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

#ifdef IS_MPI
#include <mpi.h>
#endif //is_mpi

namespace oopse {

DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) 
                   : info_(info), filename_(filename){
#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi

        dumpFile_.open(filename_.c_str(), std::ios::out | std::ios::trunc);

        if (!dumpFile_) {
            sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
                    filename_.c_str());
            painCave.isFatal = 1;
            simError();
        }

#ifdef IS_MPI

    }

    sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
    MPIcheckPoint();

#endif // is_mpi

}

DumpWriter::~DumpWriter() {

#ifdef IS_MPI

    if (worldRank == 0) {
#endif // is_mpi

        dumpFile_.close();

#ifdef IS_MPI

    }

#endif // is_mpi

}

void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {

    double currentTime;
    Mat3x3d hmat;
    double chi;
    double integralOfChiDt;
    Mat3x3d eta;
    
    currentTime = s->getTime();
    hmat = s->getHmat();
    chi = s->getChi();
    integralOfChiDt = s->getIntegralOfChiDt();
    eta = s->getEta();
    
    os << currentTime << ";\t" 
         << hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t" 
         << hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
         << hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";

    //write out additional parameters, such as chi and eta

    os << chi << "\t" << integralOfChiDt << "\t;";

    os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t" 
         << eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
         << eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
        
    os << std::endl;
}

void DumpWriter::writeFrame(std::ostream& os) {
    const int BUFFERSIZE = 2000;
    const int MINIBUFFERSIZE = 100;

    char tempBuffer[BUFFERSIZE];
    char writeLine[BUFFERSIZE];

    Quat4d q;
    Vector3d ji;
    Vector3d pos;
    Vector3d vel;

    Molecule* mol;
    StuntDouble* integrableObject;
    SimInfo::MoleculeIterator mi;
    Molecule::IntegrableObjectIterator ii;
  
    int nTotObjects;    
    nTotObjects = info_->getNGlobalIntegrableObjects();

#ifndef IS_MPI


    os << nTotObjects << "\n";
        
    writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());

    for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {

        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
            integrableObject = mol->nextIntegrableObject(ii)) { 
                

            pos = integrableObject->getPos();
            vel = integrableObject->getVel();

            sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                    integrableObject->getType().c_str(), 
                    pos[0], pos[1], pos[2],
                    vel[0], vel[1], vel[2]);

            strcpy(writeLine, tempBuffer);

            if (integrableObject->isDirectional()) {
                q = integrableObject->getQ();
                ji = integrableObject->getJ();

                sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n", 
                        q[0], q[1], q[2], q[3],
                        ji[0], ji[1], ji[2]);
                strcat(writeLine, tempBuffer);
            } else {
                strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
            }

            os << writeLine;

        }
    }

#else // is_mpi
    /*********************************************************************
     * Documentation?  You want DOCUMENTATION?
     * 
     * Why all the potatoes below?  
     *
     * To make a long story short, the original version of DumpWriter
     * worked in the most inefficient way possible.  Node 0 would 
     * poke each of the node for an individual atom's formatted data 
     * as node 0 worked its way down the global index. This was particularly 
     * inefficient since the method blocked all processors at every atom 
     * (and did it twice!).
     *
     * An intermediate version of DumpWriter could be described from Node
     * zero's perspective as follows:
     * 
     *  1) Have 100 of your friends stand in a circle.
     *  2) When you say go, have all of them start tossing potatoes at
     *     you (one at a time).
     *  3) Catch the potatoes.
     *
     * It was an improvement, but MPI has buffers and caches that could 
     * best be described in this analogy as "potato nets", so there's no 
     * need to block the processors atom-by-atom.
     * 
     * This new and improved DumpWriter works in an even more efficient 
     * way:
     * 
     *  1) Have 100 of your friend stand in a circle.
     *  2) When you say go, have them start tossing 5-pound bags of 
     *     potatoes at you.
     *  3) Once you've caught a friend's bag of potatoes,
     *     toss them a spud to let them know they can toss another bag.
     *
     * How's THAT for documentation?
     *
     *********************************************************************/
    const int masterNode = 0;

    int * potatoes;
    int myPotato;
    int nProc;
    int which_node;
    double atomData[13];
    int isDirectional;
    const char * atomTypeString;
    char MPIatomTypeString[MINIBUFFERSIZE];
    int msgLen; // the length of message actually recieved at master nodes
    int haveError;
    MPI_Status istatus;
    int nCurObj;
    
