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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

#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>
  class Communicator { 
  public: 
    
    Communicator<D>() {
      
      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);
      }

    }
    
    MPI::Intracomm getComm() { return myComm; }
    
  private:
    int rowIndex_;
    int columnIndex_;
    MPI::Intracomm myComm;
  };
  

  template<typename T>
  class Plan {
  public:
    
    Plan<T>(MPI::Intracomm comm, int nObjects) {
      myComm = comm;
      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 size_;
    vector<int> counts;
    vector<int> displacements;
    MPI::Intracomm myComm;
  }; 

#endif
}
#endif


Revision:	1798
Committed:	Thu Sep 13 14:10:11 2012 UTC (12 years, 7 months ago) by gezelter
File size:	6270 byte(s)
Log Message:	Merged trunk changes into the development branch
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
47			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
48	gezelter	1539	*/
49
50	gezelter	1544	#ifndef PARALLEL_COMMUNICATOR_HPP
51			#define PARALLEL_COMMUNICATOR_HPP
52	gezelter	1539
53			#include <config.h>
54			#include <mpi.h>
55			#include "math/SquareMatrix3.hpp"
56
57	gezelter	1551	using namespace std;
58	gezelter	1539	namespace OpenMD{
59
60			#ifdef IS_MPI
61
62	gezelter	1549	enum communicatorType {
63			Global = 0,
64			Row = 1,
65			Column = 2
66	gezelter	1539	};
67
68	gezelter	1551	template<class T>
69			class MPITraits {
70			public:
71			static MPI::Datatype Type();
72			static int Length() { return 1; };
73	gezelter	1539	};
74
75	gezelter	1798	template<> inline MPI::Datatype MPITraits<int>::Type() { return MPI::INT; }
76			template<> inline MPI::Datatype MPITraits<RealType>::Type() { return MPI::REALTYPE; }
77	gezelter	1551
78			template<class T, unsigned int Dim>
79			class MPITraits< Vector<T, Dim> > {
80			public:
81			static MPI::Datatype Type() { return MPITraits<T>::Type(); }
82			static int Length() {return Dim;}
83			};
84
85			template<class T>
86			class MPITraits< Vector3<T> > {
87			public:
88			static MPI::Datatype Type() { return MPITraits<T>::Type(); }
89			static int Length() {return 3;}
90			};
91
92			template<class T, unsigned int Row, unsigned int Col>
93			class MPITraits< RectMatrix<T, Row, Col> > {
94			public:
95			static MPI::Datatype Type() { return MPITraits<T>::Type(); }
96			static int Length() {return Row * Col;}
97			};
98
99			template<class T>
100			class MPITraits< SquareMatrix3<T> > {
101			public:
102			static MPI::Datatype Type() { return MPITraits<T>::Type(); }
103			static int Length() {return 9;}
104			};
105	gezelter	1539
106	gezelter	1551
107	gezelter	1593	template<communicatorType D>
108	gezelter	1540	class Communicator {
109	gezelter	1539	public:
110
111	gezelter	1593	Communicator<D>() {
112	gezelter	1539
113			int nProc = MPI::COMM_WORLD.Get_size();
114			int myRank = MPI::COMM_WORLD.Get_rank();
115	gezelter	1593
116	gezelter	1539	int nColumnsMax = (int) sqrt(RealType(nProc));
117
118			int nColumns;
119			for (int i = 1; i < nColumnsMax + 1; i++) {
120			if (nProc % i == 0) nColumns = i;
121			}
122
123			int nRows = nProc / nColumns;
124			rowIndex_ = myRank / nColumns;
125			columnIndex_ = myRank % nColumns;
126
127	gezelter	1549	switch(D) {
128			case Row :
129	gezelter	1539	myComm = MPI::COMM_WORLD.Split(rowIndex_, 0);
130	gezelter	1549	break;
131			case Column:
132	gezelter	1539	myComm = MPI::COMM_WORLD.Split(columnIndex_, 0);
133	gezelter	1549	break;
134			case Global:
135			myComm = MPI::COMM_WORLD.Split(myRank, 0);
136	gezelter	1539	}
137	gezelter	1593
138			}
139
140			MPI::Intracomm getComm() { return myComm; }
141
142			private:
143			int rowIndex_;
144			int columnIndex_;
145			MPI::Intracomm myComm;
146			};
147
148
149			template<typename T>
150			class Plan {
151			public:
152
153			Plan<T>(MPI::Intracomm comm, int nObjects) {
154			myComm = comm;
155	gezelter	1539	int nCommProcs = myComm.Get_size();
156	gezelter	1593
157	gezelter	1589	counts.resize(nCommProcs, 0);
158			displacements.resize(nCommProcs, 0);
159	gezelter	1593
160	gezelter	1551	planSize_ = MPITraits<T>::Length() * nObjects;
161	gezelter	1593
162	gezelter	1539	myComm.Allgather(&planSize_, 1, MPI::INT, &counts[0], 1, MPI::INT);
163	gezelter	1593
164	gezelter	1539	displacements[0] = 0;
165			for (int i = 1; i < nCommProcs; i++) {
166			displacements[i] = displacements[i-1] + counts[i-1];
167	gezelter	1541	}
168
169			size_ = 0;
170			for (int i = 0; i < nCommProcs; i++) {
171			size_ += counts[i];
172			}
173	gezelter	1539	}
174
175	gezelter	1551
176			void gather(vector<T>& v1, vector<T>& v2) {
177	gezelter	1593
178	gezelter	1589	// an assert would be helpful here to make sure the vectors are the
179			// correct geometry
180
181	gezelter	1539	myComm.Allgatherv(&v1[0],
182			planSize_,
183	gezelter	1551	MPITraits<T>::Type(),
184	gezelter	1539	&v2[0],
185			&counts[0],
186			&displacements[0],
187	gezelter	1551	MPITraits<T>::Type());
188	gezelter	1593	}
189	gezelter	1539
190	gezelter	1551	void scatter(vector<T>& v1, vector<T>& v2) {
191	gezelter	1589	// an assert would be helpful here to make sure the vectors are the
192			// correct geometry
193	gezelter	1593
194	gezelter	1539	myComm.Reduce_scatter(&v1[0], &v2[0], &counts[0],
195	gezelter	1551	MPITraits<T>::Type(), MPI::SUM);
196	gezelter	1539	}
197	gezelter	1551
198	gezelter	1541	int getSize() {
199			return size_;
200			}
201	gezelter	1539
202			private:
203			int planSize_; ///< how many are on local proc
204	gezelter	1541	int size_;
205	gezelter	1551	vector<int> counts;
206			vector<int> displacements;
207	gezelter	1539	MPI::Intracomm myComm;
208			};
209
210			#endif
211			}
212			#endif
213
214