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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 |
> |
#include "io/DumpWrite.hpp" |
2 |
> |
#include "utils/simError.h" |
3 |
> |
|
4 |
> |
#ifdef IS_MPI |
5 |
> |
#include <mpi.h> |
6 |
> |
#endif //is_mpi |
7 |
> |
namespace oopse { |
8 |
> |
DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) |
9 |
> |
: info_(info), filename_(filename){ |
10 |
> |
#ifdef IS_MPI |
11 |
> |
|
12 |
> |
if (worldRank == 0) { |
13 |
> |
#endif // is_mpi |
14 |
> |
|
15 |
> |
dumpFile.open(filename_.c_str(), ios::out | ios::trunc); |
16 |
> |
|
17 |
> |
if (!dumpFile) { |
18 |
> |
sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
19 |
> |
info_->filename_.c_str()); |
20 |
> |
painCave.isFatal = 1; |
21 |
> |
simError(); |
22 |
> |
} |
23 |
> |
|
24 |
> |
#ifdef IS_MPI |
25 |
> |
|
26 |
> |
} |
27 |
> |
|
28 |
> |
sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
29 |
> |
MPIcheckPoint(); |
30 |
> |
|
31 |
> |
#endif // is_mpi |
32 |
> |
|
33 |
> |
} |
34 |
> |
|
35 |
> |
DumpWriter::~DumpWriter() { |
36 |
> |
|
37 |
> |
#ifdef IS_MPI |
38 |
> |
|
39 |
> |
if (worldRank == 0) { |
40 |
> |
#endif // is_mpi |
41 |
> |
|
42 |
> |
dumpFile.close(); |
43 |
> |
|
44 |
> |
#ifdef IS_MPI |
45 |
> |
|
46 |
> |
} |
47 |
> |
|
48 |
> |
#endif // is_mpi |
49 |
> |
|
50 |
> |
} |
51 |
> |
|
52 |
> |
void writeCommentLine(Snapshot* s) { |
53 |
> |
|
54 |
> |
double currentTime; |
55 |
> |
Mat3x3d hmat; |
56 |
> |
double chi; |
57 |
> |
double integralOfChiDt; |
58 |
> |
Mat3x3d eta; |
59 |
> |
|
60 |
> |
currentTime = s->getTime(); |
61 |
> |
hmat = s->getHmat(); |
62 |
> |
chi = s->getChi(); |
63 |
> |
integralOfChiDt = s->getIntegralOfChiDt(); |
64 |
> |
eta = s->getEta(); |
65 |
> |
|
66 |
> |
os << currentTime << ";\t" |
67 |
> |
<< hmat[0][0] << "\t" << hmat[1][0] << "\t" << hmat[2][0] << ";\t" |
68 |
> |
<< hmat[0][1] << "\t" << hmat[1][1] << "\t" << hmat[2][1] << ";\t" |
69 |
> |
<< hmat[0][2] << "\t" << hmat[1][2] << "\t" << hmat[2][2] << ";"; |
70 |
> |
|
71 |
> |
//write out additional parameters, such as chi and eta |
72 |
> |
|
73 |
> |
os << chi << "\t" << integralOfChiDt << "\t;" |
74 |
> |
|
75 |
> |
os << eta[0][0] << "\t" << eta[1][0] << "\t" << eta[2][0] << ";\t" |
76 |
> |
<< eta[0][1] << "\t" << eta[1][1] << "\t" << eta[2][1] << ";\t" |
77 |
> |
<< eta[0][2] << "\t" << eta[1][2] << "\t" << eta[2][2] << ";"; |
78 |
> |
|
79 |
> |
os << endl; |
80 |
> |
} |
81 |
> |
|
82 |
> |
void DumpWriter::writeFrame(std::ostream& os) { |
83 |
> |
const int BUFFERSIZE = 2000; |
84 |
> |
const int MINIBUFFERSIZE = 100; |
85 |
> |
|
86 |
> |
char tempBuffer[BUFFERSIZE]; |
87 |
> |
char writeLine[BUFFERSIZE]; |
88 |
> |
|
89 |
> |
Quat4d q; |
90 |
> |
Vector3d ji; |
91 |
> |
Vector3d pos; |
92 |
> |
Vector3d vel; |
93 |
> |
|
94 |
> |
Molecule* mol; |
95 |
> |
StuntDouble* integrableObject; |
96 |
> |
typename SimInfo::MoleculeIterator mi; |
97 |
> |
typename Molecule::IntegrableObjectIterator ii; |
98 |
> |
|
99 |
> |
int nTotObjects; |
100 |
> |
nTotObjects = info_->getNGlobalIntegrableObjects(); |
101 |
> |
|
102 |
> |
#ifndef IS_MPI |
103 |
> |
|
104 |
> |
|
105 |
> |
os << nTotObjects << "\n"; |
106 |
> |
|
107 |
> |
writeCommentLine(info_->getSnapshotManager()->getCurrentSnapshot()); |
108 |
> |
|