    // code to find maximum tag value
    int * tagub;
    int flag;
    int MAXTAG;
    MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);

    if (flag) {
        MAXTAG = *tagub;
    } else {
        MAXTAG = 32767;
    }

    if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file

        // Node 0 needs a list of the magic potatoes for each processor;

        MPI_Comm_size(MPI_COMM_WORLD, &nProc);
        potatoes = new int[nProc];

        //write out the comment lines
        for(int i = 0; i < nProc; i++) {
            potatoes[i] = 0;
        }


        os << nTotObjects << "\n";
        writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());

        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {

            // Get the Node number which has this atom;

            which_node = info_->getMolToProc(i);

            if (which_node != masterNode) { //current molecule is in slave node
                if (potatoes[which_node] + 1 >= MAXTAG) {
                    // The potato was going to exceed the maximum value, 
                    // so wrap this processor potato back to 0:         

                    potatoes[which_node] = 0;
                    MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
                             MPI_COMM_WORLD);
                }

                myPotato = potatoes[which_node];

                //recieve the number of integrableObject in current molecule
                MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
                         MPI_COMM_WORLD, &istatus);
                myPotato++;

                for(int l = 0; l < nCurObj; l++) {
                    if (potatoes[which_node] + 2 >= MAXTAG) {
                        // The potato was going to exceed the maximum value, 
                        // so wrap this processor potato back to 0:         

                        potatoes[which_node] = 0;
                        MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
                                 0, MPI_COMM_WORLD);
                    }

                    MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
                             which_node, myPotato, MPI_COMM_WORLD,
                             &istatus);

                    atomTypeString = MPIatomTypeString;

                    myPotato++;

                    MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
                             MPI_COMM_WORLD, &istatus);
                    myPotato++;

                    MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);

                    if (msgLen == 13)
                        isDirectional = 1;
                    else
                        isDirectional = 0;

                    // If we've survived to here, format the line:

                    if (!isDirectional) {
                        sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                                atomTypeString, atomData[0],
                                atomData[1], atomData[2],
                                atomData[3], atomData[4],
                                atomData[5]);

                        strcat(writeLine,
                               "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
                    } else {
                        sprintf(writeLine,
                                "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
                                atomTypeString,
                                atomData[0],
                                atomData[1],
                                atomData[2],
                                atomData[3],
                                atomData[4],
                                atomData[5],
                                atomData[6],
                                atomData[7],
                                atomData[8],
                                atomData[9],
                                atomData[10],
                                atomData[11],
                                atomData[12]);
                    }

                    os << writeLine;

                } // end for(int l =0)

                potatoes[which_node] = myPotato;
            } else { //master node has current molecule

                mol = info_->getMoleculeByGlobalIndex(i);

                if (mol == NULL) {
                    sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
                    painCave.isFatal = 1;
                    simError();
                }
                
                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
                    integrableObject = mol->nextIntegrableObject(ii)) {
                        
                    atomTypeString = integrableObject->getType().c_str();

                    pos = integrableObject->getPos();
                    vel = integrableObject->getVel();

                    atomData[0] = pos[0];
                    atomData[1] = pos[1];
                    atomData[2] = pos[2];

                    atomData[3] = vel[0];
                    atomData[4] = vel[1];
                    atomData[5] = vel[2];

                    isDirectional = 0;

                    if (integrableObject->isDirectional()) {
                        isDirectional = 1;

                        q = integrableObject->getQ();
                        ji = integrableObject->getJ();

                        for(int j = 0; j < 6; j++) {
                            atomData[j] = atomData[j];
                        }

                        atomData[6] = q[0];
                        atomData[7] = q[1];
                        atomData[8] = q[2];
                        atomData[9] = q[3];

                        atomData[10] = ji[0];
                        atomData[11] = ji[1];
                        atomData[12] = ji[2];
                    }

                    // If we've survived to here, format the line:

                    if (!isDirectional) {
                        sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                                atomTypeString, atomData[0],
                                atomData[1], atomData[2],
                                atomData[3], atomData[4],
                                atomData[5]);

                        strcat(writeLine,
                               "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
                    } else {
                        sprintf(writeLine,
                                "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
                                atomTypeString,
                                atomData[0],
                                atomData[1],
                                atomData[2],
                                atomData[3],
                                atomData[4],
                                atomData[5],
                                atomData[6],
                                atomData[7],
                                atomData[8],
                                atomData[9],
                                atomData[10],
                                atomData[11],
                                atomData[12]);
                    }


                    os << writeLine;

                } //end for(iter = integrableObject.begin())
            }
        } //end for(i = 0; i < mpiSim->getNmol())

        os.flush();
        std::cout << "master" << std::endl;
        sprintf(checkPointMsg, "Sucessfully took a dump.\n");

        MPIcheckPoint();

        delete [] potatoes;
    } else {

        // worldRank != 0, so I'm a remote node.  

