src/parallel/Communicator.hpp

/**
 * @file Communicator.hpp
 * @author Charles Vardeman <cvardema.at.nd.edu>
 * @date 08/18/2010
 * @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, 234107 (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 R, unsigned int C>
  class MPITraits< RectMatrix<T, R, C> > {
  public:
    static MPI::Datatype Type() { return MPITraits<T>::Type(); }
    static int Length() {return R * C;}
  };

  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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	6239 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	User	Rev	Content
1	gezelter	1539	/**
2			* @file Communicator.hpp
3			* @author Charles Vardeman <cvardema.at.nd.edu>
4			* @date 08/18/2010
5			* @version 1.0
6			*
7			* @section LICENSE
8			* Copyright (c) 2010 The University of Notre Dame. All Rights Reserved.
9			*
10			* The University of Notre Dame grants you ("Licensee") a
11			* non-exclusive, royalty free, license to use, modify and
12			* redistribute this software in source and binary code form, provided
13			* that the following conditions are met:
14			*
15			* 1. Redistributions of source code must retain the above copyright
16			* notice, this list of conditions and the following disclaimer.
17			*
18			* 2. Redistributions in binary form must reproduce the above copyright
19			* notice, this list of conditions and the following disclaimer in the
20			* documentation and/or other materials provided with the
21			* distribution.
22			*
23			* This software is provided "AS IS," without a warranty of any
24			* kind. All express or implied conditions, representations and
25			* warranties, including any implied warranty of merchantability,
26			* fitness for a particular purpose or non-infringement, are hereby
27			* excluded. The University of Notre Dame and its licensors shall not
28			* be liable for any damages suffered by licensee as a result of
29			* using, modifying or distributing the software or its
30			* derivatives. In no event will the University of Notre Dame or its
31			* licensors be liable for any lost revenue, profit or data, or for
32			* direct, indirect, special, consequential, incidental or punitive
33			* damages, however caused and regardless of the theory of liability,
34			* arising out of the use of or inability to use software, even if the
35			* University of Notre Dame has been advised of the possibility of
36			* such damages.
37			*
38			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
39			* research, please cite the appropriate papers when you publish your
40			* work. Good starting points are:
41			*
42			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
43			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
44	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
45	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
46			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
47	gezelter	1539	*/
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	1796	template<> inline MPI::Datatype MPITraits<int>::Type() { return MPI::INT; }
75			template<> inline MPI::Datatype MPITraits<RealType>::Type() { return MPI::REALTYPE; }
76	gezelter	1551
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	gezelter	1879	template<class T, unsigned int R, unsigned int C>
92			class MPITraits< RectMatrix<T, R, C> > {
93	gezelter	1551	public:
94			static MPI::Datatype Type() { return MPITraits<T>::Type(); }
95	gezelter	1879	static int Length() {return R * C;}
96	gezelter	1551	};
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	1593	template<communicatorType D>
107	gezelter	1540	class Communicator {
108	gezelter	1539	public:
109
110	gezelter	1593	Communicator<D>() {
111	gezelter	1539
112			int nProc = MPI::COMM_WORLD.Get_size();
113			int myRank = MPI::COMM_WORLD.Get_rank();
114	gezelter	1593
115	gezelter	1539	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	gezelter	1879	// int nRows = nProc / nColumns;
123	gezelter	1539	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	gezelter	1593
137			}
138
139			MPI::Intracomm getComm() { return myComm; }
140
141			private:
142			int rowIndex_;
143			int columnIndex_;
144			MPI::Intracomm myComm;
145			};
146
147
148			template<typename T>
149			class Plan {
150			public:
151
152	gezelter	1879	Plan<T>(MPI::Intracomm comm, int nObjects) : myComm(comm) {
153	gezelter	1539	int nCommProcs = myComm.Get_size();
154	gezelter	1593
155	gezelter	1589	counts.resize(nCommProcs, 0);
156			displacements.resize(nCommProcs, 0);
157	gezelter	1593
158	gezelter	1551	planSize_ = MPITraits<T>::Length() * nObjects;
159	gezelter	1593
160	gezelter	1539	myComm.Allgather(&planSize_, 1, MPI::INT, &counts[0], 1, MPI::INT);
161	gezelter	1593
162	gezelter	1539	displacements[0] = 0;
163			for (int i = 1; i < nCommProcs; i++) {
164			displacements[i] = displacements[i-1] + counts[i-1];
165	gezelter	1541	}
166
167			size_ = 0;
168			for (int i = 0; i < nCommProcs; i++) {
169			size_ += counts[i];
170			}
171	gezelter	1539	}
172
173	gezelter	1551
174			void gather(vector<T>& v1, vector<T>& v2) {
175	gezelter	1593
176	gezelter	1589	// an assert would be helpful here to make sure the vectors are the
177			// correct geometry
178
179	gezelter	1539	myComm.Allgatherv(&v1[0],
180			planSize_,
181	gezelter	1551	MPITraits<T>::Type(),
182	gezelter	1539	&v2[0],
183			&counts[0],
184			&displacements[0],
185	gezelter	1551	MPITraits<T>::Type());
186	gezelter	1593	}
187	gezelter	1539
188	gezelter	1551	void scatter(vector<T>& v1, vector<T>& v2) {
189	gezelter	1589	// an assert would be helpful here to make sure the vectors are the
190			// correct geometry
191	gezelter	1593
192	gezelter	1539	myComm.Reduce_scatter(&v1[0], &v2[0], &counts[0],
193	gezelter	1551	MPITraits<T>::Type(), MPI::SUM);
194	gezelter	1539	}
195	gezelter	1551
196	gezelter	1541	int getSize() {
197			return size_;
198			}
199	gezelter	1539
200			private:
201			int planSize_; ///< how many are on local proc
202	gezelter	1541	int size_;
203	gezelter	1551	vector<int> counts;
204			vector<int> displacements;
205	gezelter	1539	MPI::Intracomm myComm;
206			};
207
208			#endif
209			}
210			#endif
211
212