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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 "brains/mpiSimulation.hpp" |
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|
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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 "io/ReadWrite.hpp" |
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#include "utils/simError.h" |
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|
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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|
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entry_plug = the_entry_plug; |
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|
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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dumpFile.open(entry_plug->sampleName.c_str(), 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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entry_plug->sampleName.c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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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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#endif // is_mpi |
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} |
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|
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DumpWriter::~DumpWriter( ){ |
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|
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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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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#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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/** |
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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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/** |
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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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Molecule* mols = entry_plug->molecules; |
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indexArray.clear(); |
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|
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for(int i = 0; i < entry_plug->n_mol;i++) |
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indexArray.push_back(make_pair(i, mols[i].getGlobalIndex())); |
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|
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sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
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} |
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|
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#endif |
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|
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void DumpWriter::writeDump(double currentTime){ |
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|
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ofstream finalOut; |
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vector<ofstream*> fileStreams; |
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|
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif |
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finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc ); |
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if( !finalOut ){ |
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for final dump output.\n", |
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entry_plug->finalName.c_str() ); |
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painCave.isFatal = 1; |
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simError(); |
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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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fileStreams.push_back(&finalOut); |
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fileStreams.push_back(&dumpFile); |
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|
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writeFrame(fileStreams, currentTime); |
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|
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#ifdef IS_MPI |
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finalOut.close(); |
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#endif |
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|
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} |
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|
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void DumpWriter::writeFinal(double currentTime){ |
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|
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ofstream finalOut; |
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vector<ofstream*> fileStreams; |
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|
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#ifdef IS_MPI |
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if(worldRank == 0 ){ |
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#endif // is_mpi |
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|
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finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc ); |
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|
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if( !finalOut ){ |
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sprintf( painCave.errMsg, |
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"Could not open \"%s\" for final dump output.\n", |
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entry_plug->finalName.c_str() ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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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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fileStreams.push_back(&finalOut); |