        // Set my magic potato to 0:

        myPotato = 0;

        for(int i = 0; i < info_->getNGlobalMolecules(); i++) {

            // Am I the node which has this integrableObject?
            int whichNode = info_->getMolToProc(i);
            if (whichNode == worldRank) {
                if (myPotato + 1 >= MAXTAG) {

                    // The potato was going to exceed the maximum value, 
                    // so wrap this processor potato back to 0 (and block until
                    // node 0 says we can go:

                    MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
                             &istatus);
                }

                mol = info_->getMoleculeByGlobalIndex(i);

                
                nCurObj = mol->getNIntegrableObjects();

                MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
                myPotato++;

                for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
                    integrableObject = mol->nextIntegrableObject(ii)) {

                    if (myPotato + 2 >= MAXTAG) {

                        // The potato was going to exceed the maximum value, 
                        // so wrap this processor potato back to 0 (and block until
                        // node 0 says we can go:

                        MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
                                 &istatus);
                    }

                    atomTypeString = integrableObject->getType().c_str();

                    pos = integrableObject->getPos();
                    vel = integrableObject->getVel();

                    atomData[0] = pos[0];
                    atomData[1] = pos[1];
                    atomData[2] = pos[2];

                    atomData[3] = vel[0];
                    atomData[4] = vel[1];
                    atomData[5] = vel[2];

                    isDirectional = 0;

                    if (integrableObject->isDirectional()) {
                        isDirectional = 1;

                        q = integrableObject->getQ();
                        ji = integrableObject->getJ();

                        atomData[6] = q[0];
                        atomData[7] = q[1];
                        atomData[8] = q[2];
                        atomData[9] = q[3];

                        atomData[10] = ji[0];
                        atomData[11] = ji[1];
                        atomData[12] = ji[2];
                    }

                    strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);

                    // null terminate the  std::string before sending (just in case):
                    MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';

                    MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
                             myPotato, MPI_COMM_WORLD);

                    myPotato++;

                    if (isDirectional) {
                        MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
                                 MPI_COMM_WORLD);
                    } else {
                        MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
                                 MPI_COMM_WORLD);
                    }

                    myPotato++;
                }
                    
            }
            
        }
        std::cout << "slave" << std::endl;
        sprintf(checkPointMsg, "Sucessfully took a dump.\n");
        MPIcheckPoint();
    }

