From: cvw Date: Tue, 3 Jan 2012 15:25:20 +0000 (+0000) Subject: partition of meshes MEDCoupling with MEDCouplingFieldDouble X-Git-Url: http://git.salome-platform.org/gitweb/?a=commitdiff_plain;h=refs%2Fheads%2FBR_MEDPartitioner_dev;p=tools%2Fmedcoupling.git partition of meshes MEDCoupling with MEDCouplingFieldDouble --- diff --git a/src/MEDPartitioner/MEDPARTITIONER.hxx b/src/MEDPartitioner/MEDPARTITIONER.hxx index 80e64b033..e18a0da3a 100755 --- a/src/MEDPartitioner/MEDPARTITIONER.hxx +++ b/src/MEDPartitioner/MEDPARTITIONER.hxx @@ -1,4 +1,4 @@ - // Copyright (C) 2007-2010 CEA/DEN, EDF R&D +// Copyright (C) 2007-2010 CEA/DEN, EDF R&D // // This library is free software; you can redistribute it and/or // modify it under the terms of the GNU Lesser General Public diff --git a/src/MEDPartitioner/MEDPARTITIONER_ConnectZone.cxx b/src/MEDPartitioner/MEDPARTITIONER_ConnectZone.cxx index 91e267ad6..040410714 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_ConnectZone.cxx +++ b/src/MEDPartitioner/MEDPARTITIONER_ConnectZone.cxx @@ -20,16 +20,14 @@ // See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com // -// few STL include files -// -#include - // few Med Memory include files -#include "MEDMEM_define.hxx" #include "MEDCouplingUMesh.hxx" #include "MEDPARTITIONER_SkyLineArray.hxx" #include "MEDPARTITIONER_ConnectZone.hxx" +// few STL include files +#include + using namespace MEDPARTITIONER; CONNECTZONE::CONNECTZONE(): diff --git a/src/MEDPartitioner/MEDPARTITIONER_ConnectZone.hxx b/src/MEDPartitioner/MEDPARTITIONER_ConnectZone.hxx index fd50e772e..feff431fe 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_ConnectZone.hxx +++ b/src/MEDPartitioner/MEDPARTITIONER_ConnectZone.hxx @@ -26,17 +26,12 @@ # define __MEDPARTITIONER_CONNECTZONE_HXX__ #include "MEDPARTITIONER.hxx" +#include "MEDPARTITIONER_SkyLineArray.hxx" // few STL include files #include #include -// few Med Memory include files -// #include "MEDMEM_STRING.hxx" -// #include "MEDMEM_define.hxx" -// #include "MEDMEM_Mesh.hxx" -#include "MEDPARTITIONER_SkyLineArray.hxx" - namespace MEDPARTITIONER { class MEDPARTITIONER_EXPORT CONNECTZONE { diff --git a/src/MEDPartitioner/MEDPARTITIONER_JointFinder.cxx b/src/MEDPartitioner/MEDPARTITIONER_JointFinder.cxx index 8a6ab8b78..348764b84 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_JointFinder.cxx +++ b/src/MEDPartitioner/MEDPARTITIONER_JointFinder.cxx @@ -3,6 +3,7 @@ #include "MEDPARTITIONER_Topology.hxx" #include "MEDPARTITIONER_ParaDomainSelector.hxx" #include "MEDCouplingUMesh.hxx" +#include "MEDPARTITIONER_utils.hxx" #include "BBTree.txx" @@ -14,103 +15,137 @@ JointFinder::JointFinder(const MESHCollection& mc):_mesh_collection(mc), _topolo { } +JointFinder::~JointFinder() +{ + //if (MyGlobals::_is0verbose>100) cout<<"TODO ~JointFinder"<nbDomain(); _distant_node_cell.resize(nbdomain); _node_node.resize(nbdomain); - for (int i=0; inbProcs(); - std::vector* > bbtree(nbdomain); - std::vector rev(nbdomain); - std::vectorrevIndx(nbdomain); + std::vector* > bbtree(nbdomain,(BBTree<3>*) 0); + std::vector rev(nbdomain,(DataArrayInt*) 0); + std::vector revIndx(nbdomain,(DataArrayInt*) 0); int meshDim; int spaceDim; - for (int mydomain=0;mydomainisMyDomain(mydomain)) continue; + const ParaMEDMEM::MEDCouplingUMesh* myMesh=_mesh_collection.getMesh(mydomain); + meshDim=myMesh->getMeshDimension(); + spaceDim= myMesh->getSpaceDimension(); + rev[mydomain] = ParaMEDMEM::DataArrayInt::New(); + revIndx[mydomain] = ParaMEDMEM::DataArrayInt::New(); + myMesh->getReverseNodalConnectivity(rev[mydomain],revIndx[mydomain]); + double* bbx=new double[2*spaceDim*myMesh->getNumberOfNodes()]; + for (int i=0; igetNumberOfNodes()*spaceDim; i++) + { + const double* coords=myMesh->getCoords()->getConstPointer(); + bbx[2*i]=(coords[i])-1e-12; + bbx[2*i+1]=bbx[2*i]+2e-12; + } + bbtree[mydomain]=new BBTree<3> (bbx,0,0,myMesh->getNumberOfNodes(),-1e-12); + delete[] bbx; + } + + //send my domains to other proc an receive other domains from other proc + for (int isource=0; isourceisMyDomain(mydomain)) continue; - const ParaMEDMEM::MEDCouplingUMesh* myMesh=_mesh_collection.getMesh(mydomain); + const ParaMEDMEM::MEDCouplingUMesh* sourceMesh=_mesh_collection.getMesh(isource); + if (_domain_selector->isMyDomain(isource)&&_domain_selector->isMyDomain(itarget)) continue; + if (_domain_selector->isMyDomain(isource)) + { + //preparing data for treatment on target proc + int targetProc = _domain_selector->getProcessorID(itarget); + + std::vector vec(spaceDim*sourceMesh->getNumberOfNodes()); + //cvw cout<<"\nproc "<<_domain_selector->rank()<<" : numberOfNodes "<getNumberOfNodes()<getCoords()->getConstPointer(),sourceMesh->getCoords()->getConstPointer()+sourceMesh->getNumberOfNodes()*spaceDim,&vec[0]); + sendDoubleVec(vec,targetProc); + + //retrieving target data for storage in commonDistantNodes array + std::vector localCorrespondency; + recvIntVec(localCorrespondency, targetProc); + //cvw cout<<"\nproc "<<_domain_selector->rank()<<" : nodeCellCorrespondency "; + for (int i=0; iisMyDomain(itarget)) + { + //receiving data from source proc + int sourceProc = isource%nbproc; + std::vector recvVec; + recvDoubleVec(recvVec,sourceProc); + std::map commonNodes; // (local nodes, distant nodes) list + //cvw cout<<"\nproc "<<_domain_selector->rank()<<" : commonNodes "; + for (int inode=0; inode<(recvVec.size()/meshDim); inode++) + { + double* bbox=new double[2*spaceDim]; + for (int i=0; i inodes; + bbtree[itarget]->getIntersectingElems(bbox,inodes); + delete[] bbox; - meshDim=myMesh->getMeshDimension(); - spaceDim= myMesh->getSpaceDimension(); - rev[mydomain] = ParaMEDMEM::DataArrayInt::New(); - revIndx[mydomain] = ParaMEDMEM::DataArrayInt::New(); - myMesh->getReverseNodalConnectivity(rev[mydomain],revIndx[mydomain]); - double* bbx=new double[2*spaceDim*myMesh->getNumberOfNodes()]; - for (int i=0; igetNumberOfNodes()*spaceDim;i++) + if (inodes.size()>0) + { + commonNodes.insert(std::make_pair(inodes[0],inode)); + //cvw cout<<" "< nodeCellCorrespondency; + for (std::map::iterator iter=commonNodes.begin(); iter!=commonNodes.end(); iter++) { - const double* coords=myMesh->getCoords()->getConstPointer(); - bbx[2*i]=(coords[i])-1e-12; - bbx[2*i+1]=bbx[2*i]+2e-12; + _node_node[itarget][isource].push_back(std::make_pair(iter->first, iter->second));//storing node pairs in a vector + const int* revIndxPtr=revIndx[itarget]->getConstPointer(); + const int* revPtr=rev[itarget]->getConstPointer(); + for (int icell=revIndxPtr[iter->first]; icellfirst+1]; icell++) + { + nodeCellCorrespondency.push_back(iter->second); // + int globalCell=_topology->convertCellToGlobal(itarget,revPtr[icell]); + nodeCellCorrespondency.push_back(globalCell); + //nodeCellCorrespondency.push_back(revPtr[icell]); //need to set at global numerotation + //cout<<"processor "<second<<" cellLoc "<rank()<<" : JointFinder sendIntVec "<<_domain_selector->rank()< (bbx,0,0,myMesh->getNumberOfNodes(),-1e-12); + } + } + //free rev(nbdomain) revIndx(nbdomain) bbtree(nbdomain) + for (int i=0; idecrRef(); + if (revIndx[i]!