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writeFrame(fileStreams, currentTime); |
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|
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#ifdef IS_MPI |
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finalOut.close(); |
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#endif |
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|
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} |
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|
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void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
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|
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const int BUFFERSIZE = 2000; |
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const int MINIBUFFERSIZE = 100; |
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|
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char tempBuffer[BUFFERSIZE]; |
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char writeLine[BUFFERSIZE]; |
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|
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int i; |
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unsigned int k; |
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|
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#ifdef IS_MPI |
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|
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/********************************************************************* |
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* 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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|
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int *potatoes; |
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int myPotato; |
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|
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int nProc; |
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int j, which_node, done, which_atom, local_index, currentIndex; |
| 220 |
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double atomData[13]; |
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int isDirectional; |
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char* atomTypeString; |
| 223 |
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char MPIatomTypeString[MINIBUFFERSIZE]; |
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int nObjects; |
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int msgLen; // the length of message actually recieved at master nodes |
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#endif //is_mpi |
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|
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Quat4d q; |
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Vector3d ji; |
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DirectionalAtom* dAtom; |
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Vector3d pos; |
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Vector3d vel; |
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|
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int nTotObjects; |
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StuntDouble* sd; |
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char* molName; |
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vector<StuntDouble*> integrableObjects; |
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vector<StuntDouble*>::iterator iter; |
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nTotObjects = entry_plug->getTotIntegrableObjects(); |
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#ifndef IS_MPI |
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|
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for(k = 0; k < outFile.size(); k++){ |
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*outFile[k] << nTotObjects << "\n"; |
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|
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*outFile[k] << currentTime << ";\t" |
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<< entry_plug->Hmat[0][0] << "\t" |
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<< entry_plug->Hmat[1][0] << "\t" |
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<< entry_plug->Hmat[2][0] << ";\t" |
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|
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<< entry_plug->Hmat[0][1] << "\t" |
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<< entry_plug->Hmat[1][1] << "\t" |
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<< entry_plug->Hmat[2][1] << ";\t" |
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|
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<< entry_plug->Hmat[0][2] << "\t" |
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<< entry_plug->Hmat[1][2] << "\t" |
| 256 |
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<< entry_plug->Hmat[2][2] << ";"; |
| 257 |
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|
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//write out additional parameters, such as chi and eta |
| 259 |
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*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
| 260 |
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} |
| 261 |
< |
|
| 262 |
< |
for( i=0; i< entry_plug->n_mol; i++ ){ |
| 263 |
< |
|
| 264 |
< |
integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); |
| 265 |
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molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); |
| 266 |
< |
|
| 267 |
< |
for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ |
| 268 |
< |
sd = *iter; |
| 269 |
< |
pos = sd->getPos(); |
| 270 |
< |
vel = sd->getVel(); |
| 271 |
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|
| 272 |
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sprintf( tempBuffer, |
