| 1 |
#include "io/DumpWriter.hpp" |
| 2 |
#include "primitives/Molecule.hpp" |
| 3 |
#include "utils/simError.h" |
| 4 |
|
| 5 |
#ifdef IS_MPI |
| 6 |
#include <mpi.h> |
| 7 |
#endif //is_mpi |
| 8 |
|
| 9 |
namespace oopse { |
| 10 |
|
| 11 |
DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) |
| 12 |
: info_(info), filename_(filename){ |
| 13 |
#ifdef IS_MPI |
| 14 |
|
| 15 |
if (worldRank == 0) { |
| 16 |
#endif // is_mpi |
| 17 |
|
| 18 |
dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc); |
| 19 |
|
| 20 |
if (!dumpFile_) { |
| 21 |
sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
| 22 |
filename_.c_str()); |
| 23 |
painCave.isFatal = 1; |
| 24 |
simError(); |
| 25 |
} |
| 26 |
|
| 27 |
#ifdef IS_MPI |
| 28 |
|
| 29 |
} |
| 30 |
|
| 31 |
sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
| 32 |
MPIcheckPoint(); |
| 33 |
|
| 34 |
#endif // is_mpi |
| 35 |
|
| 36 |
} |
| 37 |
|
| 38 |
DumpWriter::~DumpWriter() { |
| 39 |
|
| 40 |
#ifdef IS_MPI |
| 41 |
|
| 42 |
if (worldRank == 0) { |
| 43 |
#endif // is_mpi |
| 44 |
|
| 45 |
dumpFile_.close(); |
| 46 |
|
| 47 |
#ifdef IS_MPI |
| 48 |
|
| 49 |
} |
| 50 |
|
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#endif // is_mpi |
| 52 |
|
| 53 |
} |
| 54 |
|
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void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) { |
| 56 |
|
| 57 |
double currentTime; |
| 58 |
Mat3x3d hmat; |
| 59 |
double chi; |
| 60 |
double integralOfChiDt; |
| 61 |
Mat3x3d eta; |
| 62 |
|
| 63 |
currentTime = s->getTime(); |
| 64 |
hmat = s->getHmat(); |
| 65 |
chi = s->getChi(); |
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integralOfChiDt = s->getIntegralOfChiDt(); |
| 67 |
eta = s->getEta(); |
| 68 |
|
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os << currentTime << ";\t" |
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<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t" |
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<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t" |
| 72 |
<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t"; |
| 73 |
|
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//write out additional parameters, such as chi and eta |
| 75 |
|
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os << chi << "\t" << integralOfChiDt << "\t;"; |
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|
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os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t" |
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<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t" |
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<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";"; |
| 81 |
|
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os << std::endl; |
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} |
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|
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void DumpWriter::writeFrame(std::ostream& os) { |
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const int BUFFERSIZE = 2000; |
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const int MINIBUFFERSIZE = 100; |
| 88 |
|
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
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Quat4d q; |
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Vector3d ji; |
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Vector3d pos; |
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Vector3d vel; |
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|
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Molecule* mol; |
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StuntDouble* integrableObject; |
| 99 |
SimInfo::MoleculeIterator mi; |
| 100 |
Molecule::IntegrableObjectIterator ii; |
| 101 |
|
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int nTotObjects; |
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nTotObjects = info_->getNGlobalIntegrableObjects(); |
| 104 |
|
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#ifndef IS_MPI |
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|
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|
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os << nTotObjects << "\n"; |
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|
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writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
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|
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for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
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|
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for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii)) { |
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|
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|
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pos = integrableObject->getPos(); |
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vel = integrableObject->getVel(); |
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|
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sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
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integrableObject->getType().c_str(), |
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pos[0], pos[1], pos[2], |
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vel[0], vel[1], vel[2]); |
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|
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strcpy(writeLine, tempBuffer); |
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|
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if (integrableObject->isDirectional()) { |
