--- trunk/src/io/DumpWriter.cpp 2004/09/24 16:27:58 3 +++ trunk/src/io/DumpWriter.cpp 2008/01/23 21:23:02 1217 @@ -1,693 +1,442 @@ -#define _LARGEFILE_SOURCE64 -#define _FILE_OFFSET_BITS 64 +/* + * 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" +#include "io/basic_teebuf.hpp" +#include "io/gzstream.hpp" +#include "io/Globals.hpp" -#include -#include -#include -#include -#include - #ifdef IS_MPI #include -#include "brains/mpiSimulation.hpp" - -namespace dWrite{ - void DieDieDie( void ); -} - -using namespace dWrite; #endif //is_mpi -#include "io/ReadWrite.hpp" -#include "utils/simError.h" +namespace oopse { -DumpWriter::DumpWriter( SimInfo* the_entry_plug ){ + DumpWriter::DumpWriter(SimInfo* info) + : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){ - entry_plug = the_entry_plug; - + Globals* simParams = info->getSimParams(); + needCompression_ = simParams->getCompressDumpFile(); + needForceVector_ = simParams->getOutputForceVector(); + createDumpFile_ = true; +#ifdef HAVE_LIBZ + if (needCompression_) { + filename_ += ".gz"; + eorFilename_ += ".gz"; + } +#endif + #ifdef IS_MPI - if(worldRank == 0 ){ + + if (worldRank == 0) { #endif // is_mpi + + dumpFile_ = createOStream(filename_); - dumpFile.open(entry_plug->sampleName.c_str(), ios::out | ios::trunc ); + if (!dumpFile_) { + sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", + filename_.c_str()); + painCave.isFatal = 1; + simError(); + } - if( !dumpFile ){ +#ifdef IS_MPI - sprintf( painCave.errMsg, - "Could not open \"%s\" for dump output.\n", - entry_plug->sampleName.c_str()); - painCave.isFatal = 1; - simError(); } -#ifdef IS_MPI +#endif // is_mpi + } - //sort the local atoms by global index - sortByGlobalIndex(); - - sprintf( checkPointMsg, - "Sucessfully opened output file for dumping.\n"); - MPIcheckPoint(); -#endif // is_mpi -} -DumpWriter::~DumpWriter( ){ + DumpWriter::DumpWriter(SimInfo* info, const std::string& filename) + : info_(info), filename_(filename){ + Globals* simParams = info->getSimParams(); + eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; + + needCompression_ = simParams->getCompressDumpFile(); + needForceVector_ = simParams->getOutputForceVector(); + createDumpFile_ = true; +#ifdef HAVE_LIBZ + if (needCompression_) { + filename_ += ".gz"; + eorFilename_ += ".gz"; + } +#endif + #ifdef IS_MPI - if(worldRank == 0 ){ + + if (worldRank == 0) { #endif // is_mpi - dumpFile.close(); + + dumpFile_ = createOStream(filename_); -#ifdef IS_MPI - } -#endif // is_mpi -} + if (!dumpFile_) { + sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", + filename_.c_str()); + painCave.isFatal = 1; + simError(); + } #ifdef IS_MPI -/** - * A hook function to load balancing - */ + } -void DumpWriter::update(){ - sortByGlobalIndex(); -} - -/** - * Auxiliary sorting function - */ - -bool indexSortingCriterion(const pair& p1, const pair& p2){ - return p1.second < p2.second; -} +#endif // is_mpi -/** - * Sorting the local index by global index - */ - -void DumpWriter::sortByGlobalIndex(){ - Molecule* mols = entry_plug->molecules; - indexArray.clear(); + } - for(int i = 0; i < entry_plug->n_mol;i++) - indexArray.push_back(make_pair(i, mols[i].getGlobalIndex())); - - sort(indexArray.begin(), indexArray.end(), indexSortingCriterion); -} - + DumpWriter::DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile) + : info_(info), filename_(filename){ + + Globals* simParams = info->getSimParams(); + eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor"; + + needCompression_ = simParams->getCompressDumpFile(); + needForceVector_ = simParams->getOutputForceVector(); + +#ifdef HAVE_LIBZ + if (needCompression_) { + filename_ += ".gz"; + eorFilename_ += ".gz"; + } #endif - -void DumpWriter::writeDump(double currentTime){ - - ofstream finalOut; - vector fileStreams; - + #ifdef IS_MPI - if(worldRank == 0 ){ -#endif - finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc ); - if( !finalOut ){ - sprintf( painCave.errMsg, - "Could not open \"%s\" for final dump output.\n", - entry_plug->finalName.c_str() ); - painCave.isFatal = 1; - simError(); - } -#ifdef IS_MPI - } + + if (worldRank == 0) { #endif // is_mpi - - fileStreams.push_back(&finalOut); - fileStreams.push_back(&dumpFile); - - writeFrame(fileStreams, currentTime); - + + createDumpFile_ = writeDumpFile; + if (createDumpFile_) { + dumpFile_ = createOStream(filename_); + + if (!dumpFile_) { + sprintf(painCave.errMsg, "Could not open \"%s\" for dump output.\n", + filename_.c_str()); + painCave.isFatal = 1; + simError(); + } + } #ifdef IS_MPI - finalOut.close(); -#endif - -} + + } -void DumpWriter::writeFinal(double currentTime){ + +#endif // is_mpi + + } - ofstream finalOut; - vector fileStreams; + DumpWriter::~DumpWriter() { #ifdef IS_MPI - if(worldRank == 0 ){ + + if (worldRank == 0) { #endif // is_mpi + if (createDumpFile_){ + writeClosing(*dumpFile_); + delete dumpFile_; + } +#ifdef IS_MPI - finalOut.open( entry_plug->finalName.c_str(), ios::out | ios::trunc ); - - if( !finalOut ){ - sprintf( painCave.errMsg, - "Could not open \"%s\" for final dump output.\n", - entry_plug->finalName.c_str() ); - painCave.isFatal = 1; - simError(); } -#ifdef IS_MPI - } #endif // is_mpi - - fileStreams.push_back(&finalOut); - writeFrame(fileStreams, currentTime); -#ifdef IS_MPI - finalOut.close(); -#endif - -} + } -void DumpWriter::writeFrame( vector& outFile, double currentTime ){ + void DumpWriter::writeFrameProperties(std::ostream& os, Snapshot* s) { - const int BUFFERSIZE = 2000; - const int MINIBUFFERSIZE = 100; + char buffer[1024]; - char tempBuffer[BUFFERSIZE]; - char writeLine[BUFFERSIZE]; + os << " \n"; - int i; - unsigned int k; + RealType currentTime = s->getTime(); + sprintf(buffer, " Time: %.10g\n", currentTime); + os << buffer; -#ifdef 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? - * - *********************************************************************/ + Mat3x3d hmat; + hmat = s->getHmat(); + sprintf(buffer, " Hmat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", + hmat(0, 0), hmat(1, 0), hmat(2, 0), + hmat(0, 1), hmat(1, 1), hmat(2, 1), + hmat(0, 2), hmat(1, 2), hmat(2, 2)); + os << buffer; - int *potatoes; - int myPotato; + RealType chi = s->getChi(); + RealType integralOfChiDt = s->getIntegralOfChiDt(); + sprintf(buffer, " Thermostat: %.10g , %.10g\n", chi, integralOfChiDt); + os << buffer; - int nProc; - int j, which_node, done, which_atom, local_index, currentIndex; - double atomData[13]; - int isDirectional; - char* atomTypeString; - char MPIatomTypeString[MINIBUFFERSIZE]; - int nObjects; - int msgLen; // the length of message actually recieved at master nodes -#endif //is_mpi + Mat3x3d eta; + eta = s->getEta(); + sprintf(buffer, " Barostat: {{ %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }, { %.10g, %.10g, %.10g }}\n", + eta(0, 0), eta(1, 0), eta(2, 0), + eta(0, 1), eta(1, 1), eta(2, 