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#define _LARGEFILE_SOURCE64 |
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#define _FILE_OFFSET_BITS 64 |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#include "io/DumpWriter.hpp" |
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#include "primitives/Molecule.hpp" |
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#include "utils/simError.h" |
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#include "io/basic_teebuf.hpp" |
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#include "io/gzstream.hpp" |
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#include "io/Globals.hpp" |
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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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namespace oopse { |
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|
|
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DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ |
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DumpWriter::DumpWriter(SimInfo* info) |
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: info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ |
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|
|
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entry_plug = the_entry_plug; |
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Globals* simParams = info->getSimParams(); |
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needCompression_ = simParams->getCompressDumpFile(); |
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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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if (needCompression_) { |
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filename_ += ".gz"; |
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eorFilename_ += ".gz"; |
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} |
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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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if (worldRank == 0) { |
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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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dumpFile_ = createOStream(filename_); |
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|
|
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dumpFile.close(); |
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if (!dumpFile_) { |
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sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
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filename_.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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|
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#ifdef IS_MPI |
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} |
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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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sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
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MPIcheckPoint(); |
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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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#endif // is_mpi |
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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(); |
93 |
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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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|
|
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#endif |
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|
|
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void DumpWriter::writeDump(double currentTime){ |
93 |
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DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) |
94 |
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: info_(info), filename_(filename){ |
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|
|
96 |
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ofstream finalOut; |
97 |
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vector<ofstream*> fileStreams; |
96 |
> |
Globals* simParams = info->getSimParams(); |
97 |
> |
eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; |
98 |
|
|
99 |
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#ifdef IS_MPI |
100 |
< |
if(worldRank == 0 ){ |
101 |
< |
#endif |
102 |
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finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc ); |
111 |
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if( !finalOut ){ |
112 |
< |
sprintf( painCave.errMsg, |
113 |
< |
"Could not open \"%s\" for final dump output.\n", |
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entry_plug->finalName.c_str() ); |
115 |
< |
painCave.isFatal = 1; |
116 |
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simError(); |
99 |