=0) revIndx[i]->decrRef(); + if (bbtree[i]!=0) delete bbtree[i]; } - for (int isource=0;isourceisMyDomain(isource)&&_domain_selector->isMyDomain(itarget)) continue; - if (_domain_selector->isMyDomain(isource)) - { - //preparing data for treatment on target proc - int targetProc = _domain_selector->getProcessorID(itarget); - - std::vector vec(spaceDim*sourceMesh->getNumberOfNodes()); - std::copy(sourceMesh->getCoords()->getConstPointer(),sourceMesh->getCoords()->getConstPointer()+sourceMesh->getNumberOfNodes()*spaceDim,&vec[0]); - _domain_selector->sendDoubleVec (vec,targetProc); - - //retrieving target data for storage in commonDistantNodes array - std::vector localCorrespondency; - _domain_selector->recvIntVec(localCorrespondency, targetProc); - for (int i=0; iisMyDomain(itarget)) - { - //receiving data from source proc - int sourceProc = isource%nbproc; - std::vector recvVec; - _domain_selector->recvDoubleVec(recvVec,sourceProc); - std::map commonNodes; // (local nodes, distant nodes) list - for (int inode=0; inode<(recvVec.size()/meshDim);inode++) - { - double* bbox=new double[2*spaceDim]; - for (int i=0; i inodes; - bbtree[itarget]->getIntersectingElems(bbox,inodes); - delete[] bbox; - - if (inodes.size()>0) commonNodes.insert(std::make_pair(inodes[0],inode)); - } - std::vector nodeCellCorrespondency; - for (std::map::iterator iter=commonNodes.begin();iter!=commonNodes.end();iter++) - { - _node_node[itarget][isource].push_back(std::make_pair(iter->first, iter->second));//storing node pairs in a vector - const int*revIndxPtr=revIndx[itarget]->getConstPointer(); - const int*revPtr=rev[itarget]->getConstPointer(); - for (int icell=revIndxPtr[iter->first];icellfirst+1];icell++) - { - nodeCellCorrespondency.push_back(iter->second); - nodeCellCorrespondency.push_back(revPtr[icell]); - } - } - _domain_selector->sendIntVec(nodeCellCorrespondency, sourceProc); - } - } - + if (MyGlobals::_verbose>100) + std::cout<<"proc "<<_domain_selector->rank()<<" : end JointFinder::findCommonDistantNodes"< > > & JointFinder::getDistantNodeCell() { return _distant_node_cell; @@ -120,3 +155,40 @@ std::vector > > >& JointFinder::getNo { return _node_node; } + +void JointFinder::print() +//it is for debug on small arrays under mpi 2,3 cpus +{ + int nbdomain=_topology->nbDomain(); + //MPI_Barrier(MPI_COMM_WORLD); + if (MyGlobals::_is0verbose>0) + cout<<"\nJointFinder print node-node (nn)iproc|itarget|isource|i|inodefirst-inodesecond\n\n"<< + "JointFinder print distantNode=cell (nc)iproc|itarget|isource|inode=icell\n\n"; + for (int isource=0; isourcerank()<rank()<<" : JointFinder _distant_node_cell itarget/isource/inode=icell"<::iterator it; + for (it=_distant_node_cell[isource][itarget].begin() ; it!=_distant_node_cell[isource][itarget].end(); it++) + { + cout<<" nc"<<_domain_selector->rank()<<"|"< > >& getDistantNodeCell(); std::vector > > >& getNodeNode(); + std::vector > > _distant_node_cell; private: const MESHCollection& _mesh_collection; const ParaDomainSelector* _domain_selector; const Topology* _topology; - std::vector > > _distant_node_cell; + //std::vector > > _distant_node_cell; std::vector > > > _node_node; }; }; diff --git a/src/MEDPartitioner/MEDPARTITIONER_MESHCollection.cxx b/src/MEDPartitioner/MEDPARTITIONER_MESHCollection.cxx index 79076e873..eaab9f521 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_MESHCollection.cxx +++ b/src/MEDPartitioner/MEDPARTITIONER_MESHCollection.cxx @@ -17,8 +17,6 @@ // See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com // -#include "MEDMEM_Exception.hxx" - #include "MEDCouplingUMesh.hxx" #include "MEDCouplingNormalizedUnstructuredMesh.hxx" #include "MEDCouplingMemArray.hxx" @@ -37,7 +35,12 @@ #include "MEDPARTITIONER_MESHCollectionMedAsciiDriver.hxx" #include "MEDPARTITIONER_JointFinder.hxx" #include "MEDPARTITIONER_UserGraph.hxx" +#include "MEDLoader.hxx" +#include "MEDCouplingFieldDouble.hxx" +#ifdef HAVE_MPI2 +#include +#endif #ifdef ENABLE_METIS #include "MEDPARTITIONER_METISGraph.hxx" @@ -73,7 +76,8 @@ MESHCollection::MESHCollection() _driver_type(MEDPARTITIONER::MedXML), _subdomain_boundary_creates(false), _family_splitting(false), - _create_empty_groups(false) + _create_empty_groups(false), + _joint_finder(0) { } @@ -88,7 +92,11 @@ MESHCollection::MESHCollection() * \param topology topology containing the cell mappings */ -MESHCollection::MESHCollection(MESHCollection& initialCollection, Topology* topology, bool family_splitting, bool create_empty_groups) +MESHCollection::MESHCollection( + MESHCollection& initialCollection, + Topology* topology, + bool family_splitting, + bool create_empty_groups) //cvwat04 : _name(initialCollection._name), _topology(topology), _owns_topology(false), @@ -98,139 +106,174 @@ MESHCollection::MESHCollection(MESHCollection& initialCollection, Topology* topo _driver_type(MEDPARTITIONER::MedXML), _subdomain_boundary_creates(false), _family_splitting(family_splitting), - _create_empty_groups(create_empty_groups) + _create_empty_groups(create_empty_groups), + _joint_finder(0) { - std::vector > > new2oldIds(initialCollection.getTopology()->nbDomain()); - castCellMeshes(initialCollection, new2oldIds); + if (MyGlobals::_verbose>10) std::cout<<"proc "<(inewdomain,inewnode) createNodeMapping(initialCollection, nodeMapping); + //cvw std::cout<<"castMeshes"< > > new2oldFaceIds; - castMeshes(initialCollection.getFaceMesh(), this->getFaceMesh(),initialCollection, nodeMapping, new2oldFaceIds); + castFaceMeshes(initialCollection, nodeMapping, new2oldFaceIds); //////////////////// //treating families //////////////////// - _faceFamilyIds.resize(topology->nbDomain()); - _cellFamilyIds.resize(topology->nbDomain()); - //allocating family ids arrays - for (int inew=0; inewnbDomain();inew++) - { - if(isParallelMode() && !