| 273 |
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"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 274 |
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sd->getType(), |
| 275 |
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pos[0], |
| 276 |
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pos[1], |
| 277 |
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pos[2], |
| 278 |
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vel[0], |
| 279 |
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vel[1], |
| 280 |
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vel[2]); |
| 281 |
< |
strcpy( writeLine, tempBuffer ); |
| 282 |
< |
|
| 283 |
< |
if( sd->isDirectional() ){ |
| 284 |
< |
|
| 285 |
< |
q = sd->getQ(); |
| 286 |
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ji = sd->getJ(); |
| 287 |
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|
| 288 |
< |
sprintf( tempBuffer, |
| 289 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
| 290 |
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q[0], |
| 291 |
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q[1], |
| 292 |
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q[2], |
| 293 |
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q[3], |
| 294 |
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ji[0], |
| 295 |
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ji[1], |
| 296 |
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ji[2]); |
| 297 |
< |
strcat( writeLine, tempBuffer ); |
| 298 |
< |
} |
| 299 |
< |
else |
| 300 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 301 |
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|
| 302 |
< |
for(k = 0; k < outFile.size(); k++) |
| 303 |
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*outFile[k] << writeLine; |
| 304 |
< |
} |
| 305 |
< |
|
| 306 |
< |
} |
| 307 |
< |
|
| 308 |
< |
#else // is_mpi |
| 309 |
< |
|
| 310 |
< |
/* code to find maximum tag value */ |
| 311 |
< |
|
| 312 |
< |
int *tagub, flag, MAXTAG; |
| 313 |
< |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
| 314 |
< |
if (flag) { |
| 315 |
< |
MAXTAG = *tagub; |
| 316 |
< |
} else { |
| 317 |
< |
MAXTAG = 32767; |
| 318 |
< |
} |
| 319 |
< |
|
| 320 |
< |
int haveError; |
| 321 |
< |
|
| 322 |
< |
MPI_Status istatus; |
| 323 |
< |
int nCurObj; |
| 324 |
< |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
| 325 |
< |
|
| 326 |
< |
// write out header and node 0's coordinates |
| 327 |
< |
|
| 328 |
< |
if( worldRank == 0 ){ |
| 329 |
< |
|
| 330 |
< |
// Node 0 needs a list of the magic potatoes for each processor; |
| 331 |
< |
|
| 332 |
< |
nProc = mpiSim->getNProcessors(); |
| 333 |
< |
potatoes = new int[nProc]; |
| 334 |
< |
|
| 335 |
< |
//write out the comment lines |
| 336 |
< |
for (i = 0; i < nProc; i++) |
| 337 |
< |
potatoes[i] = 0; |
| 338 |
< |
|
| 339 |
< |
for(k = 0; k < outFile.size(); k++){ |
| 340 |
< |
*outFile[k] << nTotObjects << "\n"; |
| 341 |
< |
|
| 342 |
< |
*outFile[k] << currentTime << ";\t" |
| 343 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
| 344 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
| 345 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
| 346 |
< |
|
| 347 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
| 348 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
| 349 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
| 350 |
< |
|
| 351 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
| 352 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
| 353 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
| 354 |
< |
|
| 355 |
< |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
| 356 |
< |
} |
| 357 |
< |
|
| 358 |
< |
currentIndex = 0; |
| 359 |
< |
|
| 360 |
< |
for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { |
| 361 |
< |
|
| 362 |
< |
// Get the Node number which has this atom; |
| 363 |
< |
|
| 364 |
< |
which_node = MolToProcMap[i]; |
| 365 |
< |
|
| 366 |
< |
if (which_node != 0) { |
| 367 |
< |
|
| 368 |
< |
if (potatoes[which_node] + 1 >= MAXTAG) { |
| 369 |
< |
// The potato was going to exceed the maximum value, |
| 370 |
< |
// so wrap this processor potato back to 0: |
| 371 |
< |
|
| 372 |
< |
potatoes[which_node] = 0; |
| 373 |
< |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
| 374 |
< |
|
| 375 |
< |
} |
| 376 |
< |
|
| 377 |
< |
myPotato = potatoes[which_node]; |
| 378 |
< |
|
| 379 |
< |
//recieve the number of integrableObject in current molecule |
| 380 |
< |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
| 381 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
| 382 |
< |
myPotato++; |
| 383 |
< |
|
| 384 |
< |
for(int l = 0; l < nCurObj; l++){ |
| 385 |
< |
|
| 386 |
< |
if (potatoes[which_node] + 2 >= MAXTAG) { |
| 387 |
< |
// The potato was going to exceed the maximum value, |
| 388 |
< |
// so wrap this processor potato back to 0: |
| 389 |
< |
|
| 390 |
< |
potatoes[which_node] = 0; |
| 391 |
< |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
| 392 |
< |
|
| 393 |
< |
} |
| 394 |
< |
|
| 395 |
< |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
| 396 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
| 397 |
< |
|
| 398 |
< |
atomTypeString = MPIatomTypeString; |
| 399 |
< |
|
| 400 |
< |
myPotato++; |
| 401 |
< |
|
| 402 |
< |
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus); |
| 403 |
< |
myPotato++; |
| 404 |
< |
|
| 405 |
< |
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
| 406 |
< |
|
| 407 |
< |
if(msgLen == 13) |
| 408 |
< |
isDirectional = 1; |
| 409 |
< |
else |
| 410 |
< |
isDirectional = 0; |
| 411 |
< |
|
| 412 |
< |
// If we've survived to here, format the line: |
| 413 |
< |
|
| 414 |
< |
if (!isDirectional) { |
| 415 |
< |
|
| 416 |
< |
sprintf( writeLine, |
| 417 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 418 |
< |
atomTypeString, |
| 419 |
< |
atomData[0], |
| 420 |
< |
atomData[1], |
| 421 |
< |
atomData[2], |
| 422 |
< |
atomData[3], |
| 423 |
< |
atomData[4], |
