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 <algorithm>
#include <iostream>
#include <map>

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


namespace oopse {
  RestWriter::RestWriter(SimInfo* info) : 
    info_(info) {

    // only the master node writes to the disk
#ifdef IS_MPI
    if (worldRank == 0) {
#endif // is_mpi

      outName = info_->getRestFileName();

#ifdef IS_MPI
    }
#endif // is_mpi
  }
  
  RestWriter::~RestWriter() {}
  
  void RestWriter::writeZangle(){
    const int BUFFERSIZE = 2000;
    char tempBuffer[BUFFERSIZE];
    char writeLine[BUFFERSIZE];
    
    std::ofstream finalOut;
    
    Molecule* mol;
    StuntDouble* integrableObject;
    SimInfo::MoleculeIterator mi;
    Molecule::IntegrableObjectIterator ii;

#ifdef IS_MPI
    if(worldRank == 0 ){
#endif    
      finalOut.open( outName.c_str(), std::ios::out | std::ios::trunc );
      if( !finalOut ){
        sprintf( painCave.errMsg,
                 "Could not open \"%s\" for zAngle output.\n",
                 outName.c_str() );
        painCave.isFatal = 1;
        simError();
      }
#ifdef IS_MPI
    }
#endif // is_mpi
    
#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;
    int myNode = worldRank;
    std::vector<int> tmpNIntObjects(nproc, 0);
    std::vector<int> nIntObjectsInProc(nproc, 0);
    tmpNIntObjects[myNode] = info_->getNGlobalIntegrableObjects();
    
    //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
    MPI_Allreduce(&tmpNIntObjects[0], &nIntObjectsInProc[0], nproc, MPI_INT,
                  MPI_SUM, MPI_COMM_WORLD);
    
    MPI_Status ierr;
    int intObIndex;
    RealType zAngle;
   
    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 {
          for (mol = info_->beginMolecule(mi); mol != NULL; 
               mol = info_->nextMolecule(mi)) {
            
            for (integrableObject = mol->beginIntegrableObject(ii); 
                 integrableObject != NULL; 
                 integrableObject = mol->nextIntegrableObject(ii)) { 
              
              MPI_Recv(&intObIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
              MPI_Recv(&zAngle, 1, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr);
              zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle));
            }
          }
        }
      }
      
      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;      
      }

      finalOut.close();
      
    } else {
      for(int j = 1; j < nproc; ++j) {
        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();

            MPI_Send(&intObIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
            MPI_Send(&zAngle, 1, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
          }
        }
      }
    }