1), + eta(0, 2), eta(1, 2), eta(2, 2)); + os << buffer; - double q[4], ji[3]; - DirectionalAtom* dAtom; - double pos[3], vel[3]; - int nTotObjects; - StuntDouble* sd; - char* molName; - vector integrableObjects; - vector::iterator iter; - nTotObjects = entry_plug->getTotIntegrableObjects(); -#ifndef IS_MPI - - for(k = 0; k < outFile.size(); k++){ - *outFile[k] << nTotObjects << "\n"; - - *outFile[k] << currentTime << ";\t" - << entry_plug->Hmat[0][0] << "\t" - << entry_plug->Hmat[1][0] << "\t" - << entry_plug->Hmat[2][0] << ";\t" - - << entry_plug->Hmat[0][1] << "\t" - << entry_plug->Hmat[1][1] << "\t" - << entry_plug->Hmat[2][1] << ";\t" - - << entry_plug->Hmat[0][2] << "\t" - << entry_plug->Hmat[1][2] << "\t" - << entry_plug->Hmat[2][2] << ";"; - - //write out additional parameters, such as chi and eta - *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; + os << " \n"; } - - for( i=0; i< entry_plug->n_mol; i++ ){ - integrableObjects = entry_plug->molecules[i].getIntegrableObjects(); - molName = (entry_plug->compStamps[entry_plug->molecules[i].getStampID()])->getID(); - - for( iter = integrableObjects.begin();iter != integrableObjects.end(); ++iter){ - sd = *iter; - sd->getPos(pos); - sd->getVel(vel); + void DumpWriter::writeFrame(std::ostream& os) { - sprintf( tempBuffer, - "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t", - sd->getType(), - pos[0], - pos[1], - pos[2], - vel[0], - vel[1], - vel[2]); - strcpy( writeLine, tempBuffer ); +#ifdef IS_MPI + MPI_Status istatus; +#endif - if( sd->isDirectional() ){ + Molecule* mol; + StuntDouble* integrableObject; + SimInfo::MoleculeIterator mi; + Molecule::IntegrableObjectIterator ii; - sd->getQ( q ); - sd->getJ( ji ); +#ifndef IS_MPI + os << " \n"; + + writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); - 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 ); + os << " \n"; + for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { + + + for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)) { + os << prepareDumpLine(integrableObject); + } - else - strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" ); + } + os << " \n"; - for(k = 0; k < outFile.size(); k++) - *outFile[k] << writeLine; - } + os << " \n"; -} + os.flush(); +#else + //every node prepares the dump lines for integrable objects belong to itself + std::string buffer; + for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) { -#else // is_mpi - /* code to find maximum tag value */ - - int *tagub, flag, MAXTAG; - MPI_Attr_get(MPI_COMM_WORLD, MPI_TAG_UB, &tagub, &flag); - if (flag) { - MAXTAG = *tagub; - } else { - MAXTAG = 32767; - } + for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; + integrableObject = mol->nextIntegrableObject(ii)) { + buffer += prepareDumpLine(integrableObject); + } + } + + const int masterNode = 0; - int haveError; + if (worldRank == masterNode) { + os << " \n"; + writeFrameProperties(os, info_->getSnapshotManager()->getCurrentSnapshot()); + os << " \n"; + + os << buffer; - MPI_Status istatus; - int nCurObj; - int *MolToProcMap = mpiSim->getMolToProcMap(); + int nProc; + MPI_Comm_size(MPI_COMM_WORLD, &nProc); + for (int i = 1; i < nProc; ++i) { - // write out header and node 0's coordinates + // receive the length of the string buffer that was + // prepared by processor i - if( worldRank == 0 ){ - - // Node 0 needs a list of the magic potatoes for each processor; - - nProc = mpiSim->getNProcessors(); - potatoes = new int[nProc]; - - //write out the comment lines - for (i = 0; i < nProc; i++) - potatoes[i] = 0; - - for(k = 0; k < outFile.size(); k++){ - *outFile[k] << nTotObjects << "\n"; - - *outFile[k] << currentTime << ";\t" - << entry_plug->Hmat[0][0] << "\t" - << entry_plug->Hmat[1][0] << "\t" - << entry_plug->Hmat[2][0] << ";\t" - - << entry_plug->Hmat[0][1] << "\t" - << entry_plug->Hmat[1][1] << "\t" - << entry_plug->Hmat[2][1] << ";\t" - - << entry_plug->Hmat[0][2] << "\t" - << entry_plug->Hmat[1][2] << "\t" - << entry_plug->Hmat[2][2] << ";"; - - *outFile[k] << entry_plug->the_integrator->getAdditionalParameters() << endl; + int recvLength; + MPI_Recv(&recvLength, 1, MPI_INT, i, 0, MPI_COMM_WORLD, &istatus); + char* recvBuffer = new char[recvLength]; + if (recvBuffer == NULL) { + } else { + MPI_Recv(recvBuffer, recvLength, MPI_CHAR, i, 0, MPI_COMM_WORLD, &istatus); + os << recvBuffer; + delete recvBuffer; + } + } + os << " \n"; + + os << " \n"; + os.flush(); + } else { + int sendBufferLength = buffer.size() + 1; + MPI_Send(&sendBufferLength, 1, MPI_INT, masterNode, 0, MPI_COMM_WORLD); + MPI_Send((void *)buffer.c_str(), sendBufferLength, MPI_CHAR, masterNode, 0, MPI_COMM_WORLD); } - currentIndex = 0; +#endif // is_mpi - for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { - - // Get the Node number which has this atom; - - which_node = MolToProcMap[i]; - - if (which_node != 0) { - - 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); - - } + std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) { + + int index = integrableObject->getGlobalIntegrableObjectIndex(); + std::string type("pv"); + std::string line; + char tempBuffer[4096]; - myPotato = potatoes[which_node]; + Vector3d pos; + Vector3d vel; + pos = integrableObject->getPos(); + vel = integrableObject->getVel(); + sprintf(tempBuffer, "%18.10g %18.10g %18.10g %13e %13e %13e", + pos[0], pos[1], pos[2], + vel[0], vel[1], vel[2]); + line += tempBuffer; - //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 (integrableObject->isDirectional()) { + type += "qj"; + Quat4d q; + Vector3d ji; + q = integrableObject->getQ(); + ji = integrableObject->getJ(); + sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e %13e", + q[0], q[1], q[2], q[3], + ji[0], ji[1], ji[2]); + line += tempBuffer; + } - 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]); - - } - - for(k = 0; k < outFile.size(); k++) - *outFile[k] << writeLine; - - }// end for(int l =0) - potatoes[which_node] = myPotato; - - } - else { - - haveError = 0; - - local_index = indexArray[currentIndex].first; - - integrableObjects = (entry_plug->molecules[local_index]).getIntegrableObjects(); - - for(iter= integrableObjects.begin(); iter != integrableObjects.end(); ++iter){ - sd = *iter; - atomTypeString = sd->getType(); - - sd->getPos(pos); - sd->getVel(vel); - - atomData[0] = pos[0]; - atomData[1] = pos[1]; - atomData[2] = pos[2]; - - atomData[3] = vel[0]; - atomData[4] = vel[1]; - atomData[5] = vel[2]; + if (needForceVector_) { + type += "ft"; + Vector3d frc; + Vector3d trq; + frc = integrableObject->getFrc(); + trq = integrableObject->getTrq(); - isDirectional = 0; + sprintf(tempBuffer, " %13e %13e %13e %13e %13e %13e", + frc[0], frc[1], frc[2], + trq[0], trq[1], trq[2]); + line += tempBuffer; + } + + sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str()); + return std::string(tempBuffer); + } - if( sd->isDirectional() ){ + void