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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]; |
221 |
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int isDirectional; |
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char* atomTypeString; |
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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" |
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<< entry_plug->Hmat[2][2] << ";"; |
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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; |
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} |
261 |
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|
262 |
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for( i=0; i< entry_plug->n_mol; i++ ){ |
263 |
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|
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integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); |
265 |
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molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); |
266 |
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|
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for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ |
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sd = *iter; |
269 |
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pos = sd->getPos(); |
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vel = sd->getVel(); |
271 |
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|
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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", |
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sd->getType(), |
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pos[0], |
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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 |
< |
ji = sd->getJ(); |
287 |
< |
|
288 |
< |
sprintf( tempBuffer, |
289 |
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"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
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q[0], |
291 |
< |
q[1], |
292 |
< |
q[2], |
293 |
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q[3], |
294 |
< |
ji[0], |
295 |
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ji[1], |
296 |
< |
ji[2]); |
297 |
< |
strcat( writeLine, tempBuffer ); |
298 |
< |
} |
299 |
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else |
300 |
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strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
301 |
< |
|
302 |
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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 |