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q = integrableObject->getQ(); |
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ji = integrableObject->getJ(); |
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|
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sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[0], q[1], q[2], q[3], |
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ji[0], ji[1], ji[2]); |
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strcat(writeLine, tempBuffer); |
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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"); |
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} |
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|
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os << writeLine; |
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|
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} |
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} |
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|
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#else // is_mpi |
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/********************************************************************* |
| 147 |
* Documentation? You want DOCUMENTATION? |
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* |
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* Why all the potatoes below? |
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* |
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* To make a long story short, the original version of DumpWriter |
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* worked in the most inefficient way possible. Node 0 would |
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* poke each of the node for an individual atom's formatted data |
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* as node 0 worked its way down the global index. This was particularly |
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* inefficient since the method blocked all processors at every atom |
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* (and did it twice!). |
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* |
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* An intermediate version of DumpWriter could be described from Node |
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* zero's perspective as follows: |
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* |
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* 1) Have 100 of your friends stand in a circle. |
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* 2) When you say go, have all of them start tossing potatoes at |
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* you (one at a time). |
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* 3) Catch the potatoes. |
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* |
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* It was an improvement, but MPI has buffers and caches that could |
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* best be described in this analogy as "potato nets", so there's no |
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* need to block the processors atom-by-atom. |
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* |
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* This new and improved DumpWriter works in an even more efficient |
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* way: |
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* |
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* 1) Have 100 of your friend stand in a circle. |
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* 2) When you say go, have them start tossing 5-pound bags of |
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* potatoes at you. |
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* 3) Once you've caught a friend's bag of potatoes, |
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* toss them a spud to let them know they can toss another bag. |
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* |
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* How's THAT for documentation? |
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* |
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*********************************************************************/ |
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const int masterNode = 0; |
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|
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int * potatoes; |
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int myPotato; |
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int nProc; |
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int which_node; |
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double atomData[13]; |
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int isDirectional; |
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const char * atomTypeString; |
| 191 |
char MPIatomTypeString[MINIBUFFERSIZE]; |
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int msgLen; // the length of message actually recieved at master nodes |
| 193 |
int haveError; |
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MPI_Status istatus; |
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int nCurObj; |
| 196 |
|
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// code to find maximum tag value |
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int * tagub; |
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int flag; |
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int MAXTAG; |
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MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
| 202 |
|