109 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
110 |
> |
|
111 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
112 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
113 |
> |
|
114 |
> |
|
115 |
> |
pos = integrableObject->getPos(); |
116 |
> |
vel = integrableObject->getVel(); |
117 |
> |
|
118 |
> |
sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
119 |
> |
integrableObject->getType(), |
120 |
> |
pos[0], pos[1], pos[2], |
121 |
> |
vel[0], vel[1], vel[2]); |
122 |
> |
|
123 |
> |
strcpy(writeLine, tempBuffer); |
124 |
> |
|
125 |
> |
if (integrableObject->isDirectional()) { |
126 |
> |
q = integrableObject->getQ(); |
127 |
> |
ji = integrableObject->getJ(); |
128 |
> |
|
129 |
> |
sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
130 |
> |
q[0], q[1], q[2], q[3], |
131 |
> |
ji[0], ji[1], ji[2]); |
132 |
> |
strcat(writeLine, tempBuffer); |
133 |
> |
} else { |
134 |
> |
strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
135 |
> |
} |
136 |
> |
|
137 |
> |
os << writeLine; |
138 |
> |
|
139 |
> |
} |
140 |
> |
} |
141 |
> |
|
142 |
> |
#else // is_mpi |
143 |
> |
/********************************************************************* |
144 |
> |
* Documentation? You want DOCUMENTATION? |
145 |
> |
* |
146 |
> |
* Why all the potatoes below? |
147 |
> |
* |
148 |
> |
* To make a long story short, the original version of DumpWriter |
149 |
> |
* worked in the most inefficient way possible. Node 0 would |
150 |
> |
* poke each of the node for an individual atom's formatted data |
151 |
> |
* as node 0 worked its way down the global index. This was particularly |
152 |
> |
* inefficient since the method blocked all processors at every atom |
153 |
> |
* (and did it twice!). |
154 |
> |
* |
155 |
> |
* An intermediate version of DumpWriter could be described from Node |
156 |
> |
* zero's perspective as follows: |
157 |
> |
* |
158 |
> |
* 1) Have 100 of your friends stand in a circle. |
159 |
> |
* 2) When you say go, have all of them start tossing potatoes at |
160 |
> |
* you (one at a time). |
161 |
> |
* 3) Catch the potatoes. |
162 |
> |
* |
163 |
> |
* It was an improvement, but MPI has buffers and caches that could |
164 |
> |
* best be described in this analogy as "potato nets", so there's no |
165 |
> |
* need to block the processors atom-by-atom. |
166 |
> |
* |
167 |
> |
* This new and improved DumpWriter works in an even more efficient |
168 |
> |
* way: |
169 |
> |
* |
170 |
> |
* 1) Have 100 of your friend stand in a circle. |
171 |
> |
* 2) When you say go, have them start tossing 5-pound bags of |
172 |
> |
* potatoes at you. |
173 |
> |
* 3) Once you've caught a friend's bag of potatoes, |
174 |
> |
* toss them a spud to let them know they can toss another bag. |
175 |
> |
* |
176 |
> |
* How's THAT for documentation? |
177 |
> |
* |
178 |
> |
*********************************************************************/ |
179 |
> |
const int masterNode = 0; |
180 |
> |
|
181 |
> |
int * potatoes; |
182 |
> |
int myPotato; |
183 |
> |
int nProc; |
184 |
> |
int which_node; |
185 |
> |
double atomData[13]; |
186 |
> |
int isDirectional; |
187 |
> |
const char * atomTypeString; |
188 |
> |
char MPIatomTypeString[MINIBUFFERSIZE]; |
189 |
> |
int msgLen; // the length of message actually recieved at master nodes |
190 |
> |
int haveError; |
191 |