#endif // is_mpi

}

}//end namespace oopse
Revision:	246
Committed:	Wed Jan 12 22:41:40 2005 UTC (20 years, 9 months ago) by gezelter
Original Path:	*trunk/src/io/DumpWriter.cpp*
File size:	18988 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	246	/*
2			* 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 "io/DumpWriter.hpp"
43			#include "primitives/Molecule.hpp"
44			#include "utils/simError.h"
45	gezelter	2
46			#ifdef IS_MPI
47			#include <mpi.h>
48	gezelter	246	#endif //is_mpi
49	gezelter	2
50	gezelter	246	namespace oopse {
51	gezelter	2
52	gezelter	246	DumpWriter::DumpWriter(SimInfo* info, const std::string& filename)
53			: info_(info), filename_(filename){
54			#ifdef IS_MPI
55	gezelter	2
56	gezelter	246	if (worldRank == 0) {
57			#endif // is_mpi
58	gezelter	2
59	gezelter	246	dumpFile_.open(filename_.c_str(), std::ios::out \| std::ios::trunc);
60	gezelter	2
61	gezelter	246	if (!dumpFile_) {
62			sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n",
63			filename_.c_str());
64			painCave.isFatal = 1;
65			simError();
66			}
67	gezelter	2
68			#ifdef IS_MPI
69
70			}
71
72	gezelter	246	sprintf(checkPointMsg, "Sucessfully opened output file for dumping.\n");
73			MPIcheckPoint();
74	gezelter	2
75			#endif // is_mpi
76	gezelter	246
77	gezelter	2	}
78
79	gezelter	246	DumpWriter::~DumpWriter() {
80	gezelter	2
81			#ifdef IS_MPI
82	gezelter	246
83			if (worldRank == 0) {
84	gezelter	2	#endif // is_mpi
85
86	gezelter	246	dumpFile_.close();
87	gezelter	2
88			#ifdef IS_MPI
89	gezelter	246
90			}
91
92	gezelter	2	#endif // is_mpi
93	gezelter	246
94	gezelter	2	}
95
96	gezelter	246	void DumpWriter::writeCommentLine(std::ostream& os, Snapshot* s) {
97	gezelter	2
98	gezelter	246	double currentTime;
99			Mat3x3d hmat;
100			double chi;
101			double integralOfChiDt;
102			Mat3x3d eta;
103
104			currentTime = s->getTime();
105			hmat = s->getHmat();
106			chi = s->getChi();
107			integralOfChiDt = s->getIntegralOfChiDt();
108			eta = s->getEta();
109
110			os << currentTime << ";\t"
111			<< hmat(0, 0) << "\t" << hmat(1, 0) << "\t" << hmat(2, 0) << ";\t"
112			<< hmat(0, 1) << "\t" << hmat(1, 1) << "\t" << hmat(2, 1) << ";\t"
113			<< hmat(0, 2) << "\t" << hmat(1, 2) << "\t" << hmat(2, 2) << ";\t";
114	gezelter	2
115	gezelter	246	//write out additional parameters, such as chi and eta
116
117			os << chi << "\t" << integralOfChiDt << "\t;";
118
119			os << eta(0, 0) << "\t" << eta(1, 0) << "\t" << eta(2, 0) << ";\t"
120			<< eta(0, 1) << "\t" << eta(1, 1) << "\t" << eta(2, 1) << ";\t"
121			<< eta(0, 2) << "\t" << eta(1, 2) << "\t" << eta(2, 2) << ";";
122
123			os << std::endl;
124	gezelter	2	}
125
126	gezelter	246	void DumpWriter::writeFrame(std::ostream& os) {
127			const int BUFFERSIZE = 2000;
128			const int MINIBUFFERSIZE = 100;
129
130			char tempBuffer[BUFFERSIZE];
131			char writeLine[BUFFERSIZE];
132
133			Quat4d q;
134			Vector3d ji;
135			Vector3d pos;
136			Vector3d vel;
137
138			Molecule* mol;
139			StuntDouble* integrableObject;
140			SimInfo::MoleculeIterator mi;
141			Molecule::IntegrableObjectIterator ii;
142	gezelter	2
143	gezelter	246	int nTotObjects;
144			nTotObjects = info_->getNGlobalIntegrableObjects();
145	gezelter	2
146	gezelter	246	#ifndef IS_MPI
147	gezelter	2
148
149	gezelter	246	os << nTotObjects << "\n";
150
151			writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
152	gezelter	2
153	gezelter	246	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
154	gezelter	2
155	gezelter	246	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
156			integrableObject = mol->nextIntegrableObject(ii)) {
157
158	gezelter	2
159	gezelter	246	pos = integrableObject->getPos();
160			vel = integrableObject->getVel();
161	gezelter	2
162	gezelter	246	sprintf(tempBuffer, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
163			integrableObject->getType().c_str(),
164			pos[0], pos[1], pos[2],
165			vel[0], vel[1], vel[2]);
166	gezelter	2
167	gezelter	246	strcpy(writeLine, tempBuffer);
168	gezelter	2
169	gezelter	246	if (integrableObject->isDirectional()) {