_domain_selector->isMyDomain(inew)) continue; - _cellFamilyIds[inew]=ParaMEDMEM::DataArrayInt::New(); - int nbCells=_mesh[inew]->getNumberOfCells(); - int* ptrCellIds=new int[nbCells]; - for (int i=0; i< nbCells;i++) ptrCellIds[i]=0; - _cellFamilyIds[inew]->useArray(ptrCellIds,true, ParaMEDMEM::CPP_DEALLOC,nbCells,1); - - int nbFaces=_faceMesh[inew]->getNumberOfCells(); - _faceFamilyIds[inew]=ParaMEDMEM::DataArrayInt::New(); - int* ptrFaceIds=new int[nbFaces]; - for (int i=0; iuseArray(ptrFaceIds,true, ParaMEDMEM::CPP_DEALLOC,nbFaces,1); - } - - //casting cell and face families on new meshes - castIntField(initialCollection.getMesh(), this->getMesh(),initialCollection.getCellFamilyIds(),_cellFamilyIds); - castIntField(initialCollection.getFaceMesh(), this->getFaceMesh(),initialCollection.getFaceFamilyIds(),_faceFamilyIds); - - - /////////////////////// - ////treating groups - ////////////////////// + if (MyGlobals::_is0verbose) + if (isParallelMode()) std::cout<<"ParallelMode on "<nbDomain()<<" Domains"<nbDomain()<<" Domains"<10) std::cout<<"treating cell and face families"<getMesh(), + initialCollection.getCellFamilyIds(), + "cellFamily"); + castIntField2(initialCollection.getFaceMesh(), + this->getFaceMesh(), + initialCollection.getFaceFamilyIds(), + "faceFamily"); + + ////////////////// + //treating groups + ////////////////// + if (MyGlobals::_is0verbose) std::cout<<"treating groups"< > >& new2oldIds) +void MESHCollection::castCellMeshes( + MESHCollection& initialCollection, + std::vector > >& new2oldIds) { - if (_topology==0) throw INTERP_KERNEL::Exception("Topology has not been defined on call to castCellMeshes"); - _mesh.resize(_topology->nbDomain()); + if (_topology==0) throw INTERP_KERNEL::Exception(LOCALIZED("Topology has not been defined on call to castCellMeshes")); - //splitting the initial domains into smaller bits + int nbNewDomain=_topology->nbDomain(); + int nbOldDomain=initialCollection.getTopology()->nbDomain(); + _mesh.resize(nbNewDomain); + int rank=MyGlobals::_rank; + //if (MyGlobals::_verbose>10) std::cout<<"proc "< > splitMeshes; - splitMeshes.resize(_topology->nbDomain()); - for (int inew=0; inew<_topology->nbDomain();inew++) - { - splitMeshes[inew].resize(initialCollection.getTopology()->nbDomain()); - std::fill(&(splitMeshes[inew][0]),&(splitMeshes[inew][0])+splitMeshes[inew].size(),(ParaMEDMEM::MEDCouplingUMesh*)0); - } + splitMeshes.resize(nbNewDomain); + for (int inew=0; inewnbDomain();iold++) + for (int iold=0; ioldisMyDomain(iold)) { - if (!isParallelMode() || initialCollection._domain_selector->isMyDomain(iold)) - { - int size=(initialCollection._mesh)[iold]->getNumberOfCells(); - std::vector globalids(size); - initialCollection.getTopology()->getCellList(iold, &globalids[0]); - std::vector ilocalnew(size); - std::vector ipnew(size); - _topology->convertGlobalCellList(&globalids[0],size,&ilocalnew[0],&ipnew[0]); - new2oldIds[iold].resize(_topology->nbDomain()); - for (int i=0; inbDomain();inew++) - { - splitMeshes[inew][iold]=(ParaMEDMEM::MEDCouplingUMesh*)(initialCollection.getMesh())[iold]->buildPartOfMySelf(&new2oldIds[iold][inew][0],&new2oldIds[iold][inew][0]+new2oldIds[iold][inew].size(),true); - } - } + int size=(initialCollection._mesh)[iold]->getNumberOfCells(); + std::vector globalids(size); + initialCollection.getTopology()->getCellList(iold, &globalids[0]); + std::vector ilocalnew(size); //local + std::vector ipnew(size); //idomain old + //cvw work locally + _topology->convertGlobalCellList(&globalids[0],size,&ilocalnew[0],&ipnew[0]); + + new2oldIds[iold].resize(nbNewDomain); + for (int i=0; ibuildPartOfMySelf( + &new2oldIds[iold][inew][0], + &new2oldIds[iold][inew][0]+new2oldIds[iold][inew].size(), + true); + if (MyGlobals::_verbose>400) + std::cout<<"proc "<getNumberOfCells()<nbDomain();iold++) - for(int inew=0;inew<_topology->nbDomain();inew++) - { - if (initialCollection._domain_selector->isMyDomain(iold) && _domain_selector->isMyDomain(inew)) continue; - - if(initialCollection._domain_selector->isMyDomain(iold)) - _domain_selector->sendMesh(*(splitMeshes[inew][iold]),_domain_selector->getProcessorID(inew)); - - if (_domain_selector->isMyDomain(inew)) - _domain_selector->recvMesh(splitMeshes[inew][iold],_domain_selector->getProcessorID(iold)); - - } - } + { + //if (MyGlobals::_verbose>300) std::cout<<"proc "<isMyDomain(iold) && _domain_selector->isMyDomain(inew)) continue; + + if(initialCollection._domain_selector->isMyDomain(iold)) + _domain_selector->sendMesh(*(splitMeshes[inew][iold]),_domain_selector->getProcessorID(inew)); + + if (_domain_selector->isMyDomain(inew)) + _domain_selector->recvMesh(splitMeshes[inew][iold],_domain_selector->getProcessorID(iold)); + + } + } //fusing the split meshes - for (int inew=0; inew<_topology->nbDomain() ;inew++) - { - std::vector meshes; - - for (int i=0; i< splitMeshes[inew].size();i++) - if (splitMeshes[inew][i]!=0) meshes.push_back(splitMeshes[inew][i]); + if (MyGlobals::_verbose>200) std::cout<<"proc "< meshes; + + for (int i=0; i< splitMeshes[inew].size();i++) + if (splitMeshes[inew][i]!=0) + if (splitMeshes[inew][i]->getNumberOfCells()>0) + meshes.push_back(splitMeshes[inew][i]); - if (!isParallelMode()||_domain_selector->isMyDomain(inew)) - { - _mesh[inew]=ParaMEDMEM::MEDCouplingUMesh::MergeUMeshes(meshes); - bool areNodesMerged; - int nbNodesMerged; - ParaMEDMEM::DataArrayInt* array=_mesh[inew]->mergeNodes(1e-12,areNodesMerged,nbNodesMerged); - array->decrRef(); // array is not used in this case - _mesh[inew]->zipCoords(); - } - for (int i=0; i< splitMeshes[inew].size();i++) - if (splitMeshes[inew][i]!=0) splitMeshes[inew][i]->decrRef(); - } - + if (!isParallelMode()||_domain_selector->isMyDomain(inew)) + { + if (meshes.size()==0) + { + _mesh[inew]=createEmptyMEDCouplingUMesh(); + //throw INTERP_KERNEL::Exception(LOCALIZED("castCellMeshes fusing : no meshes")); + cout<<"WARNING : castCellMeshes fusing : no meshes try another number of processors"<mergeNodes(1e-12,areNodesMerged,nbNodesMerged); + array->decrRef(); // array is not used in this case + _mesh[inew]->zipCoords(); + } + } + for (int i=0; i< splitMeshes[inew].size(); i++) + if (splitMeshes[inew][i]!=0) splitMeshes[inew][i]->decrRef(); + } + if (MyGlobals::_verbose>300) std::cout<<"proc "<nbDomain();iold++) { @@ -253,7 +297,7 @@ void MESHCollection::createNodeMapping( MESHCollection& initialCollection, NodeM bbox=new double[nvertices*6]; ParaMEDMEM::DataArrayDouble* coords = initialCollection.getMesh(iold)->getCoords(); double* coordsPtr=coords->getPointer(); - + for (int i=0; i(bbox,0,0,nvertices,1e-9); } - - for (int inew=0; inew<_topology->nbDomain(); inew++) + + for (int inew=0; inew<_topology->nbDomain(); inew++) //cvwat12 { //sending meshes for parallel computation if (isParallelMode() && _domain_selector->isMyDomain(inew) && !