src/parallel/Communicator.hpp

/**
 * @file Communicator.hpp
 * @author Charles Vardeman <cvardema.at.nd.edu>
 * @date 08/18/2010
 * @time 11:56am
 * @version 1.0
 *
 * @section LICENSE
 * Copyright (c) 2010 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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */

#ifndef PARALLEL_COMMUNICATOR_HPP
#define PARALLEL_COMMUNICATOR_HPP

#include <config.h>
#include <mpi.h>
#include "math/SquareMatrix3.hpp"

using namespace std;
namespace OpenMD{
  
#ifdef IS_MPI

  enum communicatorType {
    Global = 0,
    Row = 1,
    Column = 2
  };
    
  template<class T>
  class MPITraits {
  public:
    static MPI::Datatype Type();
    static int Length() { return 1; };
  };
  
  template<> inline MPI::Datatype MPITraits<int>::Type() { return MPI_INT; }
  template<> inline MPI::Datatype MPITraits<RealType>::Type() { return MPI_REALTYPE; }

  template<class T, unsigned int Dim>
  class MPITraits< Vector<T, Dim> > {
  public:
    static MPI::Datatype Type() { return MPITraits<T>::Type(); }
    static int Length() {return Dim;}
  };

  template<class T>
  class MPITraits< Vector3<T> > {
  public:
    static MPI::Datatype Type() { return MPITraits<T>::Type(); }
    static int Length() {return 3;}
  };

  template<class T, unsigned int Row, unsigned int Col>
  class MPITraits< RectMatrix<T, Row, Col> > {
  public:
    static MPI::Datatype Type() { return MPITraits<T>::Type(); }
    static int Length() {return Row * Col;}
  };

  template<class T>
  class MPITraits< SquareMatrix3<T> > {
  public:
    static MPI::Datatype Type() { return MPITraits<T>::Type(); }
    static int Length() {return 9;}
  };
  
  
  template<communicatorType D, typename T>
  class Communicator { 
  public: 
    
    Communicator<D, T>(int nObjects) {
      
      int nProc = MPI::COMM_WORLD.Get_size();
      int myRank = MPI::COMM_WORLD.Get_rank();

      int nColumnsMax = (int) sqrt(RealType(nProc));

      int nColumns;
      for (int i = 1; i < nColumnsMax + 1; i++) {
        if (nProc % i == 0) nColumns = i;        
      }
        
      int nRows = nProc / nColumns;
      rowIndex_ = myRank / nColumns;      
      columnIndex_ = myRank % nColumns;

      switch(D) {
      case Row :
        myComm = MPI::COMM_WORLD.Split(rowIndex_, 0);
        break;
      case Column:
        myComm = MPI::COMM_WORLD.Split(columnIndex_, 0);
        break;
      case Global:
        myComm = MPI::COMM_WORLD.Split(myRank, 0);
      }
         
      int nCommProcs = myComm.Get_size();

      counts.resize(nCommProcs, 0);
      displacements.resize(nCommProcs, 0);

      planSize_ = MPITraits<T>::Length() * nObjects; 

      myComm.Allgather(&planSize_, 1, MPI::INT, &counts[0], 1, MPI::INT);

      displacements[0] = 0;
      for (int i = 1; i < nCommProcs; i++) {
        displacements[i] = displacements[i-1] + counts[i-1];
      }

      size_ = 0;
      for (int i = 0; i < nCommProcs; i++) {
        size_ += counts[i];
      }
    }

    
    void gather(vector<T>& v1, vector<T>& v2) {

      // an assert would be helpful here to make sure the vectors are the
      // correct geometry
      
      myComm.Allgatherv(&v1[0], 
                        planSize_, 
                        MPITraits<T>::Type(), 
                        &v2[0], 
                        &counts[0], 
                        &displacements[0], 
                        MPITraits<T>::Type());      
    }
    
