src/io/RestWriter.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */

#include "io/RestWriter.hpp"
#include "primitives/Molecule.hpp"
#include "utils/simError.h"
#include "io/basic_teebuf.hpp"

#ifdef IS_MPI
#include <mpi.h>
#define TAKE_THIS_TAG_INT 1
#define TAKE_THIS_TAG_REAL 2
#endif //is_mpi

namespace oopse {
  RestWriter::RestWriter(SimInfo* info) : 
    info_(info), outName_(info_->getRestFileName()) {
  }
  
  RestWriter::~RestWriter() {}
  
  void RestWriter::writeZAngFile() {
    std::ostream* zangStream;
    
#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi
      
      zangStream = new std::ofstream(outName_.c_str());
      
#ifdef IS_MPI
    }
#endif // is_mpi    
    
    writeZangle(*zangStream);
    
#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi
      delete zangStream;
      
#ifdef IS_MPI
    }
#endif // is_mpi  
    
  }

  void RestWriter::writeZangle(std::ostream& finalOut){
    const int BUFFERSIZE = 2000;
    char tempBuffer[BUFFERSIZE];
    char writeLine[BUFFERSIZE];
    
    Molecule* mol;
    StuntDouble* integrableObject;
    SimInfo::MoleculeIterator mi;
    Molecule::IntegrableObjectIterator ii;
    
#ifndef IS_MPI
    // first we do output for the single processor version
    finalOut
      << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
      << " : omega values at this time\n";
    
    for (mol = info_->beginMolecule(mi); mol != NULL; 
         mol = info_->nextMolecule(mi)) {
      
      for (integrableObject = mol->beginIntegrableObject(ii); 
           integrableObject != NULL; 
           integrableObject = mol->nextIntegrableObject(ii)) {    
        
        sprintf( tempBuffer,
                 "%14.10lf\n",
                 integrableObject->getZangle());
        strcpy( writeLine, tempBuffer );    
        
        finalOut << writeLine;

      }
    }
    
#else
    int nproc;
    MPI_Comm_size(MPI_COMM_WORLD, &nproc);
    const int masterNode = 0;
    
    MPI_Status ierr;
    int intObIndex;
    int vecLength;
    RealType zAngle;
    std::vector<int> gIndex;
    std::vector<RealType> zValues;

    if (worldRank == masterNode) {
      std::map<int, RealType> zAngData;
      for(int i = 0 ; i < nproc; ++i) {
        if (i == masterNode) {
          for (mol = info_->beginMolecule(mi); mol != NULL; 
               mol = info_->nextMolecule(mi)) {
            
            for (integrableObject = mol->beginIntegrableObject(ii); 
                 integrableObject != NULL; 
                 integrableObject = mol->nextIntegrableObject(ii)) { 
              
              intObIndex = integrableObject->getGlobalIndex();

              zAngle = integrableObject->getZangle();
              zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle));
            }      
          }
        } else {
          MPI_Recv(&vecLength, 1, MPI_INT, i, 
                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &ierr);
          // make sure the vectors are the right size for the incoming data
          gIndex.resize(vecLength);
          zValues.resize(vecLength);

          MPI_Recv(&gIndex[0], vecLength, MPI_INT, i, 
                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &ierr);
          MPI_Recv(&zValues[0], vecLength, MPI_REALTYPE, i, 
                   TAKE_THIS_TAG_REAL, MPI_COMM_WORLD, &ierr);
          
          for (int k = 0; k < vecLength; k++){
            zAngData.insert(std::pair<int, RealType>(gIndex[k], zValues[k]));
          }
          gIndex.clear();
          zValues.clear();
        }
      }
      
      finalOut << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
               << " : omega values at this time\n";
      
      std::map<int, RealType>::iterator l;
      for (l = zAngData.begin(); l != zAngData.end(); ++l) {

        sprintf( tempBuffer,
                 "%14.10lf\n",
                 l->second);
        strcpy( writeLine, tempBuffer );
        
        finalOut << writeLine;      
      }
      
    } else {
      // pack up and send the appropriate info to the master node
      for(int j = 1; j < nproc; ++j) {
        if (worldRank == j) {
          for (mol = info_->beginMolecule(mi); mol != NULL; 
               mol = info_->nextMolecule(mi)) {
            
            for (integrableObject = mol->beginIntegrableObject(ii); 
                 integrableObject != NULL; 
                 integrableObject = mol->nextIntegrableObject(ii)) { 
              