| 424 |
< |
atomData[5]); |
| 425 |
< |
|
| 426 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 427 |
< |
|
| 428 |
< |
} |
| 429 |
< |
else { |
| 430 |
< |
|
| 431 |
< |
sprintf( writeLine, |
| 432 |
< |
"%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", |
| 433 |
< |
atomTypeString, |
| 434 |
< |
atomData[0], |
| 435 |
< |
atomData[1], |
| 436 |
< |
atomData[2], |
| 437 |
< |
atomData[3], |
| 438 |
< |
atomData[4], |
| 439 |
< |
atomData[5], |
| 440 |
< |
atomData[6], |
| 441 |
< |
atomData[7], |
| 442 |
< |
atomData[8], |
| 443 |
< |
atomData[9], |
| 444 |
< |
atomData[10], |
| 445 |
< |
atomData[11], |
| 446 |
< |
atomData[12]); |
| 447 |
< |
|
| 448 |
< |
} |
| 449 |
< |
|
| 450 |
< |
for(k = 0; k < outFile.size(); k++) |
| 451 |
< |
*outFile[k] << writeLine; |
| 452 |
< |
|
| 453 |
< |
}// end for(int l =0) |
| 454 |
< |
potatoes[which_node] = myPotato; |
| 455 |
< |
|
| 456 |
< |
} |
| 457 |
< |
else { |
| 458 |
< |
|
| 459 |
< |
haveError = 0; |
| 460 |
< |
|
| 461 |
< |
local_index = indexArray[currentIndex].first; |
| 462 |
< |
|
| 463 |
< |
integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); |
| 464 |
< |
|
| 465 |
< |
for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){ |
| 466 |
< |
sd = *iter; |
| 467 |
< |
atomTypeString = sd->getType(); |
| 468 |
< |
|
| 469 |
< |
pos = sd->getPos(); |
| 470 |
< |
vel = sd->getVel(); |
| 471 |
< |
|
| 472 |
< |
atomData[0] = pos[0]; |
| 473 |
< |
atomData[1] = pos[1]; |
| 474 |
< |
atomData[2] = pos[2]; |
| 475 |
< |
|
| 476 |
< |
atomData[3] = vel[0]; |
| 477 |
< |
atomData[4] = vel[1]; |
| 478 |
< |
atomData[5] = vel[2]; |
| 479 |
< |
|
| 480 |
< |
isDirectional = 0; |
| 481 |
< |
|
| 482 |
< |
if( sd->isDirectional() ){ |
| 483 |
< |
|
| 484 |
< |
isDirectional = 1; |
| 485 |
< |
|
| 486 |
< |
q = sd->getQ(); |
| 487 |
< |
ji = sd->getJ(); |
| 488 |
< |
|
| 489 |
< |
for (int j = 0; j < 6 ; j++) |
| 490 |
< |
atomData[j] = atomData[j]; |
| 491 |
< |
|
| 492 |
< |
atomData[6] = q[0]; |
| 493 |
< |
atomData[7] = q[1]; |
| 494 |
< |
atomData[8] = q[2]; |
| 495 |
< |
atomData[9] = q[3]; |
| 496 |
< |
|
| 497 |
< |
atomData[10] = ji[0]; |
| 498 |
< |
atomData[11] = ji[1]; |
| 499 |
< |
atomData[12] = ji[2]; |
| 500 |
< |
} |
| 501 |
< |
|
| 502 |
< |
// If we've survived to here, format the line: |
| 503 |
< |
|
| 504 |
< |
if (!isDirectional) { |
| 505 |
< |
|
| 506 |
< |
sprintf( writeLine, |
| 507 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 508 |
< |
atomTypeString, |
| 509 |
< |
atomData[0], |
| 510 |
< |
atomData[1], |
| 511 |
< |
atomData[2], |
| 512 |
< |
atomData[3], |
| 513 |
< |
atomData[4], |
| 514 |
< |
atomData[5]); |
| 515 |
< |
|
| 516 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
| 517 |
< |
|
| 518 |
< |
} |
| 519 |
< |
else { |
| 520 |
< |
|
| 521 |
< |
sprintf( writeLine, |
| 522 |
< |
"%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", |
| 523 |
< |
atomTypeString, |
| 524 |
< |
atomData[0], |
| 525 |
< |
atomData[1], |
| 526 |
< |
atomData[2], |
| 527 |
< |
atomData[3], |
| 528 |
< |
atomData[4], |
| 529 |
< |
atomData[5], |
| 530 |
< |
atomData[6], |
| 531 |
< |
atomData[7], |
| 532 |
< |
atomData[8], |
| 533 |
< |
atomData[9], |
| 534 |
< |
atomData[10], |
| 535 |
< |
atomData[11], |
| 536 |
< |
atomData[12]); |
| 537 |
< |
|
| 538 |
< |
} |
| 539 |
< |
|
| 540 |
< |
for(k = 0; k < outFile.size(); k++) |
| 541 |
< |
*outFile[k] << writeLine; |
| 542 |
< |
|
| 543 |
< |
|
| 544 |
< |
}//end for(iter = integrableObject.begin()) |
| 545 |
< |
|
| 546 |
< |
currentIndex++; |
| 547 |
< |
} |
| 548 |
< |
|
| 549 |
< |
}//end for(i = 0; i < mpiSim->getNmol()) |
| 550 |
< |
|
| 551 |
< |
for(k = 0; k < outFile.size(); k++) |
| 552 |
< |
outFile[k]->flush(); |
| 553 |
< |
|
| 554 |
< |
sprintf( checkPointMsg, |
| 555 |
< |
"Sucessfully took a dump.\n"); |
| 556 |
< |
|
| 557 |
< |
MPIcheckPoint(); |
| 558 |
< |
|
| 559 |
< |
delete[] potatoes; |
| 560 |
< |
|
| 561 |
< |
} else { |
| 562 |
< |
|
| 563 |
< |
// worldRank != 0, so I'm a remote node. |
| 564 |
< |
|
| 565 |
< |
// Set my magic potato to 0: |
| 566 |
< |
|
| 567 |
< |
myPotato = 0; |
| 568 |
< |
currentIndex = 0; |
| 569 |
< |
|
| 570 |
< |
for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { |
| 571 |
< |
|
| 572 |
< |
// Am I the node which has this integrableObject? |
| 573 |
< |
|
| 574 |
< |
if (MolToProcMap[i] == worldRank) { |
| 575 |
< |
|
| 576 |
< |
|
| 577 |
< |
if (myPotato + 1 >= MAXTAG) { |
| 578 |
< |
|
| 579 |
< |
// The potato was going to exceed the maximum value, |
| 580 |
< |
// so wrap this processor potato back to 0 (and block until |
| 581 |
< |
// node 0 says we can go: |
| 582 |
< |
|
| 583 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
| 584 |
< |
|
| 585 |
< |
} |
| 586 |
< |
|
| 587 |
< |
local_index = indexArray[currentIndex].first; |
| 588 |
< |
integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects(); |
| 589 |
< |
|
| 590 |
< |
nCurObj = integrableObjects.size(); |
| 591 |
< |
|
| 592 |
< |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
| 593 |
< |
myPotato, MPI_COMM_WORLD); |
| 594 |
< |
myPotato++; |
| 595 |
< |
|
| 596 |
< |
for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ |
| 597 |
< |
|
| 598 |
< |
if (myPotato + 2 >= MAXTAG) { |
| 599 |
< |
|
| 600 |
< |
// The potato was going to exceed the maximum value, |
| 601 |
< |
// so wrap this processor potato back to 0 (and block until |
| 602 |
< |
// node 0 says we can go: |
| 603 |
< |
|
| 604 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
| 605 |
< |
|
| 606 |
< |
} |
| 607 |
< |
|
| 608 |
< |
sd = *iter; |
| 609 |
< |
|
| 610 |
< |
atomTypeString = sd->getType(); |
| 611 |
< |
|
| 612 |
< |
pos = sd->getPos(); |
| 613 |
< |
vel = sd->getVel(); |
| 614 |
< |
|
| 615 |
< |
atomData[0] = pos[0]; |
| 616 |
< |
atomData[1] = pos[1]; |
| 617 |
< |
atomData[2] = pos[2]; |
| 618 |
< |
|
| 619 |
< |
atomData[3] = vel[0]; |
| 620 |
< |
atomData[4] = vel[1]; |
| 621 |
< |
atomData[5] = vel[2]; |
| 622 |
< |
|
| 623 |
< |
isDirectional = 0; |