    
    
    void scatter(vector<T>& v1, vector<T>& v2) {
      // an assert would be helpful here to make sure the vectors are the
      // correct geometry
      
      myComm.Reduce_scatter(&v1[0], &v2[0], &counts[0], 
                            MPITraits<T>::Type(), MPI::SUM);
    }
    
    int getSize() {
      return size_;
    }
    
  private:
    int planSize_;     ///< how many are on local proc
    int rowIndex_;
    int columnIndex_;
    int size_;
    vector<int> counts;
    vector<int> displacements;
    MPI::Intracomm myComm;
  }; 

#endif
}
#endif


Revision:	1589
Committed:	Sun Jul 10 16:05:34 2011 UTC (13 years, 9 months ago) by gezelter
File size:	5965 byte(s)
Log Message:	Fixing some parallel bugs
#	User	Rev	Content
1	gezelter	1539	/**
2			* @file Communicator.hpp
3			* @author Charles Vardeman <cvardema.at.nd.edu>
4			* @date 08/18/2010
5			* @time 11:56am
6			* @version 1.0
7			*
8			* @section LICENSE
9			* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
10			*
11			* The University of Notre Dame grants you ("Licensee") a
12			* non-exclusive, royalty free, license to use, modify and
13			* redistribute this software in source and binary code form, provided
14			* that the following conditions are met:
15			*
16			* 1. Redistributions of source code must retain the above copyright
17			* notice, this list of conditions and the following disclaimer.
18			*
19			* 2. Redistributions in binary form must reproduce the above copyright
20			* notice, this list of conditions and the following disclaimer in the
21			* documentation and/or other materials provided with the
22			* distribution.
23			*
24			* This software is provided "AS IS," without a warranty of any
25			* kind. All express or implied conditions, representations and
26			* warranties, including any implied warranty of merchantability,
27			* fitness for a particular purpose or non-infringement, are hereby
28			* excluded. The University of Notre Dame and its licensors shall not
29			* be liable for any damages suffered by licensee as a result of
30			* using, modifying or distributing the software or its
31			* derivatives. In no event will the University of Notre Dame or its
32			* licensors be liable for any lost revenue, profit or data, or for
33			* direct, indirect, special, consequential, incidental or punitive
34			* damages, however caused and regardless of the theory of liability,
35			* arising out of the use of or inability to use software, even if the
36			* University of Notre Dame has been advised of the possibility of
37			* such damages.
38			*
39			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
40			* research, please cite the appropriate papers when you publish your
41			* work. Good starting points are:
42			*
43			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
44			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
45			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
46			* [4] Vardeman & Gezelter, in progress (2009).
47			*/
48
49	gezelter	1544	#ifndef PARALLEL_COMMUNICATOR_HPP
50			#define PARALLEL_COMMUNICATOR_HPP
51	gezelter	1539
52			#include <config.h>
53			#include <mpi.h>
54			#include "math/SquareMatrix3.hpp"
55
56	gezelter	1551	using namespace std;
57	gezelter	1539	namespace OpenMD{
58
59			#ifdef IS_MPI
60
61	gezelter	1549	enum communicatorType {
62			Global = 0,
63			Row = 1,
64			Column = 2
65	gezelter	1539	};
66
67	gezelter	1551	template<class T>
68			class MPITraits {
69			public:
70			static MPI::Datatype Type();
71			static int Length() { return 1; };
72	gezelter	1539	};
73
74	gezelter	1551	template<> inline MPI::Datatype MPITraits<int>::Type() { return MPI_INT; }