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needCompression_ = simParams->getCompressDumpFile(); |
100 |
> |
if (needCompression_) { |
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filename_ += ".gz"; |
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eorFilename_ += ".gz"; |
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|
} |
104 |
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|
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|
#ifdef IS_MPI |
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< |
} |
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|
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> |
if (worldRank == 0) { |
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|
#endif // is_mpi |
109 |
|
|
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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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dumpFile_ = createOStream(filename_); |
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|
|
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if (!dumpFile_) { |
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sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", |
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filename_.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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– |
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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|
|
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ofstream finalOut; |
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vector<ofstream*> fileStreams; |
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sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n"); |
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MPIcheckPoint(); |
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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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|
|
131 |
< |
#ifdef IS_MPI |
153 |
< |
} |
154 |
< |
#endif // is_mpi |
155 |
< |
|
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fileStreams.push_back(&finalOut); |
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writeFrame(fileStreams, currentTime); |
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> |
DumpWriter::~DumpWriter() { |
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|
|
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|
#ifdef IS_MPI |
160 |
– |
finalOut.close(); |
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– |
#endif |
162 |
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|
163 |
– |
} |
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|
|
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< |
void DumpWriter::writeFrame( vector<ofstream*>& outFile, double currentTime ){ |
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if (worldRank == 0) { |
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> |
#endif // is_mpi |
137 |
|
|
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< |
const int BUFFERSIZE = 2000; |
168 |
< |
const int MINIBUFFERSIZE = 100; |
138 |
> |
delete dumpFile_; |
139 |
|
|
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– |
char tempBuffer[BUFFERSIZE]; |
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– |
char writeLine[BUFFERSIZE]; |
172 |
– |
|
173 |
– |
int i; |
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– |
unsigned int k; |
175 |
– |
|
140 |
|
#ifdef IS_MPI |
177 |
– |
|
178 |
– |
/********************************************************************* |
179 |
– |
* Documentation? You want DOCUMENTATION? |
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– |
* |
181 |
– |
* Why all the potatoes below? |
182 |
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* |
183 |
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* To make a long story short, the original version of DumpWriter |
184 |
– |
* worked in the most inefficient way possible. Node 0 would |
185 |
– |
* poke each of the node for an individual atom's formatted data |
186 |
– |
* as node 0 worked its way down the global index. This was particularly |
187 |
– |
* inefficient since the method blocked all processors at every atom |
188 |
– |
* (and did it twice!). |
189 |
– |
* |
190 |
– |
* An intermediate version of DumpWriter could be described from Node |
191 |
– |
* zero's perspective as follows: |
192 |
– |
* |
193 |
– |
* 1) Have 100 of your friends stand in a circle. |
194 |
– |
* 2) When you say go, have all of them start tossing potatoes at |
195 |
– |
* you (one at a time). |
196 |
– |
* 3) Catch the potatoes. |
197 |
– |
* |
198 |
– |
* It was an improvement, but MPI has buffers and caches that could |
199 |
– |
* best be described in this analogy as "potato nets", so there's no |
200 |
– |
* need to block the processors atom-by-atom. |
201 |
– |
* |
202 |
– |
* This new and improved DumpWriter works in an even more efficient |
203 |
– |
* way: |
204 |
– |
* |
205 |
– |
* 1) Have 100 of your friend stand in a circle. |
206 |
– |
* 2) When you say go, have them start tossing 5-pound bags of |
207 |
– |
* potatoes at you. |
208 |
– |