| 624 |
< |
|
| 625 |
< |
if( sd->isDirectional() ){ |
| 626 |
< |
|
| 627 |
< |
isDirectional = 1; |
| 628 |
< |
|
| 629 |
< |
q = sd->getQ(); |
| 630 |
< |
ji = sd->getJ(); |
| 631 |
< |
|
| 632 |
< |
|
| 633 |
< |
atomData[6] = q[0]; |
| 634 |
< |
atomData[7] = q[1]; |
| 635 |
< |
atomData[8] = q[2]; |
| 636 |
< |
atomData[9] = q[3]; |
| 637 |
< |
|
| 638 |
< |
atomData[10] = ji[0]; |
| 639 |
< |
atomData[11] = ji[1]; |
| 640 |
< |
atomData[12] = ji[2]; |
| 641 |
< |
} |
| 642 |
< |
|
| 643 |
< |
|
| 644 |
< |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
| 645 |
< |
|
| 646 |
< |
// null terminate the string before sending (just in case): |
| 647 |
< |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
| 648 |
< |
|
| 649 |
< |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
| 650 |
< |
myPotato, MPI_COMM_WORLD); |
| 651 |
< |
|
| 652 |
< |
myPotato++; |
| 653 |
< |
|
| 654 |
< |
if (isDirectional) { |
| 655 |
< |
|
| 656 |
< |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, |
| 657 |
< |
myPotato, MPI_COMM_WORLD); |
| 658 |
< |
|
| 659 |
< |
} else { |
| 660 |
< |
|
| 661 |
< |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, |
| 662 |
< |
myPotato, MPI_COMM_WORLD); |
| 663 |
< |
} |
| 664 |
< |
|
| 665 |
< |
myPotato++; |
| 666 |
< |
|
| 667 |
< |
} |
| 668 |
< |
|
| 669 |
< |
currentIndex++; |
| 670 |
< |
|
| 671 |
< |
} |
| 672 |
< |
|
| 673 |
< |
} |
| 674 |
< |
|
| 675 |
< |
sprintf( checkPointMsg, |
| 676 |
< |
"Sucessfully took a dump.\n"); |
| 677 |
< |
MPIcheckPoint(); |
| 678 |
< |
|
| 679 |
< |
} |
| 680 |
< |
|
| 681 |
< |
|
| 682 |
< |
|
| 683 |
< |
#endif // is_mpi |
| 684 |
< |
} |
| 685 |
< |
|
| 686 |
< |
#ifdef IS_MPI |
| 687 |
< |
|
| 688 |
< |
// a couple of functions to let us escape the write loop |
| 689 |
< |
|
| 690 |
< |
void dWrite::DieDieDie( void ){ |
| 691 |
< |
|
| 692 |
< |
MPI_Finalize(); |
| 693 |
< |
exit (0); |
| 694 |
< |
} |
| 695 |
< |
|
| 696 |
< |
#endif //is_mpi |
| 1 |
> |
#define _LARGEFILE_SOURCE64 |
| 2 |
> |
#define _FILE_OFFSET_BITS 64 |
| 3 |
> |
|
| 4 |
> |
#include <string.h> |
| 5 |
> |
#include <iostream> |
| 6 |
> |
#include <fstream> |
| 7 |
> |
#include <algorithm> |
| 8 |
> |
#include <utility> |
| 9 |
> |
|
| 10 |
> |
#ifdef IS_MPI |
| 11 |
> |
|
| 12 |
> |
#include <mpi.h> |
| 13 |
> |
#include "brains/mpiSimulation.hpp" |
| 14 |
> |
|
| 15 |
> |
namespace dWrite { |
| 16 |
> |
void DieDieDie(void); |
| 17 |
> |
|
| 18 |
> |
} |
| 19 |
> |
|
| 20 |
> |
using namespace dWrite; |
| 21 |
> |
|
| 22 |
> |
#endif //is_mpi |
| 23 |
> |
|
| 24 |
> |
#include "io/ReadWrite.hpp" |
| 25 |
> |
#include "utils/simError.h" |
| 26 |
> |
|
| 27 |
> |
DumpWriter::DumpWriter(SimInfo *the_entry_plug) { |
| 28 |
> |
entry_plug = the_entry_plug; |
| 29 |
> |
|
| 30 |
> |
#ifdef IS_MPI |
| 31 |
> |
|
| 32 |
> |
if (worldRank == 0) { |
| 33 |
> |
#endif // is_mpi |
| 34 |
> |
|
| 35 |
> |
dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc); |
| 36 |
> |
|
| 37 |
> |
if (!dumpFile) { |
| 38 |
> |
sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
| 39 |
> |
entry_plug->sampleName.c_str()); |
| 40 |
> |
painCave.isFatal = 1; |
| 41 |
> |
simError(); |
| 42 |
> |
} |
| 43 |
> |
|
| 44 |
> |
#ifdef IS_MPI |
| 45 |
> |
|
| 46 |
> |
} |
| 47 |
> |
|
| 48 |
> |
//sort the local atoms by global index |
| 49 |
> |
sortByGlobalIndex(); |
| 50 |
> |
|
| 51 |
> |
sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
| 52 |
> |
MPIcheckPoint(); |
| 53 |
> |
|
| 54 |
> |
#endif // is_mpi |
| 55 |
> |
|
| 56 |
> |
} |
| 57 |
> |
|
| 58 |
> |
DumpWriter::~DumpWriter() { |
| 59 |
> |
|
| 60 |
> |
#ifdef IS_MPI |
| 61 |
> |
|
| 62 |
> |
if (worldRank == 0) { |
| 63 |
> |
#endif // is_mpi |
| 64 |
> |
|
| 65 |
> |
dumpFile.close(); |
| 66 |
> |
|
| 67 |
> |
#ifdef IS_MPI |
| 68 |
> |
|
| 69 |
> |
} |
| 70 |
> |
|
| 71 |
> |
#endif // is_mpi |
| 72 |
> |
|
| 73 |
> |
} |
| 74 |
> |
|
| 75 |
> |
#ifdef IS_MPI |
| 76 |
> |
|
| 77 |
> |
/** |
| 78 |
> |
* A hook function to load balancing |
| 79 |
> |
*/ |
| 80 |
> |
|
| 81 |
> |
void DumpWriter::update() { |
| 82 |
> |
sortByGlobalIndex(); |
| 83 |
> |
} |
| 84 |
> |
|
| 85 |
> |
/** |
| 86 |
> |
* Auxiliary sorting function |
| 87 |
> |
*/ |
| 88 |
> |
|
| 89 |
> |
bool indexSortingCriterion(const pair < int, int > &p1, const pair < int, |
| 90 |
> |
int > &p2) { |
| 91 |
> |
return p1.second < p2.second; |
| 92 |
> |
} |
| 93 |
> |
|
| 94 |
> |
/** |
| 95 |
> |
* Sorting the local index by global index |
| 96 |
> |
*/ |
| 97 |
> |
|
| 98 |
> |
void DumpWriter::sortByGlobalIndex() { |
| 99 |
> |
Molecule * mols = entry_plug->molecules; |
| 100 |
> |
indexArray.clear(); |
| 101 |
> |
|
| 102 |
> |
for(int i = 0; i < entry_plug->n_mol; i++) { |
| 103 |
> |
indexArray.push_back(make_pair(i, mols[i].getGlobalIndex())); |
| 104 |
> |
} |
| 105 |
> |
|
| 106 |
> |
sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); |
| 107 |
> |
} |
| 108 |
> |
|
| 109 |
> |
#endif |
| 110 |
> |
|
| 111 |
> |
void DumpWriter::writeDump(double currentTime) { |
| 112 |
> |
ofstream finalOut; |
| 113 |
> |
vector<ofstream *>fileStreams; |
| 114 |
> |
|
| 115 |
> |
#ifdef IS_MPI |
| 116 |
> |
|
| 117 |
> |
if (worldRank == 0) { |
| 118 |
> |
#endif |
| 119 |
> |
|
| 120 |
> |
finalOut.open(entry_plug->finalName.c_str(), ios::out | ios::trunc); |
| 121 |
> |
|
| 122 |
> |
if (!finalOut) { |
| 123 |
> |
sprintf(painCave.errMsg, |
| 124 |
> |
"Could not open \"%s\" for final dump output.\n", |
| 125 |
> |
entry_plug->finalName.c_str()); |
| 126 |
> |
painCave.isFatal = 1; |
| 127 |
> |
simError(); |
| 128 |
> |
} |
| 129 |
> |
|
| 130 |
> |
#ifdef IS_MPI |
| 131 |
> |
|
| 132 |
> |
} |
| 133 |
> |
|
| 134 |
> |
#endif // is_mpi |
| 135 |
> |
|
| 136 |
> |
fileStreams.push_back(&finalOut); |
| 137 |
> |
fileStreams.push_back(&dumpFile); |
| 138 |
> |
|
| 139 |
> |
writeFrame(fileStreams, currentTime); |
| 140 |
> |
|
| 141 |
> |
#ifdef IS_MPI |
| 142 |
> |
|
| 143 |
> |
finalOut.close(); |
| 144 |
> |
|
| 145 |
> |
#endif |
| 146 |
> |
|
| 147 |
> |
} |