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if (flag) { |
| 204 |
MAXTAG = *tagub; |
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} else { |
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MAXTAG = 32767; |
| 207 |
} |
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|
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if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file |
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|
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// Node 0 needs a list of the magic potatoes for each processor; |
| 212 |
|
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MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
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potatoes = new int[nProc]; |
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|
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//write out the comment lines |
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for(i = 0; i < nProc; i++) { |
| 218 |
potatoes[i] = 0; |
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} |
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|
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|
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os << nTotObjects << "\n"; |
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writeCommentLine(info_->getSnapshotManager()->getCurrentSnapshot()); |
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|
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for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
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|
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// Get the Node number which has this atom; |
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|
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which_node = info_->getMolToProc(i); |
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|
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if (which_node != masterNode) { //current molecule is in slave node |
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if (potatoes[which_node] + 1 >= MAXTAG) { |
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// The potato was going to exceed the maximum value, |
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// so wrap this processor potato back to 0: |
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|
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potatoes[which_node] = 0; |
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MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, |
| 238 |
MPI_COMM_WORLD); |
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} |
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|
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myPotato = potatoes[which_node]; |
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|
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//recieve the number of integrableObject in current molecule |
| 244 |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
| 245 |
MPI_COMM_WORLD, &istatus); |
| 246 |
myPotato++; |
| 247 |
|
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for(int l = 0; l < nCurObj; l++) { |
| 249 |
if (potatoes[which_node] + 2 >= MAXTAG) { |
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// The potato was going to exceed the maximum value, |
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// so wrap this processor potato back to 0: |
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|
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potatoes[which_node] = 0; |
| 254 |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, |
| 255 |
0, MPI_COMM_WORLD); |
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} |
| 257 |
|
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MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
| 259 |
which_node, myPotato, MPI_COMM_WORLD, |
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&istatus); |
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|
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atomTypeString = MPIatomTypeString; |
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|
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myPotato++; |
| 265 |
|
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MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
| 267 |
MPI_COMM_WORLD, &istatus); |
| 268 |
myPotato++; |
| 269 |
|
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MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
| 271 |
|
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if (msgLen == 13) |
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isDirectional = 1; |
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else |
| 275 |
isDirectional = 0; |
| 276 |
|
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// If we've survived to here, format the line: |
| 278 |
|
| 279 |
if (!isDirectional) { |
| 280 |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 281 |
atomTypeString, atomData[0], |
| 282 |
atomData[1], atomData[2], |
| 283 |
atomData[3], atomData[4], |
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atomData[5]); |
| 285 |
|
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strcat(writeLine, |
| 287 |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 288 |
} else { |
| 289 |
sprintf(writeLine, |
| 290 |
"%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", |
| 291 |
atomTypeString, |
| 292 |
atomData[0], |
| 293 |
atomData[1], |
| 294 |
atomData[2], |
| 295 |
atomData[3], |
| 296 |
atomData[4], |
| 297 |
atomData[5], |
| 298 |
atomData[6], |
| 299 |
atomData[7], |
| 300 |
atomData[8], |
| 301 |
atomData[9], |
| 302 |
atomData[10], |
| 303 |
atomData[11], |
| 304 |
atomData[12]); |
| 305 |
} |
| 306 |
|
| 307 |
os << writeLine; |
| 308 |
|
| 309 |