75			template<> inline MPI::Datatype MPITraits<RealType>::Type() { return MPI_REALTYPE; }
76
77			template<class T, unsigned int Dim>
78			class MPITraits< Vector<T, Dim> > {
79			public:
80			static MPI::Datatype Type() { return MPITraits<T>::Type(); }
81			static int Length() {return Dim;}
82			};
83
84			template<class T>
85			class MPITraits< Vector3<T> > {
86			public:
87			static MPI::Datatype Type() { return MPITraits<T>::Type(); }
88			static int Length() {return 3;}
89			};
90
91			template<class T, unsigned int Row, unsigned int Col>
92			class MPITraits< RectMatrix<T, Row, Col> > {
93			public:
94			static MPI::Datatype Type() { return MPITraits<T>::Type(); }
95			static int Length() {return Row * Col;}
96			};
97
98			template<class T>
99			class MPITraits< SquareMatrix3<T> > {
100			public:
101			static MPI::Datatype Type() { return MPITraits<T>::Type(); }
102			static int Length() {return 9;}
103			};
104	gezelter	1539
105	gezelter	1551
106	gezelter	1549	template<communicatorType D, typename T>
107	gezelter	1540	class Communicator {
108	gezelter	1539	public:
109
110	gezelter	1540	Communicator<D, T>(int nObjects) {
111	gezelter	1539
112			int nProc = MPI::COMM_WORLD.Get_size();
113			int myRank = MPI::COMM_WORLD.Get_rank();
114
115			int nColumnsMax = (int) sqrt(RealType(nProc));
116
117			int nColumns;
118			for (int i = 1; i < nColumnsMax + 1; i++) {
119			if (nProc % i == 0) nColumns = i;
120			}
121
122			int nRows = nProc / nColumns;
123			rowIndex_ = myRank / nColumns;
124			columnIndex_ = myRank % nColumns;
125
126	gezelter	1549	switch(D) {
127			case Row :
128	gezelter	1539	myComm = MPI::COMM_WORLD.Split(rowIndex_, 0);
129	gezelter	1549	break;
130			case Column:
131	gezelter	1539	myComm = MPI::COMM_WORLD.Split(columnIndex_, 0);
132	gezelter	1549	break;
133			case Global:
134			myComm = MPI::COMM_WORLD.Split(myRank, 0);
135	gezelter	1539	}
136
137			int nCommProcs = myComm.Get_size();
138
139	gezelter	1589	counts.resize(nCommProcs, 0);
140			displacements.resize(nCommProcs, 0);
141	gezelter	1539
142	gezelter	1551	planSize_ = MPITraits<T>::Length() * nObjects;
143	gezelter	1539
144			myComm.Allgather(&planSize_, 1, MPI::INT, &counts[0], 1, MPI::INT);
145
146			displacements[0] = 0;
147			for (int i = 1; i < nCommProcs; i++) {
148			displacements[i] = displacements[i-1] + counts[i-1];
149	gezelter	1541	}
150
151			size_ = 0;
152			for (int i = 0; i < nCommProcs; i++) {
153			size_ += counts[i];
154			}
155	gezelter	1539	}
156
157	gezelter	1551
158			void gather(vector<T>& v1, vector<T>& v2) {
159	gezelter	1589
160			// an assert would be helpful here to make sure the vectors are the
161			// correct geometry
162
163	gezelter	1539	myComm.Allgatherv(&v1[0],
164			planSize_,
165	gezelter	1551	MPITraits<T>::Type(),
166	gezelter	1539	&v2[0],
167			&counts[0],
168			&displacements[0],
169	gezelter	1551	MPITraits<T>::Type());
170	gezelter	1539	}
171
172	gezelter	1551
173
174			void scatter(vector<T>& v1, vector<T>& v2) {
175	gezelter	1589	// an assert would be helpful here to make sure the vectors are the
176			// correct geometry
177	gezelter	1551
178	gezelter	1539	myComm.Reduce_scatter(&v1[0], &v2[0], &counts[0],
179	gezelter	1551	MPITraits<T>::Type(), MPI::SUM);
180	gezelter	1539	}
181	gezelter	1551
182	gezelter	1541	int getSize() {
183			return size_;
184			}
185	gezelter	1539
186			private:
187			int planSize_; ///< how many are on local proc
188			int rowIndex_;
189			int columnIndex_;
190	gezelter	1541	int size_;
191	gezelter	1551	vector<int> counts;
192			vector<int> displacements;
193	gezelter	1539	MPI::Intracomm myComm;
194			};
195
196			#endif
197			}
198			#endif
199
200