| 148 |
> |
|
| 149 |
> |
void DumpWriter::writeFinal(double currentTime) { |
| 150 |
> |
ofstream finalOut; |
| 151 |
> |
vector<ofstream *>fileStreams; |
| 152 |
> |
|
| 153 |
> |
#ifdef IS_MPI |
| 154 |
> |
|
| 155 |
> |
if (worldRank == 0) { |
| 156 |
> |
#endif // is_mpi |
| 157 |
> |
|
| 158 |
> |
finalOut.open(entry_plug->finalName.c_str(), ios::out | ios::trunc); |
| 159 |
> |
|
| 160 |
> |
if (!finalOut) { |
| 161 |
> |
sprintf(painCave.errMsg, |
| 162 |
> |
"Could not open \"%s\" for final dump output.\n", |
| 163 |
> |
entry_plug->finalName.c_str()); |
| 164 |
> |
painCave.isFatal = 1; |
| 165 |
> |
simError(); |
| 166 |
> |
} |
| 167 |
> |
|
| 168 |
> |
#ifdef IS_MPI |
| 169 |
> |
|
| 170 |
> |
} |
| 171 |
> |
|
| 172 |
> |
#endif // is_mpi |
| 173 |
> |
|
| 174 |
> |
fileStreams.push_back(&finalOut); |
| 175 |
> |
writeFrame(fileStreams, currentTime); |
| 176 |
> |
|
| 177 |
> |
#ifdef IS_MPI |
| 178 |
> |
|
| 179 |
> |
finalOut.close(); |
| 180 |
> |
|
| 181 |
> |
#endif |
| 182 |
> |
|
| 183 |
> |
} |
| 184 |
> |
|
| 185 |
> |
void DumpWriter::writeFrame(vector<ofstream *>&outFile, double currentTime) { |
| 186 |
> |
const int BUFFERSIZE = 2000; |
| 187 |
> |
const int MINIBUFFERSIZE = 100; |
| 188 |
> |
|
| 189 |
> |
char tempBuffer[BUFFERSIZE]; |
| 190 |
> |
char writeLine[BUFFERSIZE]; |
| 191 |
> |
|
| 192 |
> |
int i; |
| 193 |
> |
unsigned int k; |
| 194 |
> |
|
| 195 |
> |
#ifdef IS_MPI |
| 196 |
> |
|
| 197 |
> |
/********************************************************************* |
| 198 |
> |
* Documentation? You want DOCUMENTATION? |
| 199 |
> |
* |
| 200 |
> |
* Why all the potatoes below? |
| 201 |
> |
* |
| 202 |
> |
* To make a long story short, the original version of DumpWriter |
| 203 |
> |
* worked in the most inefficient way possible. Node 0 would |
| 204 |
> |
* poke each of the node for an individual atom's formatted data |
| 205 |
> |
* as node 0 worked its way down the global index. This was particularly |
| 206 |
> |
* inefficient since the method blocked all processors at every atom |
| 207 |
> |
* (and did it twice!). |
| 208 |
> |
* |
| 209 |
> |
* An intermediate version of DumpWriter could be described from Node |
| 210 |
> |
* zero's perspective as follows: |
| 211 |
> |
* |
| 212 |
> |
* 1) Have 100 of your friends stand in a circle. |
| 213 |
> |
* 2) When you say go, have all of them start tossing potatoes at |
| 214 |
> |
* you (one at a time). |
| 215 |
> |
* 3) Catch the potatoes. |
| 216 |
> |
* |
| 217 |
> |
* It was an improvement, but MPI has buffers and caches that could |
| 218 |
> |
* best be described in this analogy as "potato nets", so there's no |
| 219 |
> |
* need to block the processors atom-by-atom. |
| 220 |
> |
* |
| 221 |
> |
* This new and improved DumpWriter works in an even more efficient |
| 222 |
> |
* way: |
| 223 |
> |
* |
| 224 |
> |
* 1) Have 100 of your friend stand in a circle. |
| 225 |
> |
* 2) When you say go, have them start tossing 5-pound bags of |
| 226 |
> |
* potatoes at you. |
| 227 |
> |
* 3) Once you've caught a friend's bag of potatoes, |
| 228 |
> |
* toss them a spud to let them know they can toss another bag. |
| 229 |
> |
* |
| 230 |
> |
* How's THAT for documentation? |
| 231 |
> |
* |
| 232 |
> |
*********************************************************************/ |
| 233 |
> |
|
| 234 |
> |
int * potatoes; |
| 235 |
> |
int myPotato; |
| 236 |
> |
|
| 237 |
> |
int nProc; |
| 238 |
> |
int j; |
| 239 |
> |
int which_node; |
| 240 |
> |
int done; |
| 241 |
> |
int which_atom; |
| 242 |
> |
int local_index; |
| 243 |
> |
int currentIndex; |
| 244 |
> |
double atomData[13]; |
| 245 |
> |
int isDirectional; |
| 246 |
> |
char * atomTypeString; |
| 247 |
> |
char MPIatomTypeString[MINIBUFFERSIZE]; |
| 248 |
> |
int nObjects; |
| 249 |
> |
int msgLen; // the length of message actually recieved at master nodes |
| 250 |
> |
|
| 251 |
> |
#endif //is_mpi |
| 252 |
> |
|
| 253 |
> |
Quat4d q; |
| 254 |
> |
Vector3d ji; |
| 255 |
> |
DirectionalAtom * dAtom; |
| 256 |
> |
Vector3d pos; |
| 257 |
> |
Vector3d vel; |
| 258 |
> |
|
| 259 |
> |
int nTotObjects; |
| 260 |
> |
StuntDouble * sd; |
| 261 |
> |
char * molName; |
| 262 |
> |
vector<StuntDouble *>integrableObjects; |
| 263 |
> |
vector<StuntDouble *>::iterator iter; |
| 264 |
> |
nTotObjects = entry_plug->getTotIntegrableObjects(); |
| 265 |
> |
|
| 266 |
> |
#ifndef IS_MPI |
| 267 |
> |
|
| 268 |
> |
for(k = 0; k < outFile.size(); k++) { |
| 269 |
> |
*outFile[k] << nTotObjects << "\n"; |
| 270 |
> |
|
| 271 |
> |
*outFile[k] << currentTime << ";\t" << entry_plug->Hmat[0][0] << "\t" |
| 272 |
> |
<< entry_plug->Hmat[1][0] << "\t" << entry_plug->Hmat[2][0] |
| 273 |
> |
<< ";\t" << entry_plug->Hmat[0][1] << "\t" |
| 274 |
> |
<< entry_plug->Hmat[1][1] << "\t" << entry_plug->Hmat[2][1] |
| 275 |
> |
<< ";\t" << entry_plug->Hmat[0][2] << "\t" |
| 276 |
> |
<< entry_plug->Hmat[1][2] << "\t" << entry_plug->Hmat[2][2] << ";"; |
| 277 |
> |
|
| 278 |
> |
//write out additional parameters, such as chi and eta |
| 279 |
> |
//another circular reference nightmare |
| 280 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() |
| 281 |
> |
<< endl; |
| 282 |
> |
} |
| 283 |
> |
|
| 284 |
> |
for(i = 0; i < entry_plug->n_mol; i++) { |
| 285 |
> |
integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); |
| 286 |
> |
molName |
| 287 |
> |
= (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); |
| 288 |
> |
|
| 289 |
> |
for(iter = integrableObjects.begin(); |
| 290 |
> |
iter != integrableObjects.end(); ++iter) { |
| 291 |
> |
sd = *iter; |
| 292 |
> |
pos = sd->getPos(); |
| 293 |
> |
vel = sd->getVel(); |
| 294 |
> |
|
| 295 |
> |
sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 296 |
> |
sd->getType(), pos[0], |
| 297 |
> |
pos[1], pos[2], |
| 298 |
> |
vel[0], vel[1], |
| 299 |
> |
vel[2]); |
| 300 |
> |
|
| 301 |
> |
strcpy(writeLine, tempBuffer); |
| 302 |
> |
|
| 303 |
> |
if (sd->isDirectional()) { |
| 304 |
> |
q = sd->getQ(); |
| 305 |
> |
ji = sd->getJ(); |
| 306 |
> |
|