_domain_selector->isMyDomain(iold)) @@ -275,24 +319,22 @@ void MESHCollection::createNodeMapping( MESHCollection& initialCollection, NodeM for (int inode=0; inodegetNumberOfNodes();inode++) { double* coordsPtr=coords->getPointer()+inode*3; - std::vector elems; + vector elems; tree->getElementsAroundPoint(coordsPtr,elems); - if (elems.size()==0) continue; + if (elems.size()==0) continue; nodeMapping.insert(make_pair(make_pair(iold,elems[0]),make_pair(inew,inode))); - } + } + mesh->decrRef(); } else if (!isParallelMode() || (_domain_selector->isMyDomain(inew) && _domain_selector->isMyDomain(iold))) { - ParaMEDMEM::DataArrayDouble* coords = getMesh(inew)->getCoords(); - + ParaMEDMEM::DataArrayDouble* coords = getMesh(inew)->getCoords(); for (int inode=0; inode<_mesh[inew]->getNumberOfNodes();inode++) { - double* coordsPtr=coords->getPointer()+inode*3; - - std::vector elems; + vector elems; tree->getElementsAroundPoint(coordsPtr,elems); - if (elems.size()==0) continue; + if (elems.size()==0) continue; nodeMapping.insert(make_pair(make_pair(iold,elems[0]),make_pair(inew,inode))); } } @@ -306,40 +348,95 @@ void MESHCollection::createNodeMapping( MESHCollection& initialCollection, NodeM } +//getNodeIds(meshCell, meshFace, nodeIds) +//inodeCell=nodeIds[inodeFace] +//(put the biggest mesh in One) +//if no corresponding node then inodeCell==-1 +void getNodeIds(ParaMEDMEM::MEDCouplingUMesh& meshOne, ParaMEDMEM::MEDCouplingUMesh& meshTwo, vector& nodeIds) +{ + using std::vector; + if (!&meshOne || !&meshTwo) return; //empty or not existing + double* bbox; + BBTree<3>* tree; + int nv1=meshOne.getNumberOfNodes(); + bbox=new double[nv1*6]; + ParaMEDMEM::DataArrayDouble* coords=meshOne.getCoords(); + double* coordsPtr=coords->getPointer(); + for (int i=0; i(bbox,0,0,nv1,1e-9); + + int nv2=meshTwo.getNumberOfNodes(); + nodeIds.resize(nv2,-1); + coords=meshTwo.getCoords(); + for (int inode=0; inodegetPointer()+inode*3; + vector elems; + tree->getElementsAroundPoint(coordsPtr,elems); + if (elems.size()==0) continue; + nodeIds[inode]=elems[0]; + } + delete tree; + delete[] bbox; +} + /*! creates the face meshes on the new domains from the faces on the old domain and the node mapping faces at the interface are duplicated */ - -void MESHCollection::castMeshes(std::vector& meshesCastFrom,std::vector& meshesCastTo, MESHCollection& initialCollection,const NodeMapping& nodeMapping, std::vector > >& new2oldIds) +void MESHCollection::castFaceMeshes(MESHCollection& initialCollection, + const std::multimap, std::pair >& nodeMapping, + std::vector > >& new2oldIds) { //splitMeshes structure will contain the partition of //the old faces on the new ones - // splitMeshes[4][2] contains the faces from old domain 2 - // that have to be added to domain 4 - + //splitMeshes[4][2] contains the faces from old domain 2 + //that have to be added to domain 4 + + using std::vector; + using std::map; + using std::multimap; + using std::pair; + using std::make_pair; + + vector& meshesCastFrom=initialCollection.getFaceMesh(); + vector& meshesCastTo=this->getFaceMesh(); + vector< vector > splitMeshes; int newSize=_topology->nbDomain(); - splitMeshes.resize ( newSize ); + int fromSize=meshesCastFrom.size(); + + splitMeshes.resize(newSize); + for (int inew=0;inewisMyDomain(iold)) continue; + if (meshesCastFrom[iold] != 0) { - if (isParallelMode() && !_domain_selector->isMyDomain(iold)) continue; - new2oldIds[iold].resize(newSize); - for (int ielem=0;ielemgetNumberOfCells();ielem++) - { - std::vector nodes; + for (int ielem=0; ielemgetNumberOfCells(); ielem++) + { + vector nodes; meshesCastFrom[iold]->getNodeIdsOfCell(ielem,nodes); map faces; @@ -350,140 +447,472 @@ void MESHCollection::castMeshes(std::vector& mesh //are incremented for each target node //the face is considered as going to target domains if the counter of the domain //is equal to the number of nodes - for (int inode=0;inode,pair >::const_iterator MI; int mynode=nodes[inode]; pair myRange = nodeMapping.equal_range(make_pair(iold,mynode)); for (MI iter=myRange.first; iter!=myRange.second; iter++) - { + { int inew=iter->second.first; if (faces.find(inew)==faces.end()) faces[inew]=1; else faces[inew]++; - } - } + } + } - for (map::iterator iter=faces.begin(); - iter!=faces.end(); - iter++) - { + for (map::iterator iter=faces.begin(); iter!=faces.end(); iter++) + { if (iter->second==nodes.size()) + //cvw eligible but may be have to be face of a cell of this->getMesh()[inew]? + //it is not sure here... + //done before writeMedfile on option?... see filterFaceOnCell() new2oldIds[iold][iter->first].push_back(ielem); - } - } + } + } //creating the splitMeshes from the face ids for (int inew=0;inew<_topology->nbDomain();inew++) - { - splitMeshes[inew][iold]=(ParaMEDMEM::MEDCouplingUMesh*)(meshesCastFrom[iold]->buildPartOfMySelf(&new2oldIds[iold][inew][0],&new2oldIds[iold][inew][0]+new2oldIds[iold][inew].size(),true)); - splitMeshes[inew][iold]->zipCoords(); - } + { + if (meshesCastFrom[iold]->getNumberOfCells() > 0) //cvw + { + splitMeshes[inew][iold]= + (ParaMEDMEM::MEDCouplingUMesh*) + ( meshesCastFrom[iold]->buildPartOfMySelf( + &new2oldIds[iold][inew][0], + &new2oldIds[iold][inew][0]+new2oldIds[iold][inew].size(), + true) + ); + splitMeshes[inew][iold]->zipCoords(); + } + else + { + //std::cout<<"one empty mesh from "<isMyDomain(iold)<<" "<< + _domain_selector->isMyDomain(inew)<isMyDomain(iold) && !_domain_selector->isMyDomain(inew)) - _domain_selector->sendMesh(*(splitMeshes[inew][iold]), _domain_selector->getProcessorID(inew)); + if (splitMeshes[inew][iold] != 0) { + //cvw std::cout<<"send NOT empty mesh "<getName()<<" "<sendMesh(*(splitMeshes[inew][iold]), _domain_selector->getProcessorID(inew)); + } + else { + //std::cout<<"send empty mesh "<sendMesh(*(empty), _domain_selector->getProcessorID(inew)); + } if (!_domain_selector->isMyDomain(iold) && _domain_selector->isMyDomain(inew)) - _domain_selector->recvMesh(splitMeshes[inew][iold], _domain_selector->getProcessorID(iold)); + _domain_selector->recvMesh(splitMeshes[inew][iold], _domain_selector->getProcessorID(iold)); } - - + empty->decrRef(); + } + //recollecting the bits of splitMeshes to fuse them into one + if (MyGlobals::_verbose>300) std::cout<<"proc "< myMeshes; - for (int iold=0; iold < meshesCastFrom.size();iold++) + for (int iold=0; ioldgetNumberOfCells()>0) { + myMeshes.push_back(umesh); + } + //else { + // std::cout<<"one empty mesh "<0) + { + meshesCastTo[inew]=ParaMEDMEM::MEDCouplingUMesh::MergeUMeshes(myMeshes); + } + else + { + //std::cout<<"one empty meshes to merge "<setName("emptyMesh"); + //empty->setMeshDimension(3); + //empty->allocateCells(0); + ParaMEDMEM::MEDCouplingUMesh *empty=createEmptyMEDCouplingUMesh(); + meshesCastTo[inew]=empty; + } // meshesCastTo[inew]->zipCoords(); - for (int iold=0; iold < meshesCastFrom.size();iold++) + for (int iold=0; iolddecrRef(); } + //if (MyGlobals::_verbose>1) std::cout<<"proc "<& meshesCastFrom,std::vector& meshesCastTo, std::vector& arrayFrom, std::vector& arrayTo) +void MESHCollection::remapIntField( + const ParaMEDMEM::MEDCouplingUMesh& sourceMesh, + const ParaMEDMEM::MEDCouplingUMesh& targetMesh, + const int* fromArray, + int* toArray) { - vector > splitIds; - splitIds.resize(meshesCastTo.size()); - - // send / recv operations - for (int inew=0; inew < meshesCastTo.size();inew++) - for (int iold=0; iold < meshesCastFrom.size();iold++) + using std::vector; + if (sourceMesh.getNumberOfCells()<=0) return; //empty mesh could exist + //cvw std::cout<<"remapIntField "<setCoords(sourceCoords); + vector c; + vector cI; + tmpMesh->getNodeIdsNearPoints(targetCoords->getConstPointer(),targetMesh.getNumberOfCells(),1e-10,c,cI); + if (cI.size()!