> |
MPI_Status istatus; |
192 |
> |
int nCurObj; |
193 |
> |
|
194 |
> |
// code to find maximum tag value |
195 |
> |
int * tagub; |
196 |
> |
int flag; |
197 |
> |
int MAXTAG; |
198 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
199 |
> |
|
200 |
> |
if (flag) { |
201 |
> |
MAXTAG = *tagub; |
202 |
> |
} else { |
203 |
> |
MAXTAG = 32767; |
204 |
> |
} |
205 |
> |
|
206 |
> |
if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file |
207 |
> |
|
208 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
209 |
> |
|
210 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
211 |
> |
potatoes = new int[nProc]; |
212 |
> |
|
213 |
> |
//write out the comment lines |
214 |
> |
for(i = 0; i < nProc; i++) { |
215 |
> |
potatoes[i] = 0; |
216 |
> |
} |
217 |
> |
|
218 |
> |
|
219 |
> |
os << nTotObjects << "\n"; |
220 |
> |
writeCommentLine(info_->getSnapshotManager()->getCurrentSnapshot()); |
221 |
> |
|
222 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
223 |
> |
|
224 |
> |
// Get the Node number which has this atom; |
225 |
> |
|
226 |
> |
which_node = info_->getMolToProc(i); |
227 |
> |
|
228 |
> |
if (which_node != masterNode) { //current molecule is in slave node |
229 |
> |
if (potatoes[which_node] + 1 >= MAXTAG) { |
230 |
> |
// The potato was going to exceed the maximum value, |
231 |
> |
// so wrap this processor potato back to 0: |
232 |
> |
|
233 |
> |
potatoes[which_node] = 0; |
234 |
> |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, |
235 |
> |
MPI_COMM_WORLD); |
236 |
> |
} |
237 |
> |
|
238 |
> |
myPotato = potatoes[which_node]; |
239 |
> |
|
240 |
> |
//recieve the number of integrableObject in current molecule |
241 |
> |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
242 |
> |
MPI_COMM_WORLD, &istatus); |
243 |
> |
myPotato++; |
244 |
> |
|
245 |
> |
for(int l = 0; l < nCurObj; l++) { |
246 |
> |
if (potatoes[which_node] + 2 >= MAXTAG) { |
247 |
> |
// The potato was going to exceed the maximum value, |
248 |
> |
// so wrap this processor potato back to 0: |
249 |
> |
|
250 |
> |
potatoes[which_node] = 0; |
251 |
> |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, |
252 |
> |
0, MPI_COMM_WORLD); |
253 |
> |
} |
254 |
> |
|
255 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
256 |
> |
which_node, myPotato, MPI_COMM_WORLD, |
257 |
> |
&istatus); |
258 |
> |
|
259 |
> |
atomTypeString = MPIatomTypeString; |
260 |
> |
|
261 |
> |
myPotato++; |
262 |
> |
|
263 |
> |
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
264 |
> |
MPI_COMM_WORLD, &istatus); |
265 |
> |
myPotato++; |
266 |
> |
|
267 |
> |
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
268 |
> |
|
269 |
> |
if (msgLen == 13) |
270 |
> |
isDirectional = 1; |
271 |
> |
else |
272 |
> |
isDirectional = 0; |
273 |
> |
|
274 |
> |
// If we've survived to here, format the line: |
275 |
> |
|
276 |
> |
if (!isDirectional) { |
277 |
> |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
278 |
> |
atomTypeString, atomData[0], |
279 |
> |
atomData[1], atomData[2], |
280 |
> |
atomData[3], atomData[4], |
281 |
> |
atomData[5]); |
282 |
> |
|
283 |
> |
strcat(writeLine, |
284 |
> |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
285 |
> |
} else { |
286 |
> |
sprintf(writeLine, |
287 |
> |
"%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", |