} // end for(int l =0) |
| 310 |
|
| 311 |
potatoes[which_node] = myPotato; |
| 312 |
} else { //master node has current molecule |
| 313 |
|
| 314 |
mol = info_->getMoleculeByGlobalIndex(i); |
| 315 |
|
| 316 |
if (mol == NULL) { |
| 317 |
strcpy(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
| 318 |
painCave.isFatal = 1; |
| 319 |
simError(); |
| 320 |
} |
| 321 |
|
| 322 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 323 |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 324 |
|
| 325 |
atomTypeString = integrableObject->getType().c_str(); |
| 326 |
|
| 327 |
pos = integrableObject->getPos(); |
| 328 |
vel = integrableObject->getVel(); |
| 329 |
|
| 330 |
atomData[0] = pos[0]; |
| 331 |
atomData[1] = pos[1]; |
| 332 |
atomData[2] = pos[2]; |
| 333 |
|
| 334 |
atomData[3] = vel[0]; |
| 335 |
atomData[4] = vel[1]; |
| 336 |
atomData[5] = vel[2]; |
| 337 |
|
| 338 |
isDirectional = 0; |
| 339 |
|
| 340 |
if (integrableObject->isDirectional()) { |
| 341 |
isDirectional = 1; |
| 342 |
|
| 343 |
q = integrableObject->getQ(); |
| 344 |
ji = integrableObject->getJ(); |
| 345 |
|
| 346 |
for(int j = 0; j < 6; j++) { |
| 347 |
atomData[j] = atomData[j]; |
| 348 |
} |
| 349 |
|
| 350 |
atomData[6] = q[0]; |
| 351 |
atomData[7] = q[1]; |
| 352 |
atomData[8] = q[2]; |
| 353 |
atomData[9] = q[3]; |
| 354 |
|
| 355 |
atomData[10] = ji[0]; |
| 356 |
atomData[11] = ji[1]; |
| 357 |
atomData[12] = ji[2]; |
| 358 |
} |
| 359 |
|
| 360 |
// If we've survived to here, format the line: |
| 361 |
|
| 362 |
if (!isDirectional) { |
| 363 |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 364 |
atomTypeString, atomData[0], |
| 365 |
atomData[1], atomData[2], |
| 366 |
atomData[3], atomData[4], |
| 367 |
atomData[5]); |
| 368 |
|
| 369 |
strcat(writeLine, |
| 370 |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 371 |
} else { |
| 372 |
sprintf(writeLine, |
| 373 |
"%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", |
| 374 |
atomTypeString, |
| 375 |
atomData[0], |
| 376 |
atomData[1], |
| 377 |
atomData[2], |
| 378 |
atomData[3], |
| 379 |
atomData[4], |
| 380 |
atomData[5], |
| 381 |
atomData[6], |
| 382 |
atomData[7], |
| 383 |
atomData[8], |
| 384 |
atomData[9], |
| 385 |
atomData[10], |
| 386 |
atomData[11], |
| 387 |
atomData[12]); |
| 388 |
} |
| 389 |
|
| 390 |
|
| 391 |
os << writeLine; |
| 392 |
|
| 393 |
} //end for(iter = integrableObject.begin()) |
| 394 |
} |
| 395 |
} //end for(i = 0; i < mpiSim->getNmol()) |
| 396 |
|
| 397 |
os.flush(); |
| 398 |
|
| 399 |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
| 400 |
|
| 401 |
MPIcheckPoint(); |
| 402 |
|
| 403 |
delete [] potatoes; |
| 404 |
} else { |
| 405 |
|
| 406 |
// worldRank != 0, so I'm a remote node. |
| 407 |
|
| 408 |
// Set my magic potato to 0: |
| 409 |
|
| 410 |
myPotato = 0; |
| 411 |
|
| 412 |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
| 413 |
|
| 414 |
// Am I the node which has this integrableObject? |
| 415 |
whichNode = info_->getMolToProc(i); |
| 416 |
if (whichNode == worldRank) { |
| 417 |
if (myPotato + 1 >= MAXTAG) { |
| 418 |
|
| 419 |
// The potato was going to exceed the maximum value, |
| 420 |
// so wrap this processor potato back to 0 (and block until |
| 421 |
// node 0 says we can go: |
| 422 |
|
| 423 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
| 424 |
&istatus); |
| 425 |
} |
| 426 |
|
| 427 |
mol = info_->getMoleculeByGlobalIndex(i); |
| 428 |
|
| 429 |
|
| 430 |
nCurObj = mol->getNIntegrableObjects(); |
| 431 |
|
| 432 |
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
| 433 |
myPotato++; |
| 434 |
|
| 435 |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
| 436 |
integrableObject = mol->nextIntegrableObject(ii)) { |
| 437 |
|
| 438 |
if (myPotato + 2 >= MAXTAG) { |
| 439 |
|
| 440 |
// The potato was going to exceed the maximum value, |
| 441 |
// so wrap this processor potato back to 0 (and block until |
| 442 |
// node 0 says we can go: |
| 443 |
|
| 444 |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
| 445 |
&istatus); |
| 446 |
} |
| 447 |
|
| 448 |
atomTypeString = integrableObject->getType().c_str(); |
| 449 |
|
| 450 |
pos = integrableObject->getPos(); |
| 451 |
vel = integrableObject->getVel(); |
| 452 |
|
| 453 |
atomData[0] = pos[0]; |
| 454 |
atomData[1] = pos[1]; |
| 455 |
atomData[2] = pos[2]; |
| 456 |
|
| 457 |
atomData[3] = vel[0]; |
| 458 |
atomData[4] = vel[1]; |
| 459 |
atomData[5] = vel[2]; |
| 460 |
|
| 461 |
isDirectional = 0; |
| 462 |
|
| 463 |
if (integrableObject->isDirectional()) { |
| 464 |
isDirectional = 1; |
| 465 |
|
| 466 |
q = integrableObject->getQ(); |
| 467 |
ji = integrableObject->getJ(); |
| 468 |
|
| 469 |
atomData[6] = q[0]; |
| 470 |
atomData[7] = q[1]; |
| 471 |
atomData[8] = q[2]; |
| 472 |
atomData[9] = q[3]; |
| 473 |
|
| 474 |
atomData[10] = ji[0]; |
| 475 |
atomData[11] = ji[1]; |
| 476 |
atomData[12] = ji[2]; |
| 477 |
} |
| 478 |
|
| 479 |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
| 480 |
|
| 481 |
// null terminate the std::string before sending (just in case): |
| 482 |
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
| 483 |
|
| 484 |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
| 485 |
myPotato, MPI_COMM_WORLD); |
| 486 |
|
| 487 |
myPotato++; |
| 488 |
|
| 489 |
if (isDirectional) { |
| 490 |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato, |
| 491 |
MPI_COMM_WORLD); |
| 492 |
} else { |
| 493 |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato, |
| 494 |
MPI_COMM_WORLD); |
| 495 |
} |
| 496 |
|
| 497 |
myPotato++; |
| 498 |
} |
| 499 |
|
| 500 |
} |
| 501 |
|
| 502 |
} |
| 503 |
|
| 504 |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
| 505 |
MPIcheckPoint(); |
| 506 |
} |
| 507 |
|
| 508 |
#endif // is_mpi |
| 509 |
|
| 510 |
} |
| 511 |
|
| 512 |
}//end namespace oopse |