= targetMesh.getNumberOfCells()+1) + throw INTERP_KERNEL::Exception(LOCALIZED("Error in source/target projection")); + for (int itargetnode=0; itargetnodedecrRef(); + targetCoords->decrRef(); + tmpMesh->decrRef(); +} + +void MESHCollection::castIntField2( //cvwat08 + std::vector& meshesCastFrom, + std::vector& meshesCastTo, + std::vector& arrayFrom, + std::string nameArrayTo) +{ + using std::vector; + + int ioldMax=meshesCastFrom.size(); + int inewMax=meshesCastTo.size(); + // send-recv operations + for (int inew=0; inewisMyDomain(iold) && !_domain_selector->isMyDomain(inew)) + { + //send mesh + _domain_selector->sendMesh(*meshesCastFrom[iold],_domain_selector->getProcessorID(inew)); + //send vector + int size=arrayFrom[iold]->getNumberOfTuples(); //cvw may be -1! + vectorsendIds; + if (MyGlobals::_verbose>400) std::cout<<"proc "<<_domain_selector->rank()<<" : castIntField sendIntVec size "<0) //no empty + { + sendIds.resize(size); + std::copy(arrayFrom[iold]->getPointer(),arrayFrom[iold]->getPointer()+size,&sendIds[0]); + } + else //empty + { + size=0; + sendIds.resize(size); + } + //std::cout<<"proc "<<_domain_selector->rank()<<" : castIntField sendIntVec "<getProcessorID(inew)); + } + //receiving arrays from distant domains + if (isParallelMode() && !_domain_selector->isMyDomain(iold) && _domain_selector->isMyDomain(inew)) + { + //receive mesh + vector recvIds; + ParaMEDMEM::MEDCouplingUMesh* recvMesh; + _domain_selector->recvMesh(recvMesh,_domain_selector->getProcessorID(iold)); + //receive vector + if (MyGlobals::_verbose>400) std::cout<<"proc "<<_domain_selector->rank()<<" : castIntField recIntVec "<getProcessorID(iold)); + remapIntField2(inew,iold,*recvMesh,*meshesCastTo[inew],&recvIds[0],nameArrayTo); + recvMesh->decrRef(); //cww is it correct? + } + } + } + + //local contributions and aggregation + for (int inew=0; inewisMyDomain(iold) && _domain_selector->isMyDomain(inew))) + { + remapIntField2(inew,iold,*meshesCastFrom[iold],*meshesCastTo[inew],arrayFrom[iold]->getConstPointer(),nameArrayTo); + } + } +} + +void MESHCollection::remapIntField2(int inew,int iold, + const ParaMEDMEM::MEDCouplingUMesh& sourceMesh, + const ParaMEDMEM::MEDCouplingUMesh& targetMesh, + const int* fromArray, + string nameArrayTo) +//here we store ccI for next use in future call of castAllFields and remapDoubleField2 +{ + using std::vector; + //cout<<"remapIntField2 "<setCoords(sourceCoords); + vector c; + vector cI; + vector ccI; //memorize intersection target<-source(inew,iold) + string str,cle; + str=nameArrayTo+"_toArray"; + cle=cle1ToStr(str,inew); + int* toArray; + int targetSize=targetMesh.getNumberOfCells(); + //first time iold : create and initiate + if (_mapDataArrayInt.find(cle)==_mapDataArrayInt.end()) + { + if (MyGlobals::_is0verbose>100) cout<<"create "<alloc(targetSize,1); + p->fillWithZero(); + toArray=p->getPointer(); + _mapDataArrayInt[cle]=p; + } + else //other times iold: refind and complete + { + toArray=_mapDataArrayInt.find(cle)->second->getPointer(); + } + tmpMesh->getNodeIdsNearPoints(targetCoords->getConstPointer(),targetSize,1e-10,c,cI); + if (cI.size()!=targetSize+1) + throw INTERP_KERNEL::Exception(LOCALIZED("Error in source/target projection")); + for (int itargetnode=0; itargetnode700) cout<<"proc "<decrRef(); + targetCoords->decrRef(); + tmpMesh->decrRef(); +} + +void MESHCollection::castAllFields(MESHCollection& initialCollection, string nameArrayTo) //cvwat08 +{ + using std::vector; + if (nameArrayTo!="cellFieldDouble") + throw INTERP_KERNEL::Exception(LOCALIZED("Error castAllField only on cellFieldDouble")); + + string nameTo="typeData=6"; //resume the type of field casted + // send-recv operations + int ioldMax=initialCollection.getMesh().size(); + int inewMax=this->getMesh().size(); + int iFieldMax=initialCollection.getFieldDescriptions().size(); + if (MyGlobals::_verbose>10) cout<<"castAllFields with:\n"< initialCollection.getFieldDescriptions() + //getFieldDescriptions() is a string description of field coherent and tested and set BEFORE. + //see collection.prepareFieldDescriptions() + for (int ifield=0; ifield recvIntVec; //sending arrays for distant domains if (isParallelMode() && _domain_selector->isMyDomain(iold) && !_domain_selector->isMyDomain(inew)) - { - _domain_selector->sendMesh(*meshesCastFrom[iold],_domain_selector->getProcessorID(inew)); - int size=arrayFrom[iold]->getNumberOfTuples(); - vectorsendIds(size); - std::copy(arrayFrom[iold]->getPointer(),arrayFrom[iold]->getPointer()+size,&sendIds[0]); - _domain_selector->sendIntVec(sendIds, _domain_selector->getProcessorID(inew)); - } + { + int target=_domain_selector->getProcessorID(inew); + ParaMEDMEM::DataArrayDouble* field=initialCollection.getField(descriptionField,iold); //cvwat14 + //getField look for and read it if not done, and assume decrRef() in ~MESHCollection; + if (MyGlobals::_verbose>10) + std::cout<<"proc "<<_domain_selector->rank()<<" : castAllFields sendDouble"<isMyDomain(iold) && _domain_selector->isMyDomain(inew)) - { - vector recvIds; - ParaMEDMEM::MEDCouplingUMesh* recvMesh; - _domain_selector->recvMesh(recvMesh,_domain_selector->getProcessorID(iold)); - _domain_selector->recvIntVec(recvIds, _domain_selector->getProcessorID(iold)); - remapIntField(*recvMesh,*meshesCastTo[inew],&recvIds[0],arrayTo[inew]->getPointer()); - } + if (isParallelMode() && !_domain_selector->isMyDomain(iold) && _domain_selector->isMyDomain(inew)) + { + int source=_domain_selector->getProcessorID(iold); + //receive vector + if (MyGlobals::_verbose>10) + std::cout<<"proc "<<_domain_selector->rank()<<" : castAllFields recvDouble"<isMyDomain(iold) && _domain_selector->isMyDomain(inew))) + { + ParaMEDMEM::DataArrayDouble* field=initialCollection.getField(descriptionField,iold); //cvwat14 + remapDoubleField3(inew,iold,field,nameArrayTo,descriptionField); } + } + } +} - //local contributions and aggregation - for (int inew=0; inew < meshesCastTo.size();inew++) +void MESHCollection::remapDoubleField3(int inew, int iold, + ParaMEDMEM::DataArrayDouble* fromArray, + string nameArrayTo, + string descriptionField) +//here we use 'cellFamily_ccI inew iold' set in remapIntField2 +{ + using std::vector; + if (nameArrayTo!