#endif
  }
  
}
Revision:	990
Committed:	Mon Jun 19 01:36:06 2006 UTC (18 years, 10 months ago) by chrisfen
File size:	6824 byte(s)
Log Message:	fixes for mpi thermodynamic integration, close to fully working...
#	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			#include <algorithm>
43			#include <iostream>
44			#include <map>
45
46			#include "primitives/Molecule.hpp"
47			#include "io/RestWriter.hpp"
48			#include "utils/simError.h"
49
50
51			namespace oopse {
52			RestWriter::RestWriter(SimInfo* info) :
53	gezelter	507	info_(info) {
54	chrisfen	990
55			// only the master node writes to the disk
56			#ifdef IS_MPI
57			if (worldRank == 0) {
58			#endif // is_mpi
59
60	gezelter	507	outName = info_->getRestFileName();
61	chrisfen	990
62			#ifdef IS_MPI
63	gezelter	507	}
64	chrisfen	990	#endif // is_mpi
65			}
66	chrisfen	417
67			RestWriter::~RestWriter() {}
68
69			void RestWriter::writeZangle(){
70			const int BUFFERSIZE = 2000;
71			char tempBuffer[BUFFERSIZE];
72			char writeLine[BUFFERSIZE];
73
74			std::ofstream finalOut;
75
76			Molecule* mol;
77			StuntDouble* integrableObject;
78			SimInfo::MoleculeIterator mi;
79			Molecule::IntegrableObjectIterator ii;
80	chrisfen	990
81	chrisfen	417	#ifdef IS_MPI
82			if(worldRank == 0 ){
83			#endif
84			finalOut.open( outName.c_str(), std::ios::out \| std::ios::trunc );
85			if( !finalOut ){
86			sprintf( painCave.errMsg,
87			"Could not open \"%s\" for zAngle output.\n",
88	chrisfen	423	outName.c_str() );
89	chrisfen	417	painCave.isFatal = 1;
90			simError();
91			}
92			#ifdef IS_MPI
93			}
94			#endif // is_mpi
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			strcpy( writeLine, tempBuffer );
113
114			finalOut << writeLine;
115			}
116
117			}
118
119			#else
120			int nproc;
121			MPI_Comm_size(MPI_COMM_WORLD, &nproc);
122			const int masterNode = 0;
123			int myNode = worldRank;
124			std::vector<int> tmpNIntObjects(nproc, 0);
125			std::vector<int> nIntObjectsInProc(nproc, 0);
126			tmpNIntObjects[myNode] = info_->getNGlobalIntegrableObjects();
127
128			//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups
129			MPI_Allreduce(&tmpNIntObjects[0], &nIntObjectsInProc[0], nproc, MPI_INT,
130			MPI_SUM, MPI_COMM_WORLD);
131
132			MPI_Status ierr;
133			int intObIndex;
134	tim	963	RealType zAngle;
135	chrisfen	423
136	chrisfen	990	if (worldRank == masterNode) {
137	tim	963	std::map<int, RealType> zAngData;
138	chrisfen	417	for(int i = 0 ; i < nproc; ++i) {
139			if (i == masterNode) {
140			for (mol = info_->beginMolecule(mi); mol != NULL;
141			mol = info_->nextMolecule(mi)) {
142
143			for (integrableObject = mol->beginIntegrableObject(ii);
144			integrableObject != NULL;
145			integrableObject = mol->nextIntegrableObject(ii)) {
146
147	chrisfen	990	intObIndex = integrableObject->getGlobalIndex();
148
149	chrisfen	417	zAngle = integrableObject->getZangle();
150	tim	963	zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle));
151	chrisfen	417	}
152			}
153			} else {
154	chrisfen	990	for (mol = info_->beginMolecule(mi); mol != NULL;
155			mol = info_->nextMolecule(mi)) {
156
157			for (integrableObject = mol->beginIntegrableObject(ii);
158			integrableObject != NULL;
159			integrableObject = mol->nextIntegrableObject(ii)) {
160
161			MPI_Recv(&intObIndex, 1, MPI_INT, i, 0, MPI_COMM_WORLD,&ierr);
162			MPI_Recv(&zAngle, 1, MPI_REALTYPE, i, 0, MPI_COMM_WORLD,&ierr);
163			zAngData.insert(std::pair<int, RealType>(intObIndex, zAngle));
164			}
165			}
166	chrisfen	417	}
167			}
168
169			finalOut
170			<< info_->getSnapshotManager()->getCurrentSnapshot()->getTime()
171			<< " : omega values at this time\n";
172
173	tim	963	std::map<int, RealType>::iterator l;
174	chrisfen	417	for (l = zAngData.begin(); l != zAngData.end(); ++l) {
175	chrisfen	990	sprintf( tempBuffer,
176			"%14.10lf\n",
177			l->second);
178			strcpy( writeLine, tempBuffer );
179
180			finalOut << writeLine;
181	chrisfen	417	}
182	chrisfen	990
183			finalOut.close();
184	chrisfen	417
185			} else {
186	chrisfen	990	for(int j = 1; j < nproc; ++j) {
187			for (mol = info_->beginMolecule(mi); mol != NULL;
188			mol = info_->nextMolecule(mi)) {
189
190			for (integrableObject = mol->beginIntegrableObject(ii);
191			integrableObject != NULL;
192			integrableObject = mol->nextIntegrableObject(ii)) {
193			intObIndex = integrableObject->getGlobalIndex();
194			zAngle = integrableObject->getZangle();
195
196			MPI_Send(&intObIndex, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD);
197			MPI_Send(&zAngle, 1, MPI_REALTYPE, masterNode, 0, MPI_COMM_WORLD);
198			}
199			}
200	chrisfen	417	}
201			}
202	chrisfen	990
203	chrisfen	417	#endif
204			}
205
206			}