288 |
> |
atomTypeString, |
289 |
> |
atomData[0], |
290 |
> |
atomData[1], |
291 |
> |
atomData[2], |
292 |
> |
atomData[3], |
293 |
> |
atomData[4], |
294 |
> |
atomData[5], |
295 |
> |
atomData[6], |
296 |
> |
atomData[7], |
297 |
> |
atomData[8], |
298 |
> |
atomData[9], |
299 |
> |
atomData[10], |
300 |
> |
atomData[11], |
301 |
> |
atomData[12]); |
302 |
> |
} |
303 |
> |
|
304 |
> |
os << writeLine; |
305 |
> |
|
306 |
> |
} // end for(int l =0) |
307 |
> |
|
308 |
> |
potatoes[which_node] = myPotato; |
309 |
> |
} else { //master node has current molecule |
310 |
> |
|
311 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
312 |
> |
|
313 |
> |
if (mol == NULL) { |
314 |
> |
strcpy(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
315 |
> |
painCave.isFatal = 1; |
316 |
> |
simError(); |
317 |
> |
} |
318 |
> |
|
319 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
320 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
321 |
> |
|
322 |
> |
atomTypeString = integrableObject->getType().c_str(); |
323 |
> |
|
324 |
> |
pos = integrableObject->getPos(); |
325 |
> |
vel = integrableObject->getVel(); |
326 |
> |
|
327 |
> |
atomData[0] = pos[0]; |
328 |
> |
atomData[1] = pos[1]; |
329 |
> |
atomData[2] = pos[2]; |
330 |
> |
|
331 |
> |
atomData[3] = vel[0]; |
332 |
> |
atomData[4] = vel[1]; |
333 |
> |
atomData[5] = vel[2]; |
334 |
> |
|
335 |
> |
isDirectional = 0; |
336 |
> |
|
337 |
> |
if (integrableObject->isDirectional()) { |
338 |
> |
isDirectional = 1; |
339 |
> |
|
340 |
> |
q = integrableObject->getQ(); |
341 |
> |
ji = integrableObject->getJ(); |
342 |
> |
|
343 |
> |
for(int j = 0; j < 6; j++) { |
344 |
> |
atomData[j] = atomData[j]; |
345 |
> |
} |
346 |
> |
|
347 |
> |
atomData[6] = q[0]; |
348 |
> |
atomData[7] = q[1]; |
349 |
> |
atomData[8] = q[2]; |
350 |
> |
atomData[9] = q[3]; |
351 |
> |
|
352 |
> |
atomData[10] = ji[0]; |
353 |
> |
atomData[11] = ji[1]; |
354 |
> |
atomData[12] = ji[2]; |
355 |
> |
} |
356 |
> |
|
357 |
> |
// If we've survived to here, format the line: |
358 |
> |
|
359 |
> |
if (!isDirectional) { |
360 |
> |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
361 |
> |
atomTypeString, atomData[0], |
362 |
> |
atomData[1], atomData[2], |
363 |
> |
atomData[3], atomData[4], |
364 |
> |
atomData[5]); |
365 |
> |
|
366 |
> |
strcat(writeLine, |
367 |
> |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
368 |
> |
} else { |
369 |
> |
sprintf(writeLine, |
370 |
> |
"%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", |
371 |
> |
atomTypeString, |
372 |
> |
atomData[0], |
373 |
> |
atomData[1], |
374 |
> |
atomData[2], |
375 |
> |
atomData[3], |
376 |
> |
atomData[4], |
377 |
> |
atomData[5], |
378 |
> |
atomData[6], |
379 |
> |
atomData[7], |
380 |
> |
atomData[8], |
381 |
> |
atomData[9], |
382 |
> |
atomData[10], |
383 |
> |
atomData[11], |
384 |
> |
atomData[12]); |
385 |
> |
} |
386 |
> |
|
387 |
> |
|
388 |
> |
os << writeLine; |
389 |
> |
|
390 |
> |
} //end for(iter = integrableObject.begin()) |
391 |
> |
} |
392 |
> |
} //end for(i = 0; i < mpiSim->getNmol()) |
393 |
> |
|
394 |
> |
os.flush(); |
395 |
> |
|
396 |
> |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
397 |
> |
|
398 |
> |
MPIcheckPoint(); |
399 |
> |
|
400 |
> |
delete [] potatoes; |
401 |
> |
} else { |
402 |
> |
|
403 |