="cellFieldDouble") + throw INTERP_KERNEL::Exception(LOCALIZED("Error remapDoubleField3 only on cellFieldDouble")); + string cle=cle2ToStr("cellFamily_ccI",inew,iold); + + map::iterator it1; + it1=_mapDataArrayInt.find(cle); + if (it1==_mapDataArrayInt.end()) + { + cerr<<"proc "<second; + if (MyGlobals::_verbose>300) cout<<"proc "<getNbOfElems()<getMesh()[inew]->getNumberOfCells(); //number of cell of mesh + int nbcomp=fromArray->getNumberOfComponents(); + int nbPtGauss=strToInt(extractFromDescription(descriptionField, "nbPtGauss=")); + + //int nbk=fromArray->getNumberOfTuples(); + + //cle=reprGenericDescription(descriptionField)+" "+intToStr(inew); + string tag="inewFieldDouble="+intToStr(inew); + cle=descriptionField+serializeFromString(tag); + //cout<<"descriptionField in remapDoubleField3 : "<getNbOfElems(); + int fromArrayNbOfComp=fromArray->getNumberOfComponents(); + int fromArrayNbOfCell=fromArrayNbOfElem/fromArrayNbOfComp/nbPtGauss; + + if (MyGlobals::_verbose>1000) + { + cout<<"proc "<getNumberOfTuples()<< + " nbcells "<getNumberOfComponents()<::iterator it2; + it2=_mapDataArrayDouble.find(cle); + if (it2==_mapDataArrayDouble.end()) + { + if (MyGlobals::_verbose>300) cout<<"proc "<alloc(nbcell*nbPtGauss,nbcomp); + field->fillWithZero(); + } + else + { + field=it2->second; + if (field->getNumberOfTuples()!=nbcell*nbPtGauss || field->getNumberOfComponents()!=nbcomp) { - for (int iold=0; iold < meshesCastFrom.size();iold++) - if (!isParallelMode() || ( _domain_selector->isMyDomain(iold) && _domain_selector->isMyDomain(inew))) - { - remapIntField(*meshesCastFrom[iold],*meshesCastTo[inew],arrayFrom[iold]->getConstPointer(),arrayTo[inew]->getPointer()); - } + cerr<<"proc "<getNbOfElems()<setPartOfValuesAdv(fromArray,ccI); + } + else + { + //replaced by setPartOfValuesAdv if nbPtGauss==1 + int iMax=ccI->getNbOfElems(); + int* pccI=ccI->getPointer(); + double* pField=field->getPointer(); + double* pFrom=fromArray->getPointer(); + int itarget, isource, delta=nbPtGauss*nbcomp; + for (int i=0; i=nbcell) || (isource<0) || (isource>=fromArrayNbOfCell)) + throw INTERP_KERNEL::Exception(LOCALIZED("Error field override")); + int ita=itarget*delta; + int iso=isource*delta; + for (int k=0; ksetCoords(sourceCoords); - vectorc; + vector c; vector cI; tmpMesh->getNodeIdsNearPoints(targetCoords->getConstPointer(),targetMesh.getNumberOfCells(),1e-10,c,cI); - if (cI.size()!= targetMesh.getNumberOfCells()+1) throw INTERP_KERNEL::Exception("Error in source/target projection"); + if (cI.size()!= targetMesh.getNumberOfCells()+1) + throw INTERP_KERNEL::Exception(LOCALIZED("Error in source/target projection")); + for (int itargetnode=0; itargetnodedecrRef(); targetCoords->decrRef(); tmpMesh->decrRef(); - - } +*/ + /*! constructing the MESH collection from a distributed file * * \param filename name of the master file containing the list of all the MED files */ -MESHCollection::MESHCollection(const string& filename) +MESHCollection::MESHCollection(const std::string& filename) : _topology(0), _owns_topology(true), _driver(0), @@ -492,7 +921,8 @@ MESHCollection::MESHCollection(const string& filename) _driver_type(MEDPARTITIONER::Undefined), _subdomain_boundary_creates(false), _family_splitting(false), - _create_empty_groups(false) + _create_empty_groups(false), + _joint_finder(0) { // char filenamechar[256]; // strcpy(filenamechar,filename.c_str()); @@ -501,22 +931,22 @@ MESHCollection::MESHCollection(const string& filename) _driver=new MESHCollectionMedXMLDriver(this); _driver->read (filename.c_str()); _driver_type = MedXML; - } - catch(MEDMEM::MEDEXCEPTION){ - delete _driver; - try - { - _driver=new MESHCollectionMedAsciiDriver(this); - _driver->read (filename.c_str()); - _driver_type=MedAscii; - } - catch(MEDMEM::MEDEXCEPTION&) - { - delete _driver; - throw MEDMEM::MEDEXCEPTION("file does not comply with any recognized format"); - } - } + catch(...) + { // Handle all exceptions + if ( _driver ) delete _driver; _driver=0; + try + { + _driver=new MESHCollectionMedAsciiDriver(this); + _driver->read (filename.c_str()); + _driver_type=MedAscii; + } + catch(...) + { + if ( _driver ) delete _driver; _driver=0; + throw INTERP_KERNEL::Exception(LOCALIZED("file does not comply with any recognized format")); + } + } for ( int idomain = 0; idomain < _mesh.size(); ++idomain ) if ( _mesh[idomain] && _mesh[idomain]->getNumberOfNodes() > 0 ) _i_non_empty_mesh = idomain; @@ -527,46 +957,166 @@ MESHCollection::MESHCollection(const string& filename) * \param filename - name of the master file containing the list of all the MED files * \param domainSelector - selector of domains to load */ -MESHCollection::MESHCollection(const string& filename, ParaDomainSelector& domainSelector) +MESHCollection::MESHCollection(const std::string& filename, ParaDomainSelector& domainSelector) //cvwat01 : _topology(0), _owns_topology(true), _driver(0), - _domain_selector( domainSelector.nbProcs() > 1 ? & domainSelector : 0 ), + //cvw _domain_selector( domainSelector.nbProcs() > 1 ? & domainSelector : 0 ), + _domain_selector( &domainSelector ), _i_non_empty_mesh(-1), _driver_type(MEDPARTITIONER::Undefined), _subdomain_boundary_creates(false), _family_splitting(false), - _create_empty_groups(false) + _create_empty_groups(false), + _joint_finder(0) { - try + std::string myfile=filename; + std::size_t found=myfile.find(".xml"); + if (found!=std::string::npos) //file .xml + { + try { - _driver=new MESHCollectionMedXMLDriver(this); + _driver=new MESHCollectionMedXMLDriver(this); //cvwat02 _driver->read ( (char*)filename.c_str(), _domain_selector ); _driver_type = MedXML; } - catch(MEDMEM::MEDEXCEPTION&) + catch(...) + { // Handle all exceptions + if ( _driver ) delete _driver; _driver=0; + throw INTERP_KERNEL::Exception(LOCALIZED("file .xml does not comply with any recognized format")); + } + } + else + { + found=myfile.find(".med"); + if (found!