170			q = integrableObject->getQ();
171			ji = integrableObject->getJ();
172	gezelter	2
173	gezelter	246	sprintf(tempBuffer, "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
174			q[0], q[1], q[2], q[3],
175			ji[0], ji[1], ji[2]);
176			strcat(writeLine, tempBuffer);
177			} else {
178			strcat(writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
179			}
180	gezelter	2
181	gezelter	246	os << writeLine;
182	gezelter	2
183	gezelter	246	}
184	gezelter	2	}
185
186	gezelter	246	#else // is_mpi
187			/*********************************************************************
188			* Documentation? You want DOCUMENTATION?
189			*
190			* Why all the potatoes below?
191			*
192			* To make a long story short, the original version of DumpWriter
193			* worked in the most inefficient way possible. Node 0 would
194			* poke each of the node for an individual atom's formatted data
195			* as node 0 worked its way down the global index. This was particularly
196			* inefficient since the method blocked all processors at every atom
197			* (and did it twice!).
198			*
199			* An intermediate version of DumpWriter could be described from Node
200			* zero's perspective as follows:
201			*
202			* 1) Have 100 of your friends stand in a circle.
203			* 2) When you say go, have all of them start tossing potatoes at
204			* you (one at a time).
205			* 3) Catch the potatoes.
206			*
207			* It was an improvement, but MPI has buffers and caches that could
208			* best be described in this analogy as "potato nets", so there's no
209			* need to block the processors atom-by-atom.
210			*
211			* This new and improved DumpWriter works in an even more efficient
212			* way:
213			*
214			* 1) Have 100 of your friend stand in a circle.
215			* 2) When you say go, have them start tossing 5-pound bags of
216			* potatoes at you.
217			* 3) Once you've caught a friend's bag of potatoes,
218			* toss them a spud to let them know they can toss another bag.
219			*
220			* How's THAT for documentation?
221			*
222			*********************************************************************/
223			const int masterNode = 0;
224	gezelter	2
225	gezelter	246	int * potatoes;
226			int myPotato;
227			int nProc;
228			int which_node;
229			double atomData[13];
230			int isDirectional;
231			const char * atomTypeString;
232			char MPIatomTypeString[MINIBUFFERSIZE];
233			int msgLen; // the length of message actually recieved at master nodes
234			int haveError;
235			MPI_Status istatus;
236			int nCurObj;
237
238			// code to find maximum tag value
239			int * tagub;
240			int flag;
241			int MAXTAG;
242			MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag);
243	gezelter	2
244	gezelter	246	if (flag) {
245			MAXTAG = *tagub;
246			} else {
247			MAXTAG = 32767;
248			}
249	gezelter	2
250	gezelter	246	if (worldRank == masterNode) { //master node (node 0) is responsible for writing the dump file
251	gezelter	2
252	gezelter	246	// Node 0 needs a list of the magic potatoes for each processor;
253	gezelter	2
254	gezelter	246	MPI_Comm_size(MPI_COMM_WORLD, &nProc);
255			potatoes = new int[nProc];
256	gezelter	2
257	gezelter	246	//write out the comment lines
258			for(int i = 0; i < nProc; i++) {
259			potatoes[i] = 0;
260			}
261	gezelter	2
262
263	gezelter	246	os << nTotObjects << "\n";
264			writeCommentLine(os, info_->getSnapshotManager()->getCurrentSnapshot());
265	gezelter	2
266	gezelter	246	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
267	gezelter	2
268	gezelter	246	// Get the Node number which has this atom;
269	gezelter	2
270	gezelter	246	which_node = info_->getMolToProc(i);
271	gezelter	2
272	gezelter	246	if (which_node != masterNode) { //current molecule is in slave node
273			if (potatoes[which_node] + 1 >= MAXTAG) {
274			// The potato was going to exceed the maximum value,
275			// so wrap this processor potato back to 0:
276	gezelter	2
277	gezelter	246	potatoes[which_node] = 0;
278			MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node, 0,
279			MPI_COMM_WORLD);
280			}
281	gezelter	2