| 307 |
> |
sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", q[0], |
| 308 |
> |
q[1], q[2], q[3], |
| 309 |
> |
ji[0], ji[1], ji[2]); |
| 310 |
> |
strcat(writeLine, tempBuffer); |
| 311 |
> |
} else { |
| 312 |
> |
strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 313 |
> |
} |
| 314 |
> |
|
| 315 |
> |
for(k = 0; k < outFile.size(); k++) { |
| 316 |
> |
*outFile[k] << writeLine; |
| 317 |
> |
} |
| 318 |
> |
} |
| 319 |
> |
} |
| 320 |
> |
|
| 321 |
> |
#else // is_mpi |
| 322 |
> |
|
| 323 |
> |
/* code to find maximum tag value */ |
| 324 |
> |
|
| 325 |
> |
int * tagub, flag, MAXTAG; |
| 326 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
| 327 |
> |
|
| 328 |
> |
if (flag) { |
| 329 |
> |
MAXTAG = *tagub; |
| 330 |
> |
} else { |
| 331 |
> |
MAXTAG = 32767; |
| 332 |
> |
} |
| 333 |
> |
|
| 334 |
> |
int haveError; |
| 335 |
> |
|
| 336 |
> |
MPI_Status istatus; |
| 337 |
> |
int nCurObj; |
| 338 |
> |
int * MolToProcMap = mpiSim->getMolToProcMap(); |
| 339 |
> |
|
| 340 |
> |
// write out header and node 0's coordinates |
| 341 |
> |
|
| 342 |
> |
if (worldRank == 0) { |
| 343 |
> |
|
| 344 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
| 345 |
> |
|
| 346 |
> |
nProc = mpiSim->getNProcessors(); |
| 347 |
> |
potatoes = new int[nProc]; |
| 348 |
> |
|
| 349 |
> |
//write out the comment lines |
| 350 |
> |
for(i = 0; i < nProc; i++) { |
| 351 |
> |
potatoes[i] = 0; |
| 352 |
> |
} |
| 353 |
> |
|
| 354 |
> |
for(k = 0; k < outFile.size(); k++) { |
| 355 |
> |
*outFile[k] << nTotObjects << "\n"; |
| 356 |
> |
|
| 357 |
> |
*outFile[k] << currentTime << ";\t" << entry_plug->Hmat[0][0] |
| 358 |
> |
<< "\t" << entry_plug->Hmat[1][0] << "\t" |
| 359 |
> |
<< entry_plug->Hmat[2][0] << ";\t" << entry_plug->Hmat[0][1] |
| 360 |
> |
<< "\t" << entry_plug->Hmat[1][1] << "\t" |
| 361 |
> |
<< entry_plug->Hmat[2][1] << ";\t" << entry_plug->Hmat[0][2] |
| 362 |
> |
<< "\t" << entry_plug->Hmat[1][2] << "\t" |
| 363 |
> |
<< entry_plug->Hmat[2][2] << ";"; |
| 364 |
> |
|
| 365 |
> |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() |
| 366 |
> |
<< endl; |
| 367 |
> |
} |
| 368 |
> |
|
| 369 |
> |
currentIndex = 0; |
| 370 |
> |
|
| 371 |
> |
for(i = 0; i < mpiSim->getNMolGlobal(); i++) { |
| 372 |
> |
|
| 373 |
> |
// Get the Node number which has this atom; |
| 374 |
> |
|
| 375 |
> |
which_node = MolToProcMap[i]; |
| 376 |
> |
|
| 377 |
> |
if (which_node != 0) { |
| 378 |
> |
if (potatoes[which_node] + 1 >= MAXTAG) { |
| 379 |
> |
// The potato was going to exceed the maximum value, |
| 380 |
> |
// so wrap this processor potato back to 0: |
| 381 |
> |
|
| 382 |
> |
potatoes[which_node] = 0; |
| 383 |
> |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, |
| 384 |
> |
MPI_COMM_WORLD); |
| 385 |
> |
} |
| 386 |
> |
|
| 387 |
> |
myPotato = potatoes[which_node]; |
| 388 |
> |
|
| 389 |
> |
//recieve the number of integrableObject in current molecule |
| 390 |
> |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
| 391 |
> |
MPI_COMM_WORLD, &istatus); |
| 392 |
> |
myPotato++; |
| 393 |
> |
|
| 394 |
> |
for(int l = 0; l < nCurObj; l++) { |
| 395 |
> |
if (potatoes[which_node] + 2 >= MAXTAG) { |
| 396 |
> |
// The potato was going to exceed the maximum value, |
| 397 |
> |
// so wrap this processor potato back to 0: |
| 398 |
> |
|
| 399 |
> |
potatoes[which_node] = 0; |
| 400 |
> |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, |
| 401 |
> |
0, MPI_COMM_WORLD); |
| 402 |
> |
} |
| 403 |
> |
|
| 404 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
| 405 |
> |
which_node, myPotato, MPI_COMM_WORLD, |
| 406 |
> |
&istatus); |
| 407 |
> |
|
| 408 |
> |
atomTypeString = MPIatomTypeString; |
| 409 |
> |
|
| 410 |
> |
myPotato++; |
| 411 |
> |
|
| 412 |
> |
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
| 413 |
> |
MPI_COMM_WORLD, &istatus); |
| 414 |
> |
myPotato++; |
| 415 |
> |
|
| 416 |
> |
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
| 417 |
> |
|
| 418 |
> |
if (msgLen == 13) |
| 419 |
> |
isDirectional = 1; |
| 420 |
> |
else |
| 421 |
> |
isDirectional = 0; |
| 422 |
> |
|
| 423 |
> |
// If we've survived to here, format the line: |
| 424 |
> |
|
| 425 |
> |
if (!isDirectional) { |
| 426 |
> |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 427 |
> |
atomTypeString, atomData[0], |
| 428 |
> |
atomData[1], atomData[2], |
| 429 |
> |
atomData[3], atomData[4], |
| 430 |
> |
atomData[5]); |
| 431 |
> |
|
| 432 |
> |
strcat(writeLine, |
| 433 |
> |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 434 |
> |
} else { |
| 435 |
> |
sprintf(writeLine, |
| 436 |
> |
"%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", |
| 437 |
> |
atomTypeString, |
| 438 |
> |
atomData[0], |
| 439 |
> |
atomData[1], |
| 440 |
> |
atomData[2], |
| 441 |
> |
atomData[3], |
| 442 |
> |
atomData[4], |
| 443 |
> |
atomData[5], |
| 444 |
> |
atomData[6], |
| 445 |
> |
atomData[7], |
| 446 |
> |
atomData[8], |
| 447 |
> |
atomData[9], |
| 448 |
> |
atomData[10], |
| 449 |
> |
atomData[11], |
| 450 |
> |
atomData[12]); |
| 451 |
> |
} |
| 452 |
> |
|
| 453 |
> |
for(k = 0; k < outFile.size(); k++) { |
| 454 |
> |
*outFile[k] << writeLine; |
| 455 |
> |
} |
| 456 |
> |
} // end for(int l =0) |
| 457 |
> |
|
| 458 |
> |
potatoes[which_node] = myPotato; |
| 459 |
> |
} else { |
| 460 |
> |
haveError = 0; |
| 461 |
> |
|
| 462 |
> |
local_index = indexArray[currentIndex].first; |
| 463 |
> |
|
| 464 |
> |
integrableObjects |
| 465 |
> |
= (entry_plug->molecules[local_index]).getIntegrableObjects(); |
| 466 |
> |
|
| 467 |
> |
for(iter = integrableObjects.begin(); |
| 468 |
> |
iter != integrableObjects.end(); ++iter) { |
| 469 |
> |
sd = *iter; |
| 470 |
> |
atomTypeString = sd->getType(); |
| 471 |
> |
|
| 472 |
> |
pos = sd->getPos(); |
| 473 |
> |
vel = sd->getVel(); |
| 474 |
> |
|
| 475 |
> |
atomData[0] = pos[0]; |
| 476 |
> |
atomData[1] = pos[1]; |
| 477 |
> |
atomData[2] = pos[2]; |
| 478 |
> |
|
| 479 |
> |
atomData[3] = vel[0]; |
| 480 |
> |
atomData[4] = vel[1]; |
| 481 |
> |