* 3) Once you've caught a friend's bag of potatoes, |
209 |
– |
* toss them a spud to let them know they can toss another bag. |
210 |
– |
* |
211 |
– |
* How's THAT for documentation? |
212 |
– |
* |
213 |
– |
*********************************************************************/ |
141 |
|
|
142 |
< |
int *potatoes; |
216 |
< |
int myPotato; |
142 |
> |
} |
143 |
|
|
144 |
< |
int nProc; |
219 |
< |
int j, which_node, done, which_atom, local_index, currentIndex; |
220 |
< |
double atomData[13]; |
221 |
< |
int isDirectional; |
222 |
< |
char* atomTypeString; |
223 |
< |
char MPIatomTypeString[MINIBUFFERSIZE]; |
224 |
< |
int nObjects; |
225 |
< |
int msgLen; // the length of message actually recieved at master nodes |
226 |
< |
#endif //is_mpi |
144 |
> |
#endif // is_mpi |
145 |
|
|
228 |
– |
double q[4], ji[3]; |
229 |
– |
DirectionalAtom* dAtom; |
230 |
– |
double pos[3], vel[3]; |
231 |
– |
int nTotObjects; |
232 |
– |
StuntDouble* sd; |
233 |
– |
char* molName; |
234 |
– |
vector<StuntDouble*> integrableObjects; |
235 |
– |
vector<StuntDouble*>::iterator iter; |
236 |
– |
nTotObjects = entry_plug->getTotIntegrableObjects(); |
237 |
– |
#ifndef IS_MPI |
238 |
– |
|
239 |
– |
for(k = 0; k < outFile.size(); k++){ |
240 |
– |
*outFile[k] << nTotObjects << "\n"; |
241 |
– |
|
242 |
– |
*outFile[k] << currentTime << ";\t" |
243 |
– |
<< entry_plug->Hmat[0][0] << "\t" |
244 |
– |
<< entry_plug->Hmat[1][0] << "\t" |
245 |
– |
<< entry_plug->Hmat[2][0] << ";\t" |
246 |
– |
|
247 |
– |
<< entry_plug->Hmat[0][1] << "\t" |
248 |
– |
<< entry_plug->Hmat[1][1] << "\t" |
249 |
– |
<< entry_plug->Hmat[2][1] << ";\t" |
250 |
– |
|
251 |
– |
<< entry_plug->Hmat[0][2] << "\t" |
252 |
– |
<< entry_plug->Hmat[1][2] << "\t" |
253 |
– |
<< entry_plug->Hmat[2][2] << ";"; |
254 |
– |
|
255 |
– |
//write out additional parameters, such as chi and eta |
256 |
– |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; |
146 |
|
} |
258 |
– |
|
259 |
– |
for( i=0; i< entry_plug->n_mol; i++ ){ |
147 |
|
|
148 |
< |
integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); |
149 |
< |
molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); |
148 |
> |
void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) { |
149 |
> |
|
150 |
> |
double currentTime; |
151 |
> |
Mat3x3d hmat; |
152 |
> |
double chi; |
153 |
> |
double integralOfChiDt; |
154 |
> |
Mat3x3d eta; |
155 |
|
|
156 |
< |
for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ |
157 |
< |
sd = *iter; |
158 |
< |
sd->getPos(pos); |
159 |
< |
sd->getVel(vel); |
156 |
> |
currentTime = s->getTime(); |
157 |
> |
hmat = s->getHmat(); |
158 |
> |
chi = s->getChi(); |
159 |
> |
integralOfChiDt = s->getIntegralOfChiDt(); |
160 |
> |
eta = s->getEta(); |
161 |
> |
|
162 |
> |
os << currentTime << ";\t" |
163 |
> |
<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t" |
164 |
> |
<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t" |
165 |
> |
<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t"; |
166 |
|
|
167 |
< |
sprintf( tempBuffer, |
270 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
271 |
< |
sd->getType(), |
272 |
< |
pos[0], |
273 |
< |
pos[1], |
274 |
< |
pos[2], |
275 |
< |
vel[0], |
276 |
< |
vel[1], |
277 |
< |
vel[2]); |
278 |
< |
strcpy( writeLine, tempBuffer ); |
167 |
> |
//write out additional parameters, such as chi and eta |
168 |
|
|
169 |
< |
if( sd->isDirectional() ){ |
169 |
> |
os << chi << "\t" << integralOfChiDt << "\t;"; |
170 |
|
|
171 |
< |
sd->getQ( q ); |
172 |
< |
sd->getJ( ji ); |
173 |
< |
|
174 |
< |
sprintf( tempBuffer, |
175 |
< |
"%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
287 |
< |
q[0], |
288 |
< |
q[1], |
289 |
< |
q[2], |
290 |
< |
q[3], |
291 |
< |
ji[0], |
292 |
< |
ji[1], |
293 |
< |
ji[2]); |
294 |
< |
strcat( writeLine, tempBuffer ); |
295 |
< |
} |
296 |
< |
else |
297 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
298 |
< |
|
299 |
< |
for(k = 0; k < outFile.size(); k++) |
300 |
< |
*outFile[k] << writeLine; |
301 |
< |
} |
302 |
< |
|
171 |
> |
os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t" |
172 |
> |
<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t" |
173 |
> |
<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";"; |
174 |
> |
|
175 |
> |
os << "\n"; |
176 |
|
} |
177 |
|
|
178 |
< |
#else // is_mpi |
178 |
> |
void DumpWriter::writeFrame(std::ostream& os) { |
179 |
> |
const int BUFFERSIZE = 2000; |
180 |
> |
const int MINIBUFFERSIZE = 100; |
181 |
|
|
182 |
< |
/* code to find maximum tag value */ |
182 |
> |
char tempBuffer[BUFFERSIZE]; |
183 |
> |
char writeLine[BUFFERSIZE]; |
184 |
> |
|
185 |
> |
Quat4d q; |
186 |
> |
Vector3d ji; |
187 |
> |
Vector3d pos; |
188 |
> |
Vector3d vel; |
189 |
> |
|
190 |
> |
Molecule* mol; |
191 |
> |
StuntDouble* integrableObject; |
192 |
> |
SimInfo::MoleculeIterator mi; |
193 |
> |
Molecule::IntegrableObjectIterator ii; |
194 |
|
|
195 |
< |
int *tagub, flag, MAXTAG; |
196 |
< |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
311 |
< |
if (flag) { |
312 |
< |
MAXTAG = *tagub; |
313 |
< |
} else { |
314 |
< |
MAXTAG = 32767; |
315 |
< |
} |
195 |
> |
int nTotObjects; |