282	gezelter	246	myPotato = potatoes[which_node];
283	gezelter	2
284	gezelter	246	//recieve the number of integrableObject in current molecule
285			MPI_Recv(&nCurObj, 1, MPI_INT, which_node, myPotato,
286			MPI_COMM_WORLD, &istatus);
287			myPotato++;
288	gezelter	2
289	gezelter	246	for(int l = 0; l < nCurObj; l++) {
290			if (potatoes[which_node] + 2 >= MAXTAG) {
291			// The potato was going to exceed the maximum value,
292			// so wrap this processor potato back to 0:
293	gezelter	2
294	gezelter	246	potatoes[which_node] = 0;
295			MPI_Send(&potatoes[which_node], 1, MPI_INT, which_node,
296			0, MPI_COMM_WORLD);
297			}
298	gezelter	2
299	gezelter	246	MPI_Recv(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR,
300			which_node, myPotato, MPI_COMM_WORLD,
301			&istatus);
302	gezelter	2
303	gezelter	246	atomTypeString = MPIatomTypeString;
304	gezelter	2
305	gezelter	246	myPotato++;
306	gezelter	2
307	gezelter	246	MPI_Recv(atomData, 13, MPI_DOUBLE, which_node, myPotato,
308			MPI_COMM_WORLD, &istatus);
309			myPotato++;
310	gezelter	2
311	gezelter	246	MPI_Get_count(&istatus, MPI_DOUBLE, &msgLen);
312	gezelter	2
313	gezelter	246	if (msgLen == 13)
314			isDirectional = 1;
315			else
316			isDirectional = 0;
317	gezelter	2
318	gezelter	246	// If we've survived to here, format the line:
319	gezelter	2
320	gezelter	246	if (!isDirectional) {
321			sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
322			atomTypeString, atomData[0],
323			atomData[1], atomData[2],
324			atomData[3], atomData[4],
325			atomData[5]);
326	gezelter	2
327	gezelter	246	strcat(writeLine,
328			"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
329			} else {
330			sprintf(writeLine,
331			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
332			atomTypeString,
333			atomData[0],
334			atomData[1],
335			atomData[2],
336			atomData[3],
337			atomData[4],
338			atomData[5],
339			atomData[6],
340			atomData[7],
341			atomData[8],
342			atomData[9],
343			atomData[10],
344			atomData[11],
345			atomData[12]);
346			}
347	gezelter	2
348	gezelter	246	os << writeLine;
349	gezelter	2
350	gezelter	246	} // end for(int l =0)
351	gezelter	2
352	gezelter	246	potatoes[which_node] = myPotato;
353			} else { //master node has current molecule
354	gezelter	2
355	gezelter	246	mol = info_->getMoleculeByGlobalIndex(i);
356	gezelter	2
357	gezelter	246	if (mol == NULL) {
358			sprintf(painCave.errMsg, "Molecule not found on node %d!", worldRank);
359			painCave.isFatal = 1;
360			simError();
361			}
362
363			for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
364			integrableObject = mol->nextIntegrableObject(ii)) {
365
366			atomTypeString = integrableObject->getType().c_str();
367	gezelter	2
368	gezelter	246	pos = integrableObject->getPos();
369			vel = integrableObject->getVel();
370	gezelter	2
371	gezelter	246	atomData[0] = pos[0];
372			atomData[1] = pos[1];
373			atomData[2] = pos[2];
374	gezelter	2
375	gezelter	246	atomData[3] = vel[0];
376			atomData[4] = vel[1];
377			atomData[5] = vel[2];
378	gezelter	2
379	gezelter	246	isDirectional = 0;
380	gezelter	2
381	gezelter	246	if (integrableObject->isDirectional()) {
382			isDirectional = 1;
383	gezelter	2
384	gezelter	246	q = integrableObject->getQ();
385			ji = integrableObject->getJ();
386	gezelter	2
387	gezelter	246	for(int j = 0; j < 6; j++) {
388			atomData[j] = atomData[j];
389			}
390	gezelter	2
391	gezelter	246	atomData[6] = q[0];
392			atomData[7] = q[1];
393			atomData[8] = q[2];
394			atomData[9] = q[3];
395	gezelter	2
396	gezelter	246	atomData[10] = ji[0];
397			atomData[11] = ji[1];
398			atomData[12] = ji[2];
399			}
400	gezelter	2
401	gezelter	246	// If we've survived to here, format the line:
402	gezelter	2
403	gezelter	246	if (!isDirectional) {
404			sprintf(writeLine, "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
405			atomTypeString, atomData[0],
406			atomData[1], atomData[2],
407			atomData[3], atomData[4],
408			atomData[5]);
409	gezelter	2
410	gezelter	246	strcat(writeLine,
411			"0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n");