=std::string::npos) //file .med single + { + //make a temporary file .xml and retry MedXMLDriver + std::string xml="\ +\n \ +\n \ + \n \ + \n \ + \n \ + \n \ + \n \ + \n \ + \n \ + \n \ + \n \ + \n \ + \n \ + $fileName\n \ + localhost\n \ + \n \ + \n \ + \n \ + \n \ + \n \ + $meshName\n \ + \n \ + \n \ + \n \ +\n"; + std::vector meshNames=MEDLoader::GetMeshNames(myfile.c_str()); + xml.replace(xml.find("$fileName"),9,myfile); + xml.replace(xml.find("$meshName"),9,meshNames[0]); + xml.replace(xml.find("$meshName"),9,meshNames[0]); + xml.replace(xml.find("$meshName"),9,meshNames[0]); + //std::cout<rank()==0) //only on to write it + { + std::ofstream f(nameFileXml.c_str()); + f<read ( (char*)nameFileXml.c_str(), _domain_selector ); + _driver_type = MedXML; + } + catch(...) + { // Handle all exceptions + if ( _driver ) delete _driver; _driver=0; + throw INTERP_KERNEL::Exception(LOCALIZED("file medpartitioner_xxx.xml does not comply with any recognized format")); + } + } + else //no extension { - delete _driver; try { _driver=new MESHCollectionMedAsciiDriver(this); _driver->read ( (char*)filename.c_str(), _domain_selector ); _driver_type=MedAscii; } - catch(MEDMEM::MEDEXCEPTION&) + catch(...) { - delete _driver; - throw MEDMEM::MEDEXCEPTION("file does not comply with any recognized format"); + if ( _driver ) delete _driver; _driver=0; + throw INTERP_KERNEL::Exception(LOCALIZED("file name with no extension does not comply with any recognized format")); } } + } + + /*done in MESHCollectionMedXMLDriver read if ( isParallelMode() ) // to know nb of cells on each proc to compute global cell ids from locally global - _domain_selector->gatherNbOf( getMesh() ); + _domain_selector->gatherNbOf( getMesh() );*/ // find non-empty domain mesh for ( int idomain = 0; idomain < _mesh.size(); ++idomain ) if ( _mesh[idomain] && _mesh[idomain]->getNumberOfNodes() > 0 ) _i_non_empty_mesh = idomain; + + try + { + //check for all proc/file compatibility of _fieldDescriptions + //*MyGlobals::_fileNames=allgathervVectorOfString(*MyGlobals::_fileNames); + _fieldDescriptions=allgathervVectorOfString(MyGlobals::_fieldDescriptions); //cvwat07 + } + catch(INTERP_KERNEL::Exception& e) + { + cerr<<"proc "< v2=allgathervVectorOfString(vectorizeFromMapOfStringInt(_familyInfo)); + _familyInfo=devectorizeToMapOfStringInt(v2); + } + catch(INTERP_KERNEL::Exception& e) + { + cerr<<"proc "< v2=allgathervVectorOfString( + vectorizeFromMapOfStringVectorOfString(_groupInfo)); + _groupInfo=deleteDuplicatesInMapOfStringVectorOfString( + devectorizeToMapOfStringVectorOfString(v2)); + } + catch(INTERP_KERNEL::Exception& e) + { + cerr<<"proc "< _meshes=MEDLoader::GetMeshNames(filename); + //std::vector< std::string > _fields=MEDLoader::GetAllFieldNamesOnMesh(filename,meshname[0]); + //cout<<"number of fields "<<_fields.size()<readSeq (filename.c_str(),meshname.c_str()); } - catch ( MED_EXCEPTION& e ) + catch (...) { if ( _driver ) delete _driver; _driver=0; - throw e; + throw INTERP_KERNEL::Exception(LOCALIZED("problem reading .med files")); } if ( _mesh[0] && _mesh[0]->getNumberOfNodes() > 0 ) _i_non_empty_mesh = 0; @@ -606,22 +1157,29 @@ MESHCollection::MESHCollection(const string& filename, const string& meshname) MESHCollection::~MESHCollection() { for (int i=0; i<_mesh.size();i++) - { - if (_mesh[i]!=0) _mesh[i]->decrRef(); - if (_cellFamilyIds[i]!=0) _cellFamilyIds[i]->decrRef(); - } + if (_mesh[i]!=0) _mesh[i]->decrRef(); + + for (int i=0; i<_cellFamilyIds.size();i++) + if (_cellFamilyIds[i]!=0) _cellFamilyIds[i]->decrRef(); for (int i=0; i<_faceMesh.size();i++) - { - if (_faceMesh[i]!=0) _faceMesh[i]->decrRef(); - if (_faceFamilyIds[i]!=0) _faceFamilyIds[i]->decrRef(); - } + if (_faceMesh[i]!=0) _faceMesh[i]->decrRef(); + + for (int i=0; i<_faceFamilyIds.size();i++) + if (_faceFamilyIds[i]!=0) _faceFamilyIds[i]->decrRef(); + + for (map::iterator it=_mapDataArrayInt.begin() ; it!=_mapDataArrayInt.end(); it++ ) + if ((*it).second!=0) (*it).second->decrRef(); + + for (map::iterator it=_mapDataArrayDouble.begin() ; it!=_mapDataArrayDouble.end(); it++ ) + if ((*it).second!=0) (*it).second->decrRef(); if (_driver !=0) {delete _driver; _driver=0;} if (_topology!=0 && _owns_topology) {delete _topology; _topology=0;} + + if (_joint_finder!=0) {delete _joint_finder; _joint_finder=0;} } - /*! constructing the MESH collection from a file * * The method creates as many MED-files as there are domains in the @@ -632,13 +1190,13 @@ MESHCollection::~MESHCollection() * \param filename name of the master file that will contain the list of the MED files * */ -void MESHCollection::write(const string& filename) +void MESHCollection::write(const std::string& filename) { //building the connect zones necessary for writing joints // if (_topology->nbDomain()>1) // buildConnectZones(); //suppresses link with driver so that it can be changed for writing - if (_driver!=0)delete _driver; + if (_driver!=0) delete _driver; _driver=0; //char filenamechar[256]; @@ -661,10 +1219,9 @@ MESHCollectionDriver* MESHCollection::retrieveDriver() _driver=new MESHCollectionMedAsciiDriver(this); break; default: - throw MEDMEM::MEDEXCEPTION("Unrecognized driver"); + throw INTERP_KERNEL::Exception(LOCALIZED("Unrecognized driver")); } } - return _driver; } @@ -672,67 +1229,250 @@ MESHCollectionDriver* MESHCollection::retrieveDriver() /*! gets an existing driver * */ -MESHCollectionDriver* MESHCollection::getDriver() const -{ +MESHCollectionDriver* MESHCollection::getDriver() const { return _driver; } + // /*! retrieves the mesh dimension*/ -int MESHCollection::getMeshDimension() const -{ +int MESHCollection::getMeshDimension() const { return _i_non_empty_mesh < 0 ? -1 : _mesh[_i_non_empty_mesh]->getMeshDimension(); } -vector& MESHCollection::getMesh() -{ +std::vector& MESHCollection::getMesh() { return _mesh; } -vector& MESHCollection::getFaceMesh() -{ + +std::vector& MESHCollection::getFaceMesh() { return _faceMesh; } -ParaMEDMEM::MEDCouplingUMesh* MESHCollection::getMesh(int idomain) const -{ + +ParaMEDMEM::MEDCouplingUMesh* MESHCollection::getMesh(int idomain) const { return _mesh[idomain]; } -ParaMEDMEM::MEDCouplingUMesh* MESHCollection::getFaceMesh(int idomain) -{ +ParaMEDMEM::MEDCouplingUMesh* MESHCollection::getFaceMesh(int idomain) { return _faceMesh[idomain]; } -vector& MESHCollection::getCZ() -{ + +std::vector& MESHCollection::getCZ() { return _connect_zones; } -Topology* MESHCollection::getTopology() const -{ +Topology* MESHCollection::getTopology() const { return _topology; } -void MESHCollection::setTopology(Topology* topo) -{ +void MESHCollection::setTopology(Topology* topo) { if (_topology!