> |
// worldRank != 0, so I'm a remote node. |
404 |
> |
|
405 |
> |
// Set my magic potato to 0: |
406 |
> |
|
407 |
> |
myPotato = 0; |
408 |
> |
|
409 |
> |
for(i = 0; i < info_->getNGlobalMolecules(); i++) { |
410 |
> |
|
411 |
> |
// Am I the node which has this integrableObject? |
412 |
> |
whichNode = info_->getMolToProc(i); |
413 |
> |
if (whichNode == worldRank) { |
414 |
> |
if (myPotato + 1 >= MAXTAG) { |
415 |
> |
|
416 |
> |
// The potato was going to exceed the maximum value, |
417 |
> |
// so wrap this processor potato back to 0 (and block until |
418 |
> |
// node 0 says we can go: |
419 |
> |
|
420 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
421 |
> |
&istatus); |
422 |
> |
} |
423 |
> |
|
424 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
425 |
> |
|
426 |
> |
|
427 |
> |
nCurObj = mol->getNIntegrableObjects(); |
428 |
> |
|
429 |
> |
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
430 |
> |
myPotato++; |
431 |
> |
|
432 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
433 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
434 |
> |
|
435 |
> |
if (myPotato + 2 >= MAXTAG) { |
436 |
> |
|
437 |
> |
// The potato was going to exceed the maximum value, |
438 |
> |
// so wrap this processor potato back to 0 (and block until |
439 |
> |
// node 0 says we can go: |
440 |
> |
|
441 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
442 |
> |
&istatus); |
443 |
> |
} |
444 |
> |
|
445 |
> |
atomTypeString = integrableObject->getType().c_str(); |
446 |
> |
|
447 |
> |
pos = integrableObject->getPos(); |
448 |
> |
vel = integrableObject->getVel(); |
449 |
> |
|
450 |
> |
atomData[0] = pos[0]; |
451 |
> |
atomData[1] = pos[1]; |
452 |
> |
atomData[2] = pos[2]; |
453 |
> |
|
454 |
> |
atomData[3] = vel[0]; |
455 |
> |
atomData[4] = vel[1]; |
456 |
> |
atomData[5] = vel[2]; |
457 |
> |
|
458 |
> |
isDirectional = 0; |
459 |
> |
|
460 |
> |
if (integrableObject->isDirectional()) { |
461 |
> |
isDirectional = 1; |
462 |
> |
|
463 |
> |
q = integrableObject->getQ(); |
464 |
> |
ji = integrableObject->getJ(); |
465 |
> |
|
466 |
> |
atomData[6] = q[0]; |
467 |
> |
atomData[7] = q[1]; |
468 |
> |
atomData[8] = q[2]; |
469 |
> |
atomData[9] = q[3]; |
470 |
> |
|
471 |
> |
atomData[10] = ji[0]; |
472 |
> |
atomData[11] = ji[1]; |
473 |
> |
atomData[12] = ji[2]; |
474 |
> |
} |
475 |
> |
|
476 |
> |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
477 |
> |
|
478 |
> |
// null terminate the string before sending (just in case): |
479 |
> |
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
480 |
> |
|
481 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
482 |
> |
myPotato, MPI_COMM_WORLD); |
483 |
> |
|
484 |
> |
myPotato++; |
485 |
> |
|
486 |
> |
if (isDirectional) { |
487 |
> |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato, |
488 |
> |
MPI_COMM_WORLD); |
489 |
> |
} else { |
490 |
> |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato, |
491 |
> |
MPI_COMM_WORLD); |
492 |
> |
} |
493 |
> |
|
494 |
> |
myPotato++; |
495 |
> |
} |
496 |
> |
|
497 |
> |
} |
498 |
> |
|
499 |
> |
} |
500 |
> |
|
501 |
> |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
502 |
> |
MPIcheckPoint(); |
503 |
> |
} |
504 |
> |
|
505 |
> |
#endif // is_mpi |
506 |
> |
|
507 |
> |
} |
508 |
> |
|
509 |
> |
}//end namespace oopse |