atomData[5] = vel[2]; |
| 482 |
> |
|
| 483 |
> |
isDirectional = 0; |
| 484 |
> |
|
| 485 |
> |
if (sd->isDirectional()) { |
| 486 |
> |
isDirectional = 1; |
| 487 |
> |
|
| 488 |
> |
q = sd->getQ(); |
| 489 |
> |
ji = sd->getJ(); |
| 490 |
> |
|
| 491 |
> |
for(int j = 0; j < 6; j++) { |
| 492 |
> |
atomData[j] = atomData[j]; |
| 493 |
> |
} |
| 494 |
> |
|
| 495 |
> |
atomData[6] = q[0]; |
| 496 |
> |
atomData[7] = q[1]; |
| 497 |
> |
atomData[8] = q[2]; |
| 498 |
> |
atomData[9] = q[3]; |
| 499 |
> |
|
| 500 |
> |
atomData[10] = ji[0]; |
| 501 |
> |
atomData[11] = ji[1]; |
| 502 |
> |
atomData[12] = ji[2]; |
| 503 |
> |
} |
| 504 |
> |
|
| 505 |
> |
// If we've survived to here, format the line: |
| 506 |
> |
|
| 507 |
> |
if (!isDirectional) { |
| 508 |
> |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
| 509 |
> |
atomTypeString, atomData[0], |
| 510 |
> |
atomData[1], atomData[2], |
| 511 |
> |
atomData[3], atomData[4], |
| 512 |
> |
atomData[5]); |
| 513 |
> |
|
| 514 |
> |
strcat(writeLine, |
| 515 |
> |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
| 516 |
> |
} else { |
| 517 |
> |
sprintf(writeLine, |
| 518 |
> |
"%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", |
| 519 |
> |
atomTypeString, |
| 520 |
> |
atomData[0], |
| 521 |
> |
atomData[1], |
| 522 |
> |
atomData[2], |
| 523 |
> |
atomData[3], |
| 524 |
> |
atomData[4], |
| 525 |
> |
atomData[5], |
| 526 |
> |
atomData[6], |
| 527 |
> |
atomData[7], |
| 528 |
> |
atomData[8], |
| 529 |
> |
atomData[9], |
| 530 |
> |
atomData[10], |
| 531 |
> |
atomData[11], |
| 532 |
> |
atomData[12]); |
| 533 |
> |
} |
| 534 |
> |
|
| 535 |
> |
for(k = 0; k < outFile.size(); k++) { |
| 536 |
> |
*outFile[k] << writeLine; |
| 537 |
> |
} |
| 538 |
> |
} //end for(iter = integrableObject.begin()) |
| 539 |
> |
|
| 540 |
> |
currentIndex++; |
| 541 |
> |
} |
| 542 |
> |
} //end for(i = 0; i < mpiSim->getNmol()) |
| 543 |
> |
|
| 544 |
> |
for(k = 0; k < outFile.size(); k++) { |
| 545 |
> |
outFile[k]->flush(); |
| 546 |
> |
} |
| 547 |
> |
|
| 548 |
> |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
| 549 |
> |
|
| 550 |
> |
MPIcheckPoint(); |
| 551 |
> |
|
| 552 |
> |
delete [] potatoes; |
| 553 |
> |
} else { |
| 554 |
> |
|
| 555 |
> |
// worldRank != 0, so I'm a remote node. |
| 556 |
> |
|
| 557 |
> |
// Set my magic potato to 0: |
| 558 |
> |
|
| 559 |
> |
myPotato = 0; |
| 560 |
> |
currentIndex = 0; |
| 561 |
> |
|
| 562 |
> |
for(i = 0; i < mpiSim->getNMolGlobal(); i++) { |
| 563 |
> |
|
| 564 |
> |
// Am I the node which has this integrableObject? |
| 565 |
> |
|
| 566 |
> |
if (MolToProcMap[i] == worldRank) { |
| 567 |
> |
if (myPotato + 1 >= MAXTAG) { |
| 568 |
> |
|
| 569 |
> |
// The potato was going to exceed the maximum value, |
| 570 |
> |
// so wrap this processor potato back to 0 (and block until |
| 571 |
> |
// node 0 says we can go: |
| 572 |
> |
|
| 573 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
| 574 |
> |
&istatus); |
| 575 |
> |
} |
| 576 |
> |
|
| 577 |
> |
local_index = indexArray[currentIndex].first; |
| 578 |
> |
integrableObjects = |
| 579 |
> |
entry_plug->molecules[local_index].getIntegrableObjects(); |
| 580 |
> |
|
| 581 |
> |
nCurObj = integrableObjects.size(); |
| 582 |
> |
|
| 583 |
> |
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
| 584 |
> |
myPotato++; |
| 585 |
> |
|
| 586 |
> |
for(iter = integrableObjects.begin(); |
| 587 |
> |
iter != integrableObjects.end(); iter++) { |
| 588 |
> |
if (myPotato + 2 >= MAXTAG) { |
| 589 |
> |
|
| 590 |
> |
// The potato was going to exceed the maximum value, |
| 591 |
> |
// so wrap this processor potato back to 0 (and block until |
| 592 |
> |
// node 0 says we can go: |
| 593 |
> |
|
| 594 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
| 595 |
> |
&istatus); |
| 596 |
> |
} |
| 597 |
> |
|
| 598 |
> |
sd = *iter; |
| 599 |
> |
|
| 600 |
> |
atomTypeString = sd->getType(); |
| 601 |
> |
|
| 602 |
> |
pos = sd->getPos(); |
| 603 |
> |
vel = sd->getVel(); |
| 604 |
> |
|
| 605 |
> |
atomData[0] = pos[0]; |
| 606 |
> |
atomData[1] = pos[1]; |
| 607 |
> |
atomData[2] = pos[2]; |
| 608 |
> |
|
| 609 |
> |
atomData[3] = vel[0]; |
| 610 |
> |
atomData[4] = vel[1]; |
| 611 |
> |
atomData[5] = vel[2]; |
| 612 |
> |
|
| 613 |
> |
isDirectional = 0; |
| 614 |
> |
|
| 615 |
> |
if (sd->isDirectional()) { |
| 616 |
> |
isDirectional = 1; |
| 617 |
> |
|
| 618 |
> |
q = sd->getQ(); |
| 619 |
> |
ji = sd->getJ(); |
| 620 |
> |
|
| 621 |
> |
atomData[6] = q[0]; |
| 622 |
> |
atomData[7] = q[1]; |
| 623 |
> |
atomData[8] = q[2]; |
| 624 |
> |
atomData[9] = q[3]; |
| 625 |
> |
|
| 626 |
> |
atomData[10] = ji[0]; |
| 627 |
> |
atomData[11] = ji[1]; |
| 628 |
> |
atomData[12] = ji[2]; |
| 629 |
> |
} |
| 630 |
> |
|
| 631 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
| 632 |
> |
|
| 633 |
> |
// null terminate the string before sending (just in case): |
| 634 |
> |
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
| 635 |
> |
|
| 636 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
| 637 |
> |
myPotato, MPI_COMM_WORLD); |
| 638 |
> |
|
| 639 |
> |
myPotato++; |
| 640 |
> |
|
| 641 |
> |
if (isDirectional) { |
| 642 |
> |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato, |
| 643 |
> |
MPI_COMM_WORLD); |
| 644 |
> |
} else { |
| 645 |
> |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato, |
| 646 |
> |
MPI_COMM_WORLD); |
| 647 |
> |
} |
| 648 |
> |
|
| 649 |
> |
myPotato++; |
| 650 |
> |
} |
| 651 |
> |
|
| 652 |
> |
currentIndex++; |
| 653 |
> |
} |
| 654 |
> |
} |
| 655 |
> |
|
| 656 |
> |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
| 657 |
> |
MPIcheckPoint(); |
| 658 |
> |
} |
| 659 |
> |
|
| 660 |
> |
#endif // is_mpi |
| 661 |
> |
|
| 662 |
> |
} |
| 663 |
> |
|
| 664 |
> |
#ifdef IS_MPI |
| 665 |
> |
|
| 666 |
> |
// a couple of functions to let us escape the write loop |
| 667 |
> |
|
| 668 |
> |
void dWrite::DieDieDie(void) { |
| 669 |
> |
MPI_Finalize(); |
| 670 |
> |
exit(0); |
| 671 |
> |
} |
| 672 |
> |
|
| 673 |
> |
#endif //is_mpi |