196 |
> |
nTotObjects = info_->getNGlobalIntegrableObjects(); |
197 |
|
|
198 |
< |
int haveError; |
198 |
> |
#ifndef IS_MPI |
199 |
|
|
319 |
– |
MPI_Status istatus; |
320 |
– |
int nCurObj; |
321 |
– |
int *MolToProcMap = mpiSim->getMolToProcMap(); |
200 |
|
|
201 |
< |
// write out header and node 0's coordinates |
201 |
> |
os << nTotObjects << "\n"; |
202 |
> |
|
203 |
> |
writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
204 |
|
|
205 |
< |
if( worldRank == 0 ){ |
205 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { |
206 |
|
|
207 |
< |
// Node 0 needs a list of the magic potatoes for each processor; |
207 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
208 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
209 |
> |
|
210 |
|
|
211 |
< |
nProc = mpiSim->getNProcessors(); |
212 |
< |
potatoes = new int[nProc]; |
211 |
> |
pos = integrableObject->getPos(); |
212 |
> |
vel = integrableObject->getVel(); |
213 |
|
|
214 |
< |
//write out the comment lines |
215 |
< |
for (i = 0; i < nProc; i++) |
216 |
< |
potatoes[i] = 0; |
217 |
< |
|
218 |
< |
for(k = 0; k < outFile.size(); k++){ |
219 |
< |
*outFile[k] << nTotObjects << "\n"; |
220 |
< |
|
221 |
< |
*outFile[k] << currentTime << ";\t" |
222 |
< |
<< entry_plug->Hmat[0][0] << "\t" |
223 |
< |
<< entry_plug->Hmat[1][0] << "\t" |
224 |
< |
<< entry_plug->Hmat[2][0] << ";\t" |
225 |
< |
|
226 |
< |
<< entry_plug->Hmat[0][1] << "\t" |
227 |
< |
<< entry_plug->Hmat[1][1] << "\t" |
228 |
< |
<< entry_plug->Hmat[2][1] << ";\t" |
229 |
< |
|
230 |
< |
<< entry_plug->Hmat[0][2] << "\t" |
231 |
< |
<< entry_plug->Hmat[1][2] << "\t" |
232 |
< |
<< entry_plug->Hmat[2][2] << ";"; |
233 |
< |
|
234 |
< |
*outFile[k] << entry_plug->the_integrator->getAdditionalParameters() |
235 |
< |
<< endl; |
214 |
> |
sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
215 |
> |
integrableObject->getType().c_str(), |
216 |
> |
pos[0], pos[1], pos[2], |
217 |
> |
vel[0], vel[1], vel[2]); |
218 |
> |
|
219 |
> |
strcpy(writeLine, tempBuffer); |
220 |
> |
|
221 |
> |
if (integrableObject->isDirectional()) { |
222 |
> |
q = integrableObject->getQ(); |
223 |
> |
ji = integrableObject->getJ(); |
224 |
> |
|
225 |
> |
sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", |
226 |
> |
q[0], q[1], q[2], q[3], |
227 |
> |
ji[0], ji[1], ji[2]); |
228 |
> |
strcat(writeLine, tempBuffer); |
229 |
> |
} else { |
230 |
> |
strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
231 |
> |
} |
232 |
> |
|
233 |
> |
os << writeLine; |
234 |
> |
|
235 |
> |
} |
236 |
|
} |
237 |
+ |
|
238 |
+ |
os.flush(); |
239 |
+ |
#else // is_mpi |
240 |
+ |
/********************************************************************* |
241 |
+ |
* Documentation? You want DOCUMENTATION? |
242 |
+ |
* |
243 |
+ |
* Why all the potatoes below? |
244 |
+ |
* |
245 |
+ |
* To make a long story short, the original version of DumpWriter |
246 |
+ |
* worked in the most inefficient way possible. Node 0 would |
247 |
+ |
* poke each of the node for an individual atom's formatted data |
248 |
+ |
* as node 0 worked its way down the global index. This was particularly |
249 |
+ |
* inefficient since the method blocked all processors at every atom |
250 |
+ |
* (and did it twice!). |
251 |
+ |
* |
252 |
+ |
* An intermediate version of DumpWriter could be described from Node |
253 |
+ |
* zero's perspective as follows: |
254 |
+ |
* |
255 |
+ |
* 1) Have 100 of your friends stand in a circle. |
256 |
+ |
* 2) When you say go, have all of them start tossing potatoes at |
257 |
+ |
* you (one at a time). |
258 |
+ |
* 3) Catch the potatoes. |
259 |
+ |
* |
260 |
+ |
* It was an improvement, but MPI has buffers and caches that could |
261 |
+ |
* best be described in this analogy as "potato nets", so there's no |
262 |
+ |
* need to block the processors atom-by-atom. |
263 |
+ |
* |
264 |
+ |
* This new and improved DumpWriter works in an even more efficient |
265 |
+ |
* way: |
266 |
+ |
* |
267 |
+ |
* 1) Have 100 of your friend stand in a circle. |
268 |
+ |
* 2) When you say go, have them start tossing 5-pound bags of |
269 |
+ |
* potatoes at you. |
270 |
+ |
* 3) Once you've caught a friend's bag of potatoes, |
271 |
+ |
* toss them a spud to let them know they can toss another bag. |
272 |
+ |
* |
273 |
+ |
* How's THAT for documentation? |
274 |
+ |
* |
275 |
+ |
*********************************************************************/ |
276 |
+ |
const int masterNode = 0; |
277 |
+ |
|
278 |
+ |
int * potatoes; |
279 |
+ |
int myPotato; |
280 |
+ |
int nProc; |
281 |
+ |
int which_node; |
282 |
+ |
double atomData[13]; |
283 |
+ |
int isDirectional; |
284 |
+ |
char MPIatomTypeString[MINIBUFFERSIZE]; |
285 |
+ |
int msgLen; // the length of message actually recieved at master nodes |
286 |
+ |
int haveError; |
287 |
+ |
MPI_Status istatus; |
288 |
+ |
int nCurObj; |
289 |
|
|
290 |
< |
currentIndex = 0; |
291 |
< |
|
292 |
< |
for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { |
293 |
< |
|
294 |
< |
// Get the Node number which has this atom; |
361 |
< |
|
362 |
< |
which_node = MolToProcMap[i]; |
363 |
< |
|
364 |
< |
if (which_node != 0) { |