DumpWriter::writeDump() { + writeFrame(*dumpFile_); + } - isDirectional = 1; - - sd->getQ( q ); - sd->getJ( ji ); - - 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]); - - } - - for(k = 0; k < outFile.size(); k++) - *outFile[k] << writeLine; - - - }//end for(iter = integrableObject.begin()) - - currentIndex++; - } - - }//end for(i = 0; i < mpiSim->getNmol()) + void DumpWriter::writeEor() { + std::ostream* eorStream; - for(k = 0; k < outFile.size(); k++) - outFile[k]->flush(); - - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - - MPIcheckPoint(); - - delete[] potatoes; - - } else { +#ifdef IS_MPI + if (worldRank == 0) { +#endif // is_mpi - // worldRank != 0, so I'm a remote node. + eorStream = createOStream(eorFilename_); - // Set my magic potato to 0: +#ifdef IS_MPI + } +#endif // is_mpi - myPotato = 0; - currentIndex = 0; - - for (i = 0 ; i < mpiSim->getNMolGlobal(); i++ ) { - - // Am I the node which has this integrableObject? - - if (MolToProcMap[i] == worldRank) { + writeFrame(*eorStream); +#ifdef IS_MPI + if (worldRank == 0) { +#endif // is_mpi + writeClosing(*eorStream); + delete eorStream; +#ifdef IS_MPI + } +#endif // is_mpi - 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); - - } + } - local_index = indexArray[currentIndex].first; - integrableObjects = entry_plug->molecules[local_index].getIntegrableObjects(); - - nCurObj = integrableObjects.size(); - - MPI_Send(&nCurObj, 1, MPI_INT, 0, - myPotato, MPI_COMM_WORLD); - myPotato++; - for( iter = integrableObjects.begin(); iter != integrableObjects.end(); iter++){ + void DumpWriter::writeDumpAndEor() { + std::vector buffers; + std::ostream* eorStream; +#ifdef IS_MPI + if (worldRank == 0) { +#endif // is_mpi - 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); - - } - - sd = *iter; - - atomTypeString = sd->getType(); + buffers.push_back(dumpFile_->rdbuf()); - sd->getPos(pos); - sd->getVel(vel); + eorStream = createOStream(eorFilename_); - 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( sd->isDirectional() ){ - - isDirectional = 1; - - sd->getQ( q ); - sd->getJ( ji ); - - - 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 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++; - - } - - currentIndex++; - - } - - } - - sprintf( checkPointMsg, - "Sucessfully took a dump.\n"); - MPIcheckPoint(); - + buffers.push_back(eorStream->rdbuf()); + +#ifdef IS_MPI } +#endif // is_mpi + TeeBuf tbuf(buffers.begin(), buffers.end()); + std::ostream os(&tbuf); - -#endif // is_mpi -} + writeFrame(os); #ifdef IS_MPI + if (worldRank == 0) { +#endif // is_mpi + writeClosing(*eorStream); + delete eorStream; +#ifdef IS_MPI + } +#endif // is_mpi + + } -// a couple of functions to let us escape the write loop + std::ostream* DumpWriter::createOStream(const std::string& filename) { -void dWrite::DieDieDie( void ){ + std::ostream* newOStream; +#ifdef HAVE_LIBZ + if (needCompression_) { + newOStream = new ogzstream(filename.c_str()); + } else { + newOStream = new std::ofstream(filename.c_str()); + } +#else + newOStream = new std::ofstream(filename.c_str()); +#endif + //write out MetaData first + (*newOStream) << "" << std::endl; + (*newOStream) << " " << std::endl; + (*newOStream) << info_->getRawMetaData(); + (*newOStream) << " " << std::endl; + return newOStream; + } - MPI_Finalize(); - exit (0); -} + void DumpWriter::writeClosing(std::ostream& os) { -#endif //is_mpi + os << "\n"; + os.flush(); + } + +}//end namespace oopse