              // build a vector of the indicies 
              intObIndex = integrableObject->getGlobalIndex();
              gIndex.push_back(intObIndex);
                     
              // build a vector of the zAngle values
              zAngle = integrableObject->getZangle();
              zValues.push_back(zAngle);

            }      
          }

          // let's send these vectors to the master node so that it
          // can sort them and write to the disk
          vecLength = gIndex.size();

          MPI_Send(&vecLength, 1, MPI_INT, masterNode, 
                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
          MPI_Send(&gIndex[0], vecLength, MPI_INT, masterNode, 
                   TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
          MPI_Send(&zValues[0], vecLength, MPI_REALTYPE, masterNode, 
                   TAKE_THIS_TAG_REAL, MPI_COMM_WORLD);
        
        }
      }
    }

#endif
  }
  
}
Revision:	993
Committed:	Thu Jun 22 15:21:01 2006 UTC (19 years, 4 months ago) by chrisfen
File size:	7005 byte(s)
Log Message:	MPI thermodynamic integration works now.
#	User	Rev	Content
1	gezelter	507	/*
2	chrisfen	417	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	chrisfen	993	#include "io/RestWriter.hpp"
43	chrisfen	417	#include "primitives/Molecule.hpp"
44			#include "utils/simError.h"
45	chrisfen	993	#include "io/basic_teebuf.hpp"
46	chrisfen	417
47	chrisfen	993	#ifdef IS_MPI
48			#include <mpi.h>
49			#define TAKE_THIS_TAG_INT 1
50			#define TAKE_THIS_TAG_REAL 2
51			#endif //is_mpi
52	chrisfen	417
53			namespace oopse {
54			RestWriter::RestWriter(SimInfo* info) :
55	chrisfen	993	info_(info), outName_(info_->getRestFileName()) {
56			}
57
58			RestWriter::~RestWriter() {}
59
60			void RestWriter::writeZAngFile() {
61			std::ostream* zangStream;
62
63	chrisfen	990	#ifdef IS_MPI
64			if (worldRank == 0) {
65			#endif // is_mpi
66	chrisfen	993
67			zangStream = new std::ofstream(outName_.c_str());
68
69	chrisfen	990	#ifdef IS_MPI
70	gezelter	507	}
71	chrisfen	993	#endif // is_mpi
72
73			writeZangle(*zangStream);
74
75			#ifdef IS_MPI
76			if (worldRank == 0) {
77	chrisfen	990	#endif // is_mpi
78	chrisfen	993	delete zangStream;
79
80			#ifdef IS_MPI
81			}
82			#endif // is_mpi
83
84	chrisfen	990	}
85	chrisfen	993
86			void RestWriter::writeZangle(std::ostream& finalOut){
87	chrisfen	417	const int BUFFERSIZE = 2000;
88			char tempBuffer[BUFFERSIZE];
89			char writeLine[BUFFERSIZE];
90
91			Molecule* mol;
92			StuntDouble* integrableObject;
93			SimInfo::MoleculeIterator mi;
94			Molecule::IntegrableObjectIterator ii;
95
96			#ifndef IS_MPI
97			// first we do output for the single processor version
98			finalOut
99			<< info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
100			<< " : omega values at this time\n";
101
102			for (mol = info_->beginMolecule(mi); mol != NULL;
103			mol = info_->nextMolecule(mi)) {
104
105			for (integrableObject = mol->beginIntegrableObject(ii);
106			integrableObject != NULL;
107			integrableObject = mol->nextIntegrableObject(ii)) {
108
109			sprintf( tempBuffer,
110			"%14.10lf\n",
111			integrableObject->getZangle());
112	chrisfen	993	strcpy( writeLine, tempBuffer );
113
114			finalOut << writeLine;
115
116	chrisfen	417	}
117			}
118
119			#else
120			int nproc;
121			MPI_Comm_size(MPI_COMM_WORLD, &nproc);
122			const int masterNode = 0;
123