365 |
< |
|
366 |
< |
if (potatoes[which_node] + 1 >= MAXTAG) { |
367 |
< |
// The potato was going to exceed the maximum value, |
368 |
< |
// so wrap this processor potato back to 0: |
290 |
> |
// code to find maximum tag value |
291 |
> |
int * tagub; |
292 |
> |
int flag; |
293 |
> |
int MAXTAG; |
294 |
> |
MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); |
295 |
|
|
296 |
< |
potatoes[which_node] = 0; |
297 |
< |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, |
298 |
< |
MPI_COMM_WORLD); |
299 |
< |
|
300 |
< |
} |
296 |
> |
if (flag) { |
297 |
> |
MAXTAG = *tagub; |
298 |
> |
} else { |
299 |
> |
MAXTAG = 32767; |
300 |
> |
} |
301 |
|
|
302 |
< |
myPotato = potatoes[which_node]; |
302 |
> |
if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file |
303 |
|
|
304 |
< |
//recieve the number of integrableObject in current molecule |
379 |
< |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, |
380 |
< |
myPotato, MPI_COMM_WORLD, &istatus); |
381 |
< |
myPotato++; |
382 |
< |
|
383 |
< |
for(int l = 0; l < nCurObj; l++){ |
304 |
> |
// Node 0 needs a list of the magic potatoes for each processor; |
305 |
|
|
306 |
< |
if (potatoes[which_node] + 2 >= MAXTAG) { |
307 |
< |
// The potato was going to exceed the maximum value, |
387 |
< |
// so wrap this processor potato back to 0: |
306 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &nProc); |
307 |
> |
potatoes = new int[nProc]; |
308 |
|
|
309 |
< |
potatoes[which_node] = 0; |
310 |
< |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, MPI_COMM_WORLD); |
311 |
< |
|
312 |
< |
} |
309 |
> |
//write out the comment lines |
310 |
> |
for(int i = 0; i < nProc; i++) { |
311 |
> |
potatoes[i] = 0; |
312 |
> |
} |
313 |
|
|
394 |
– |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, which_node, |
395 |
– |
myPotato, MPI_COMM_WORLD, &istatus); |
314 |
|
|
315 |
< |
atomTypeString = MPIatomTypeString; |
315 |
> |
os << nTotObjects << "\n"; |
316 |
> |
writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot()); |
317 |
|
|
318 |
< |
myPotato++; |
318 |
> |
for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
319 |
|
|
320 |
< |
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, MPI_COMM_WORLD, &istatus); |
402 |
< |
myPotato++; |
320 |
> |
// Get the Node number which has this atom; |
321 |
|
|
322 |
< |
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
322 |
> |
which_node = info_->getMolToProc(i); |
323 |
> |
|
324 |
> |
if (which_node != masterNode) { //current molecule is in slave node |
325 |
> |
if (potatoes[which_node] + 1 >= MAXTAG) { |
326 |
> |
// The potato was going to exceed the maximum value, |
327 |
> |
// so wrap this processor potato back to 0: |
328 |
> |
|
329 |
> |
potatoes[which_node] = 0; |
330 |
> |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0, |
331 |
> |
MPI_COMM_WORLD); |
332 |
> |
} |
333 |
> |
|
334 |
> |
myPotato = potatoes[which_node]; |
335 |
> |
|
336 |
> |
//recieve the number of integrableObject in current molecule |
337 |
> |
MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato, |
338 |
> |
MPI_COMM_WORLD, &istatus); |
339 |
> |
myPotato++; |
340 |
> |
|
341 |
> |
for(int l = 0; l < nCurObj; l++) { |
342 |
> |
if (potatoes[which_node] + 2 >= MAXTAG) { |
343 |
> |
// The potato was going to exceed the maximum value, |
344 |
> |
// so wrap this processor potato back to 0: |
345 |
> |
|
346 |
> |
potatoes[which_node] = 0; |
347 |
> |
MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, |
348 |
> |
0, MPI_COMM_WORLD); |
349 |
> |
} |
350 |
> |
|
351 |
> |
MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, |
352 |
> |
which_node, myPotato, MPI_COMM_WORLD, |
353 |
> |
&istatus); |
354 |
|
|
355 |
< |
if(msgLen == 13) |
407 |
< |
isDirectional = 1; |
408 |
< |
else |
409 |
< |
isDirectional = 0; |
410 |
< |
|
411 |
< |
// If we've survived to here, format the line: |
412 |
< |
|
413 |
< |
if (!isDirectional) { |
414 |
< |
|
415 |
< |
sprintf( writeLine, |
416 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
417 |
< |
atomTypeString, |
418 |
< |
atomData[0], |
419 |
< |
atomData[1], |
420 |
< |
atomData[2], |
421 |
< |
atomData[3], |
422 |
< |
atomData[4], |
423 |
< |
atomData[5]); |
424 |
< |
|
425 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
426 |
< |
|
427 |
< |
} |
428 |
< |
else { |
429 |
< |
|
430 |
< |
sprintf( writeLine, |
431 |
< |
"%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", |
432 |
< |
atomTypeString, |
433 |
< |
atomData[0], |
434 |
< |
atomData[1], |
435 |
< |
atomData[2], |
436 |
< |
atomData[3], |
437 |
< |
atomData[4], |
438 |
< |
atomData[5], |
439 |
< |
atomData[6], |
440 |
< |
atomData[7], |
441 |
< |
atomData[8], |
442 |
< |
atomData[9], |
443 |
< |
atomData[10], |
444 |
< |
atomData[11], |
445 |
< |
atomData[12]); |
446 |
< |
|
447 |
< |
} |
448 |
< |
|
449 |
< |
for(k = 0; k < outFile.size(); k++) |
450 |
< |
*outFile[k] << writeLine; |
355 |
> |
myPotato++; |
356 |
|
|
357 |
< |
}// end for(int l =0) |
358 |
< |
potatoes[which_node] = myPotato; |
359 |
< |
|
455 |
< |
} |
456 |
< |
else { |
457 |
< |
|
458 |
< |
haveError = 0; |
459 |
< |
|
460 |
< |
