |
< |
<< info_->getSnapshotManager()->getCurrentSnapshot()->getTime() |
| 171 |
< |
<< " : omega values at this time\n"; |
| 168 |
> |
finalOut << info_->getSnapshotManager()->getCurrentSnapshot()->getTime() |
| 169 |
> |
<< " : omega values at this time\n"; |
| 170 |
|
|
| 171 |
|
std::map<int, RealType>::iterator l; |
| 172 |
|
for (l = zAngData.begin(); l != zAngData.end(); ++l) { |
| 173 |
+ |
|
| 174 |
|
sprintf( tempBuffer, |
| 175 |
|
"%14.10lf\n", |
| 176 |
|
l->second); |
| 178 |
|
|
| 179 |
|
finalOut << writeLine; |
| 180 |
|
} |
| 182 |
– |
|
| 183 |
– |
finalOut.close(); |
| 181 |
|
|
| 182 |
|
} else { |
| 183 |
+ |
// pack up and send the appropriate info to the master node |
| 184 |
|
for(int j = 1; j < nproc; ++j) { |
| 185 |
< |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 186 |
< |
mol = info_->nextMolecule(mi)) { |
| 187 |
< |
|
| 188 |
< |
for (integrableObject = mol->beginIntegrableObject(ii); |
| 189 |
< |
integrableObject != NULL; |
| 190 |
< |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 191 |
< |
intObIndex = integrableObject->getGlobalIndex(); |
| 192 |
< |
zAngle = integrableObject->getZangle(); |
| 185 |
> |
if (worldRank == j) { |
| 186 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 187 |
> |
mol = info_->nextMolecule(mi)) { |
| 188 |
> |
|
| 189 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); |
| 190 |
> |
integrableObject != NULL; |
| 191 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 192 |
> |
|
| 193 |
> |
// build a vector of the indicies |
| 194 |
> |
intObIndex = integrableObject->getGlobalIndex(); |
| 195 |
> |
gIndex.push_back(intObIndex); |
| 196 |
> |
|
| 197 |
> |
// build a vector of the zAngle values |
| 198 |
> |
zAngle = integrableObject->getZangle(); |
| 199 |
> |
zValues.push_back(zAngle); |
| 200 |
|
|
| 201 |
< |
MPI_Send(&intObIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); |
| 197 |
< |
MPI_Send(&zAngle, 1, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD); |
| 201 |
> |
} |
| 202 |
|
} |
| 203 |
+ |
|
| 204 |
+ |
// let's send these vectors to the master node so that it |
| 205 |
+ |
// can sort them and write to the disk |
| 206 |
+ |
vecLength = gIndex.size(); |
| 207 |
+ |
|
| 208 |
+ |
MPI_Send(&vecLength, 1, MPI_INT, masterNode, |
| 209 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 210 |
+ |
MPI_Send(&gIndex[0], vecLength, MPI_INT, masterNode, |
| 211 |
+ |
TAKE_THIS_TAG_INT, MPI_COMM_WORLD); |
| 212 |
+ |
MPI_Send(&zValues[0], vecLength, MPI_REALTYPE, masterNode, |
| 213 |
+ |
TAKE_THIS_TAG_REAL, MPI_COMM_WORLD); |
| 214 |
+ |
|
| 215 |
|
} |
| 216 |
|
} |
| 217 |
|
} |