124			MPI_Status ierr;
125			int intObIndex;
126	chrisfen	993	int vecLength;
127	tim	963	RealType zAngle;
128	chrisfen	993	std::vector<int> gIndex;
129			std::vector<RealType> zValues;
130
131	chrisfen	990	if (worldRank == masterNode) {
132	tim	963	std::map<int, RealType> zAngData;
133	chrisfen	417	for(int i = 0 ; i < nproc; ++i) {
134			if (i == masterNode) {
135			for (mol = info_->beginMolecule(mi); mol != NULL;
136			mol = info_->nextMolecule(mi)) {
137
138			for (integrableObject = mol->beginIntegrableObject(ii);
139			integrableObject != NULL;
140			integrableObject = mol->nextIntegrableObject(ii)) {
141
142	chrisfen	990	intObIndex = integrableObject->getGlobalIndex();
143
144	chrisfen	417	zAngle = integrableObject->getZangle();
145	tim	963	zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle));
146	chrisfen	417	}
147			}
148			} else {
149	chrisfen	993	MPI_Recv(&vecLength, 1, MPI_INT, i,
150			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &ierr);
151			// make sure the vectors are the right size for the incoming data
152			gIndex.resize(vecLength);
153			zValues.resize(vecLength);
154
155			MPI_Recv(&gIndex[0], vecLength, MPI_INT, i,
156			TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &ierr);
157			MPI_Recv(&zValues[0], vecLength, MPI_REALTYPE, i,
158			TAKE_THIS_TAG_REAL, MPI_COMM_WORLD, &ierr);
159
160			for (int k = 0; k < vecLength; k++){
161			zAngData.insert(std::pair<int, RealType>(gIndex[k], zValues[k]));
162	chrisfen	990	}
163	chrisfen	993	gIndex.clear();
164			zValues.clear();
165	chrisfen	417	}
166			}
167
168	chrisfen	993	finalOut << info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
169			<< " : omega values at this time\n";
170	chrisfen	417
171	tim	963	std::map<int, RealType>::iterator l;
172	chrisfen	417	for (l = zAngData.begin(); l != zAngData.end(); ++l) {
173	chrisfen	993
174	chrisfen	990	sprintf( tempBuffer,
175			"%14.10lf\n",
176			l->second);
177			strcpy( writeLine, tempBuffer );
178
179			finalOut << writeLine;
180	chrisfen	417	}
181
182			} else {
183	chrisfen	993	// pack up and send the appropriate info to the master node
184	chrisfen	990	for(int j = 1; j < nproc; ++j) {
185	chrisfen	993	if (worldRank == j) {
186			for (mol = info_->beginMolecule(mi); mol != NULL;
187			mol = info_->nextMolecule(mi)) {
188
189			for (integrableObject = mol->beginIntegrableObject(ii);
190			integrableObject != NULL;
191			integrableObject = mol->nextIntegrableObject(ii)) {
192
193			// build a vector of the indicies
194			intObIndex = integrableObject->getGlobalIndex();
195			gIndex.push_back(intObIndex);
196
197			// build a vector of the zAngle values
198			zAngle = integrableObject->getZangle();
199			zValues.push_back(zAngle);
200	chrisfen	990
201	chrisfen	993	}
202	chrisfen	990	}
203	chrisfen	993
204			// let's send these vectors to the master node so that it
205			// can sort them and write to the disk
206			vecLength = gIndex.size();
207
208			MPI_Send(&vecLength, 1, MPI_INT, masterNode,
209			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
210			MPI_Send(&gIndex[0], vecLength, MPI_INT, masterNode,
211			TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
212			MPI_Send(&zValues[0], vecLength, MPI_REALTYPE, masterNode,
213			TAKE_THIS_TAG_REAL, MPI_COMM_WORLD);
214
215	chrisfen	990	}
216	chrisfen	417	}
217			}
218	chrisfen	990
219	chrisfen	417	#endif
220			}
221
222			}