local_index = indexArray[currentIndex].first; |
461 |
< |
|
462 |
< |
integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); |
357 |
> |
MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato, |
358 |
> |
MPI_COMM_WORLD, &istatus); |
359 |
> |
myPotato++; |
360 |
|
|
361 |
< |
for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){ |
465 |
< |
sd = *iter; |
466 |
< |
atomTypeString = sd->getType(); |
467 |
< |
|
468 |
< |
sd->getPos(pos); |
469 |
< |
sd->getVel(vel); |
470 |
< |
|
471 |
< |
atomData[0] = pos[0]; |
472 |
< |
atomData[1] = pos[1]; |
473 |
< |
atomData[2] = pos[2]; |
361 |
> |
MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen); |
362 |
|
|
363 |
< |
atomData[3] = vel[0]; |
364 |
< |
atomData[4] = vel[1]; |
365 |
< |
atomData[5] = vel[2]; |
366 |
< |
|
479 |
< |
isDirectional = 0; |
363 |
> |
if (msgLen == 13) |
364 |
> |
isDirectional = 1; |
365 |
> |
else |
366 |
> |
isDirectional = 0; |
367 |
|
|
368 |
< |
if( sd->isDirectional() ){ |
368 |
> |
// If we've survived to here, format the line: |
369 |
|
|
370 |
< |
isDirectional = 1; |
371 |
< |
|
372 |
< |
sd->getQ( q ); |
373 |
< |
sd->getJ( ji ); |
370 |
> |
if (!isDirectional) { |
371 |
> |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
372 |
> |
MPIatomTypeString, atomData[0], |
373 |
> |
atomData[1], atomData[2], |
374 |
> |
atomData[3], atomData[4], |
375 |
> |
atomData[5]); |
376 |
|
|
377 |
< |
for (int j = 0; j < 6 ; j++) |
378 |
< |
atomData[j] = atomData[j]; |
379 |
< |
|
380 |
< |
atomData[6] = q[0]; |
381 |
< |
atomData[7] = q[1]; |
382 |
< |
atomData[8] = q[2]; |
383 |
< |
atomData[9] = q[3]; |
384 |
< |
|
385 |
< |
atomData[10] = ji[0]; |
386 |
< |
atomData[11] = ji[1]; |
387 |
< |
atomData[12] = ji[2]; |
388 |
< |
} |
389 |
< |
|
390 |
< |
// If we've survived to here, format the line: |
391 |
< |
|
392 |
< |
if (!isDirectional) { |
393 |
< |
|
394 |
< |
sprintf( writeLine, |
395 |
< |
"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
396 |
< |
atomTypeString, |
508 |
< |
atomData[0], |
509 |
< |
atomData[1], |
510 |
< |
atomData[2], |
511 |
< |
atomData[3], |
512 |
< |
atomData[4], |
513 |
< |
atomData[5]); |
514 |
< |
|
515 |
< |
strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); |
516 |
< |
|
517 |
< |
} |
518 |
< |
else { |
519 |
< |
|
520 |
< |
sprintf( writeLine, |
521 |
< |
"%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", |
522 |
< |
atomTypeString, |
523 |
< |
atomData[0], |
524 |
< |
atomData[1], |
525 |
< |
atomData[2], |
526 |
< |
atomData[3], |
527 |
< |
atomData[4], |
528 |
< |
atomData[5], |
529 |
< |
atomData[6], |
530 |
< |
atomData[7], |
531 |
< |
atomData[8], |
532 |
< |
atomData[9], |
533 |
< |
atomData[10], |
534 |
< |
atomData[11], |
535 |
< |
atomData[12]); |
536 |
< |
|
537 |
< |
} |
538 |
< |
|
539 |
< |
for(k = 0; k < outFile.size(); k++) |
540 |
< |
*outFile[k] << writeLine; |
541 |
< |
|
542 |
< |
|
543 |
< |
}//end for(iter = integrableObject.begin()) |
544 |
< |
|
545 |
< |
currentIndex++; |
546 |
< |
} |
377 |
> |
strcat(writeLine, |
378 |
> |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
379 |
> |
} else { |
380 |
> |
sprintf(writeLine, |
381 |
> |
"%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", |
382 |
> |
MPIatomTypeString, |
383 |
> |
atomData[0], |
384 |
> |
atomData[1], |
385 |
> |
atomData[2], |
386 |
> |
atomData[3], |
387 |
> |
atomData[4], |
388 |
> |
atomData[5], |
389 |
> |
atomData[6], |
390 |
> |
atomData[7], |
391 |
> |
atomData[8], |
392 |
> |
atomData[9], |
393 |
> |
atomData[10], |
394 |
> |
atomData[11], |
395 |
> |
atomData[12]); |
396 |
> |
} |
397 |
|
|
398 |
< |
}//end for(i = 0; i < mpiSim->getNmol()) |
549 |
< |
|
550 |
< |
for(k = 0; k < outFile.size(); k++) |
551 |
< |
outFile[k]->flush(); |
552 |
< |
|
553 |
< |
sprintf( checkPointMsg, |
554 |
< |
"Sucessfully took a dump.\n"); |
555 |
< |
|
556 |
< |
MPIcheckPoint(); |
557 |
< |
|
558 |
< |
delete[] potatoes; |
559 |
< |
|
560 |
< |
} else { |
398 |
> |
os << writeLine; |
399 |
|
|
400 |
< |
// worldRank != 0, so I'm a remote node. |
400 |
> |
} // end for(int l =0) |
401 |
|
|
402 |
< |
// Set my magic potato to 0: |
402 |
> |
potatoes[which_node] = myPotato; |
403 |
> |
} else { //master node has current molecule |
404 |
|
|
405 |
< |
myPotato = 0; |
567 |
< |
currentIndex = 0; |
568 |
< |
|
569 |
< |
for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { |
570 |
< |
|
571 |
< |
// Am I the node which has this integrableObject? |
572 |
< |
|
573 |
< |
if (MolToProcMap[i] == worldRank) { |
405 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
406 |
|
|
407 |
+ |
if (mol == NULL) { |
408 |
+ |
sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank); |
409 |
+ |
painCave.isFatal = 1; |
410 |
+ |
simError(); |
411 |
+ |
} |
412 |
+ |
|
413 |
+ |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
414 |
+ |
integrableObject = mol->nextIntegrableObject(ii)) { |
415 |
|
|
416 |
< |
if (myPotato + 1 >= MAXTAG) { |
417 |
< |
|
578 |
< |
// The potato was going to exceed the maximum value, |
579 |
< |
// so wrap this processor potato back to 0 (and block until |
580 |
< |
// node 0 says we can go: |
581 |