412			} else {
413			sprintf(writeLine,
414			"%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
415			atomTypeString,
416			atomData[0],
417			atomData[1],
418			atomData[2],
419			atomData[3],
420			atomData[4],
421			atomData[5],
422			atomData[6],
423			atomData[7],
424			atomData[8],
425			atomData[9],
426			atomData[10],
427			atomData[11],
428			atomData[12]);
429			}
430	gezelter	2
431
432	gezelter	246	os << writeLine;
433	gezelter	2
434	gezelter	246	} //end for(iter = integrableObject.begin())
435			}
436			} //end for(i = 0; i < mpiSim->getNmol())
437	gezelter	2
438	gezelter	246	os.flush();
439			std::cout << "master" << std::endl;
440			sprintf(checkPointMsg, "Sucessfully took a dump.\n");
441	gezelter	2
442	gezelter	246	MPIcheckPoint();
443	gezelter	2
444	gezelter	246	delete [] potatoes;
445			} else {
446	gezelter	2
447	gezelter	246	// worldRank != 0, so I'm a remote node.
448	gezelter	2
449	gezelter	246	// Set my magic potato to 0:
450	gezelter	2
451	gezelter	246	myPotato = 0;
452	gezelter	2
453	gezelter	246	for(int i = 0; i < info_->getNGlobalMolecules(); i++) {
454	gezelter	2
455	gezelter	246	// Am I the node which has this integrableObject?
456			int whichNode = info_->getMolToProc(i);
457			if (whichNode == worldRank) {
458			if (myPotato + 1 >= MAXTAG) {
459	gezelter	2
460	gezelter	246	// The potato was going to exceed the maximum value,
461			// so wrap this processor potato back to 0 (and block until
462			// node 0 says we can go:
463	gezelter	2
464	gezelter	246	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
465			&istatus);
466			}
467	gezelter	2
468	gezelter	246	mol = info_->getMoleculeByGlobalIndex(i);
469
470	gezelter	2
471	gezelter	246	nCurObj = mol->getNIntegrableObjects();
472	gezelter	2
473	gezelter	246	MPI_Send(&nCurObj, 1, MPI_INT, 0, myPotato, MPI_COMM_WORLD);
474			myPotato++;
475	gezelter	2
476	gezelter	246	for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;
477			integrableObject = mol->nextIntegrableObject(ii)) {
478	gezelter	2
479	gezelter	246	if (myPotato + 2 >= MAXTAG) {
480	gezelter	2
481	gezelter	246	// The potato was going to exceed the maximum value,
482			// so wrap this processor potato back to 0 (and block until
483			// node 0 says we can go:
484	gezelter	2
485	gezelter	246	MPI_Recv(&myPotato, 1, MPI_INT, 0, 0, MPI_COMM_WORLD,
486			&istatus);
487			}
488	gezelter	2
489	gezelter	246	atomTypeString = integrableObject->getType().c_str();
490	gezelter	2
491	gezelter	246	pos = integrableObject->getPos();
492			vel = integrableObject->getVel();
493	gezelter	2
494	gezelter	246	atomData[0] = pos[0];
495			atomData[1] = pos[1];
496			atomData[2] = pos[2];
497	gezelter	2
498	gezelter	246	atomData[3] = vel[0];
499			atomData[4] = vel[1];
500			atomData[5] = vel[2];
501	gezelter	2
502	gezelter	246	isDirectional = 0;
503	gezelter	2
504	gezelter	246	if (integrableObject->isDirectional()) {
505			isDirectional = 1;
506	gezelter	2
507	gezelter	246	q = integrableObject->getQ();
508			ji = integrableObject->getJ();
509	gezelter	2
510	gezelter	246	atomData[6] = q[0];
511			atomData[7] = q[1];
512			atomData[8] = q[2];
513			atomData[9] = q[3];
514
515			atomData[10] = ji[0];
516			atomData[11] = ji[1];
517			atomData[12] = ji[2];
518			}
519
520			strncpy(MPIatomTypeString, atomTypeString, MINIBUFFERSIZE);
521
522			// null terminate the std::string before sending (just in case):
523			MPIatomTypeString[MINIBUFFERSIZE - 1] = '\0';
524
525			MPI_Send(MPIatomTypeString, MINIBUFFERSIZE, MPI_CHAR, 0,
526			myPotato, MPI_COMM_WORLD);
527
528			myPotato++;
529
530			if (isDirectional) {
531			MPI_Send(atomData, 13, MPI_DOUBLE, 0, myPotato,
532			MPI_COMM_WORLD);
533			} else {
534			MPI_Send(atomData, 6, MPI_DOUBLE, 0, myPotato,
535			MPI_COMM_WORLD);
536			}
537
538			myPotato++;
539			}
540
541			}
542
543			}
544			std::cout << "slave" << std::endl;
545			sprintf(checkPointMsg, "Sucessfully took a dump.\n");
546			MPIcheckPoint();
547			}
548
549			#endif // is_mpi
550
551	gezelter	2	}
552
553	gezelter	246	}//end namespace oopse