< |
|
582 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
583 |
< |
|
584 |
< |
} |
416 |
> |
pos = integrableObject->getPos(); |
417 |
> |
vel = integrableObject->getVel(); |
418 |
|
|
419 |
< |
local_index = indexArray[currentIndex].first; |
420 |
< |
integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects(); |
421 |
< |
|
589 |
< |
nCurObj = integrableObjects.size(); |
590 |
< |
|
591 |
< |
MPI_Send(&nCurObj, 1, MPI_INT, 0, |
592 |
< |
myPotato, MPI_COMM_WORLD); |
593 |
< |
myPotato++; |
419 |
> |
atomData[0] = pos[0]; |
420 |
> |
atomData[1] = pos[1]; |
421 |
> |
atomData[2] = pos[2]; |
422 |
|
|
423 |
< |
for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ |
423 |
> |
atomData[3] = vel[0]; |
424 |
> |
atomData[4] = vel[1]; |
425 |
> |
atomData[5] = vel[2]; |
426 |
|
|
427 |
< |
if (myPotato + 2 >= MAXTAG) { |
598 |
< |
|
599 |
< |
// The potato was going to exceed the maximum value, |
600 |
< |
// so wrap this processor potato back to 0 (and block until |
601 |
< |
// node 0 says we can go: |
602 |
< |
|
603 |
< |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, &istatus); |
604 |
< |
|
605 |
< |
} |
606 |
< |
|
607 |
< |
sd = *iter; |
608 |
< |
|
609 |
< |
atomTypeString = sd->getType(); |
427 |
> |
isDirectional = 0; |
428 |
|
|
429 |
< |
sd->getPos(pos); |
430 |
< |
sd->getVel(vel); |
429 |
> |
if (integrableObject->isDirectional()) { |
430 |
> |
isDirectional = 1; |
431 |
|
|
432 |
< |
atomData[0] = pos[0]; |
433 |
< |
atomData[1] = pos[1]; |
616 |
< |
atomData[2] = pos[2]; |
432 |
> |
q = integrableObject->getQ(); |
433 |
> |
ji = integrableObject->getJ(); |
434 |
|
|
435 |
< |
atomData[3] = vel[0]; |
436 |
< |
atomData[4] = vel[1]; |
437 |
< |
atomData[5] = vel[2]; |
621 |
< |
|
622 |
< |
isDirectional = 0; |
435 |
> |
for(int j = 0; j < 6; j++) { |
436 |
> |
atomData[j] = atomData[j]; |
437 |
> |
} |
438 |
|
|
439 |
< |
if( sd->isDirectional() ){ |
439 |
> |
atomData[6] = q[0]; |
440 |
> |
atomData[7] = q[1]; |
441 |
> |
atomData[8] = q[2]; |
442 |
> |
atomData[9] = q[3]; |
443 |
|
|
444 |
< |
isDirectional = 1; |
445 |
< |
|
446 |
< |
sd->getQ( q ); |
447 |
< |
sd->getJ( ji ); |
448 |
< |
|
444 |
> |
atomData[10] = ji[0]; |
445 |
> |
atomData[11] = ji[1]; |
446 |
> |
atomData[12] = ji[2]; |
447 |
> |
} |
448 |
> |
|
449 |
> |
// If we've survived to here, format the line: |
450 |
> |
|
451 |
> |
if (!isDirectional) { |
452 |
> |
sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", |
453 |
> |
integrableObject->getType().c_str(), atomData[0], |
454 |
> |
atomData[1], atomData[2], |
455 |
> |
atomData[3], atomData[4], |
456 |
> |
atomData[5]); |
457 |
> |
|
458 |
> |
strcat(writeLine, |
459 |
> |
"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n"); |
460 |
> |
} else { |
461 |
> |
sprintf(writeLine, |
462 |
> |
"%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", |
463 |
> |
integrableObject->getType().c_str(), |
464 |
> |
atomData[0], |
465 |
> |
atomData[1], |
466 |
> |
atomData[2], |
467 |
> |
atomData[3], |
468 |
> |
atomData[4], |
469 |
> |
atomData[5], |
470 |
> |
atomData[6], |
471 |
> |
atomData[7], |
472 |
> |
atomData[8], |
473 |
> |
atomData[9], |
474 |
> |
atomData[10], |
475 |
> |
atomData[11], |
476 |
> |
atomData[12]); |
477 |
> |
} |
478 |
> |
|
479 |
> |
|
480 |
> |
os << writeLine; |
481 |
> |
|
482 |
> |
} //end for(iter = integrableObject.begin()) |
483 |
> |
} |
484 |
> |
} //end for(i = 0; i < mpiSim->getNmol()) |
485 |
> |
|
486 |
> |
os.flush(); |
487 |
> |
|
488 |
> |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
489 |
> |
MPIcheckPoint(); |
490 |
> |
|
491 |
> |
delete [] potatoes; |
492 |
> |
} else { |
493 |
> |
|
494 |
> |
// worldRank != 0, so I'm a remote node. |
495 |
> |
|
496 |
> |
// Set my magic potato to 0: |
497 |
> |
|
498 |
> |
myPotato = 0; |
499 |
> |
|
500 |
> |
for(int i = 0; i < info_->getNGlobalMolecules(); i++) { |
501 |
> |
|
502 |
> |
// Am I the node which has this integrableObject? |
503 |
> |
int whichNode = info_->getMolToProc(i); |
504 |
> |
if (whichNode == worldRank) { |
505 |
> |
if (myPotato + 1 >= MAXTAG) { |
506 |
> |
|
507 |
> |
// The potato was going to exceed the maximum value, |
508 |
> |
// so wrap this processor potato back to 0 (and block until |
509 |
> |
// node 0 says we can go: |
510 |
> |
|
511 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
512 |
> |
&istatus); |
513 |
> |
} |
514 |
> |
|
515 |
> |
mol = info_->getMoleculeByGlobalIndex(i); |
516 |
> |
|
517 |
|
|
518 |
< |
atomData[6] = q[0]; |
633 |
< |
atomData[7] = q[1]; |
634 |
< |
atomData[8] = q[2]; |
635 |
< |
atomData[9] = q[3]; |
636 |
< |
|
637 |
< |
atomData[10] = ji[0]; |
638 |
< |
atomData[11] = ji[1]; |
639 |
< |
atomData[12] = ji[2]; |
640 |
< |
} |
518 |
> |
nCurObj = mol->getNIntegrableObjects(); |
519 |
|
|
520 |
< |
|
521 |
< |
strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE); |
520 |
> |
MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD); |
521 |
> |
myPotato++; |
522 |
|
|
523 |
< |
// null terminate the string before sending (just in case): |
524 |
< |
MPIatomTypeString[MINIBUFFERSIZE-1] = '\0'; |
523 |
> |
for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; |
524 |
> |
integrableObject = mol->nextIntegrableObject(ii)) { |
525 |
|
|
526 |
< |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
649 |
< |
myPotato, MPI_COMM_WORLD); |
650 |
< |
|
651 |
< |
myPotato++; |
652 |
< |
|
653 |
< |
if (isDirectional) { |
526 |
> |
if (myPotato + 2 >= MAXTAG) { |
527 |
|
|
528 |
< |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, |
529 |
< |
myPotato, MPI_COMM_WORLD); |
530 |
< |
|
658 |
< |
} else { |
528 |
> |
// The potato was going to exceed the maximum value, |
529 |
> |
// so wrap this processor potato back to 0 (and block until |
530 |
> |
// node 0 says we can go: |
531 |
|
|
532 |
< |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, |
533 |
< |
myPotato, MPI_COMM_WORLD); |
534 |
< |
} |
532 |
> |
MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD, |
533 |
> |
&istatus); |
534 |
> |
} |
535 |
|
|
536 |
< |
myPotato++; |
536 |
> |
pos = integrableObject->getPos(); |
537 |
> |
vel = integrableObject->getVel(); |
538 |
|
|
539 |
< |
} |
539 |
> |
atomData[0] = pos[0]; |
540 |
> |
atomData[1] = pos[1]; |
541 |
> |
atomData[2] = pos[2]; |
542 |
|
|
543 |
< |
currentIndex++; |
544 |
< |
|
545 |
< |
} |
546 |
< |
|
543 |
> |
atomData[3] = vel[0]; |
544 |
> |
atomData[4] = vel[1]; |
545 |
> |
atomData[5] = vel[2]; |
546 |
> |
|
547 |
> |
isDirectional = 0; |
548 |
> |
|
549 |
> |
if (integrableObject->isDirectional()) { |
550 |
> |
isDirectional = 1; |
551 |
> |
|
552 |
> |
q = integrableObject->getQ(); |
553 |
> |
ji = integrableObject->getJ(); |
554 |
> |
|
555 |
> |
atomData[6] = q[0]; |
556 |
> |
atomData[7] = q[1]; |
557 |
> |
atomData[8] = q[2]; |
558 |
> |
atomData[9] = q[3]; |
559 |
> |
|
560 |
> |
atomData[10] = ji[0]; |
561 |
> |
atomData[11] = ji[1]; |
562 |
> |
atomData[12] = ji[2]; |
563 |
> |
} |
564 |
> |
|
565 |
> |
strncpy(MPIatomTypeString, integrableObject->getType().c_str(), MINIBUFFERSIZE); |
566 |
> |
|
567 |
> |
// null terminate the std::string before sending (just in case): |
568 |
> |
MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0'; |
569 |
> |
|
570 |
> |
MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0, |
571 |
> |
myPotato, MPI_COMM_WORLD); |
572 |
> |
|
573 |
> |
myPotato++; |
574 |
> |
|
575 |
> |
if (isDirectional) { |
576 |
> |
MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato, |
577 |
> |
MPI_COMM_WORLD); |
578 |
> |
} else { |
579 |
> |
MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato, |
580 |
> |
MPI_COMM_WORLD); |
581 |
> |
} |
582 |
> |
|
583 |
> |
myPotato++; |
584 |
> |
} |
585 |
> |
|
586 |
> |
} |
587 |
> |
|
588 |
|
} |
589 |
+ |
sprintf(checkPointMsg, "Sucessfully took a dump.\n"); |
590 |
+ |
MPIcheckPoint(); |
591 |
+ |
} |
592 |
|
|
593 |
< |
sprintf( checkPointMsg, |
594 |
< |
"Successfully took a dump.\n"); |
595 |
< |
MPIcheckPoint(); |
593 |
> |
#endif // is_mpi |
594 |
> |
|
595 |
> |
} |
596 |
> |
|
597 |
> |
void DumpWriter::writeDump() { |
598 |
> |
writeFrame(*dumpFile_); |
599 |
> |
} |
600 |
> |
|
601 |
> |
void DumpWriter::writeEor() { |
602 |
> |
std::ostream* eorStream; |
603 |
|
|
604 |
+ |
#ifdef IS_MPI |
605 |
+ |
if (worldRank == 0) { |
606 |
+ |
#endif // is_mpi |
607 |
+ |
|
608 |
+ |
eorStream = createOStream(eorFilename_); |
609 |
+ |
|
610 |
+ |
#ifdef IS_MPI |
611 |
+ |
} |
612 |
+ |
#endif // is_mpi |
613 |
+ |
|
614 |
+ |
writeFrame(*eorStream); |
615 |
+ |
|
616 |
+ |
#ifdef IS_MPI |
617 |
+ |
if (worldRank == 0) { |
618 |
+ |
#endif // is_mpi |
619 |
+ |
delete eorStream; |
620 |
+ |
|
621 |
+ |
#ifdef IS_MPI |
622 |
+ |
} |
623 |
+ |
#endif // is_mpi |
624 |
+ |
|
625 |
|
} |
626 |
< |
|
626 |
> |
|
627 |
> |
|
628 |
> |
void DumpWriter::writeDumpAndEor() { |
629 |
> |
std::vector<std::streambuf*> buffers; |
630 |
> |
std::ostream* eorStream; |
631 |
> |
#ifdef IS_MPI |
632 |
> |
if (worldRank == 0) { |
633 |
|
#endif // is_mpi |
681 |
– |
} |
634 |
|
|
635 |
+ |
buffers.push_back(dumpFile_->rdbuf()); |
636 |
+ |
|
637 |
+ |
eorStream = createOStream(eorFilename_); |
638 |
+ |
|
639 |
+ |
buffers.push_back(eorStream->rdbuf()); |
640 |
+ |
|
641 |
|
#ifdef IS_MPI |
642 |
+ |
} |
643 |
+ |
#endif // is_mpi |
644 |
|
|
645 |
< |
// a couple of functions to let us escape the write loop |
645 |
> |
TeeBuf tbuf(buffers.begin(), buffers.end()); |
646 |
> |
std::ostream os(&tbuf); |
647 |
|
|
648 |
< |
void dWrite::DieDieDie( void ){ |
648 |
> |
writeFrame(os); |
649 |
|
|
650 |
< |
MPI_Finalize(); |
651 |
< |
exit (0); |
650 |
> |
#ifdef IS_MPI |
651 |
> |
if (worldRank == 0) { |
652 |
> |
#endif // is_mpi |
653 |
> |
delete eorStream; |
654 |
> |
|
655 |
> |
#ifdef IS_MPI |
656 |
> |
} |
657 |
> |
#endif // is_mpi |
658 |
> |
|
659 |
> |
} |
660 |
> |
|
661 |
> |
std::ostream* DumpWriter::createOStream(const std::string& filename) { |
662 |
> |
std::ostream* newOStream; |
663 |
> |
if (needCompression_) { |
664 |
> |
newOStream = new ogzstream(filename.c_str()); |
665 |
> |
} else { |
666 |
> |
newOStream = new std::ofstream(filename.c_str()); |
667 |
> |
} |
668 |
> |
return newOStream; |
669 |
|
} |
670 |
|
|
671 |
< |
#endif //is_mpi |
671 |
> |
}//end namespace oopse |