=0) { - throw MEDMEM::MEDEXCEPTION("Erreur : topology is already set"); + throw INTERP_KERNEL::Exception(LOCALIZED("topology is already set")); } else _topology = topo; } - /*! Method creating the cell graph * * \param array returns the pointer to the structure that contains the graph * \param edgeweight returns the pointer to the table that contains the edgeweights * (only used if indivisible regions are required) */ - -void MESHCollection::buildCellGraph(MEDPARTITIONER::MEDSKYLINEARRAY* & array,int *& edgeweights ) +void MESHCollection::buildCellGraph(MEDPARTITIONER::MEDSKYLINEARRAY* & array, int *& edgeweights ) //cvwat09 { - + using std::multimap; + using std::vector; + using std::make_pair; + using std::pair; + multimap< int, int > node2cell; multimap< int, int > cell2cell; + multimap< int, int > cell2node; + + vector > > commonDistantNodes; + int nbdomain=_topology->nbDomain(); + if (isParallelMode()) + { + _joint_finder=new JointFinder(*this); + _joint_finder->findCommonDistantNodes(); + commonDistantNodes=_joint_finder->getDistantNodeCell(); + } + + if (MyGlobals::_verbose>500) _joint_finder->print(); + + //looking for reverse nodal connectivity i global numbering + for (int idomain=0; idomainisMyDomain(idomain)) continue; + + /*obsolete + int offsetCell=0, offsetNode=0; + if (isParallelMode()) + { + offsetCell=_domain_selector->getDomainCellShift(idomain); + offsetNode=_domain_selector->getDomainNodeShift(idomain); + }*/ + + ParaMEDMEM::DataArrayInt* index=ParaMEDMEM::DataArrayInt::New(); + ParaMEDMEM::DataArrayInt* revConn=ParaMEDMEM::DataArrayInt::New(); + int nbNodes=_mesh[idomain]->getNumberOfNodes(); + //cout<<"proc "<getReverseNodalConnectivity(revConn,index); + //problem saturation over 1 000 000 nodes for 1 proc + if (MyGlobals::_verbose>100) cout<<"proc "<getPointer(); + int* revConnPtr=revConn->getPointer(); + //if (MyGlobals::_verbose>100) cout<<"proc "<convertNodeToGlobal(idomain,i); + int globalCell=_topology->convertCellToGlobal(idomain,revConnPtr[icell]); + node2cell.insert(make_pair(globalNode, globalCell)); + //cvw cout<<" "<decrRef(); + index->decrRef(); + //vector > > dNC=getDistantNodeCell() + for (int iother=0; iother::iterator it; + int isource=idomain; + int itarget=iother; + for (it=_joint_finder->_distant_node_cell[isource][itarget].begin(); + it!=_joint_finder->_distant_node_cell[isource][itarget].end(); it++) + { + int globalNode=_topology->convertNodeToGlobal(idomain,(*it).first); + int globalCell=(*it).second; + node2cell.insert(make_pair(globalNode, globalCell)); + //cout<<"processor "<100) cout<<"proc "<nbNodes()<nbNodes(); inode++) //on all nodes + { + typedef multimap::const_iterator MI; + pair myRange=node2cell.equal_range(inode); + for (MI cell1=myRange.first; cell1!=myRange.second; cell1++) //on cells with inode + { + pair myNodes1=cell2node.equal_range(cell1->second); //nodes of one cell + for (MI cell2=myRange.first; cell2!=myRange.second; cell2++) //on one of these cell + { + if (cell1->second!=cell2->second) //in cells of my domain + { + pair myNodes2=cell2node.equal_range(cell2->second); //on nodes of this cell + int nbcn=0; //number of common nodes between cells: at least 3 for cells + for (MI it1=myNodes1.first; it1!=myNodes1.second; ++it1) + { + for (MI it2=myNodes2.first; it2!=myNodes2.second; ++it2) + { + if ((*it1).second==(*it2).second) + { + nbcn=nbcn+1 ; break; + } + } + } + if (nbcn>=3) //cvw TODO if 2d cells set at 2 + cell2cell.insert(make_pair(cell1->second,cell2->second)); + //note here there is some global numerotation of cell which come from other domain (not mydomain) + //cout<<" "<second<<"!"<second; //cvw + } + } + } + } + + if (MyGlobals::_verbose>100) cout<<"proc "< index,value; + index.push_back(0); + int idep=0; + + for (int idomain=0; idomainisMyDomain(idomain)) continue; + int nbCells=_mesh[idomain]->getNumberOfCells(); + for (int icell=0; icellconvertCellToGlobal(idomain,icell); + multimap::iterator it; + pair::iterator,multimap::iterator> ret; + ret=cell2cell.equal_range(globalCell); + //cout<<" "<100) + { + std::cout<<"\nproc "<<_domain_selector->rank()<<" : end MESHCollection::buildCellGraph "<< + index.size()-1<<" "<1) + { + for (int i=0; i<10; ++i) cout< node2cell; + multimap< int, int > cell2cell; + vector > > commonDistantNodes; int nbdomain=_topology->nbDomain(); if (isParallelMode()) @@ -743,14 +1483,14 @@ void MESHCollection::buildCellGraph(MEDPARTITIONER::MEDSKYLINEARRAY* & array,int } //looking for reverse nodal connectivity i global numbering - for (int idomain=0; idomainisMyDomain(idomain)) continue; int offset=0, procOffset=0; if (isParallelMode()) { - offset=_domain_selector->getDomainShift(idomain); - procOffset=_domain_selector->getProcShift()+1; + offset=_domain_selector->getDomainCellShift(idomain); + procOffset=_domain_selector->getProcShift(); } ParaMEDMEM::DataArrayInt* index=ParaMEDMEM::DataArrayInt::New(); ParaMEDMEM::DataArrayInt* revConn=ParaMEDMEM::DataArrayInt::New(); @@ -774,8 +1514,10 @@ void MESHCollection::buildCellGraph(MEDPARTITIONER::MEDSKYLINEARRAY* & array,int int* globalRevConnPtr=globalRevConn->getPointer(); for (int i=0; i<_mesh[idomain]->getNumberOfNodes();i++) { - for (int icell=index_ptr[i]; icellfirst; int icell=iter->second; - - node2cell.insert(make_pair(globalNodeIds[ilocnode],icell+offset)); + node2cell.insert(make_pair(globalNodeIds[ilocnode],icell+offset)); } - // } } } @@ -807,33 +1547,41 @@ void MESHCollection::buildCellGraph(MEDPARTITIONER::MEDSKYLINEARRAY* & array,int // means 6 arcs (0,1), (0,2), (0,3), (1,2), (1,3), (2,3) // in present version arcs are not doubled but reflexive (1,1) arcs are present for each cell + //warning here one node have effective number of cell with it + //but cell could have more than effective nodes + //is it normal??? because other equals nodes in other domain (with other inode)??? + int mincell,maxcell; if (isParallelMode()) { - mincell=_domain_selector->getProcShift()+1; + mincell=_domain_selector->getProcShift(); maxcell=mincell; for (int i=0; iisMyDomain(i)) maxcell+=_mesh[i]->getNumberOfCells(); - } else { mincell=0; maxcell=_topology->nbCells(); } - for (int inode=0; inode<_topology->nbNodes();inode++) + for (int inode=0; inode<_topology->nbNodes(); inode++) //on all nodes { typedef multimap::const_iterator MI; pair myRange = node2cell.equal_range(inode); - for (MI cell1=myRange.first; cell1!=myRange.second; cell1++) + + + for (MI cell1=myRange.first; cell1!=myRange.second; cell1++) //on cells with inode { - for (MI cell2 = myRange.first; cell2!=myRange.second; cell2++) + for (MI cell2 = myRange.first; cell2!=myRange.second; cell2++) //on one of these cell { - if (cell1->second!=cell2->second&&cell1->second>=mincell&&cell1->secondsecond,cell2->second)); + if (cell1->second!=cell2->second && cell1->second>=mincell && cell1->secondsecond,cell2->second)); + } } } } - + //cout<<"proc "<::const_iterator iter; @@ -841,26 +1589,34 @@ void MESHCollection::buildCellGraph(MEDPARTITIONER::MEDSKYLINEARRAY* & array,int iter=cell2cell.begin(); vector index,value; index.push_back(0); + int idep=0; while (iter != cell2cell.end()) + { + multimap::const_iterator next_iter = cell2cell.upper_bound(iter->first); + int size=0; + for (multimap::const_iterator current_iter=iter; current_iter!=next_iter; current_iter++) { - multimap::const_iterator next_iter = cell2cell.upper_bound(iter->first); - int size=0; - for (multimap::const_iterator current_iter=iter; current_iter!=next_iter; current_iter++) + int ival=current_iter->second; //no adding one existing yet + for (int i=idep ; isecond); - size++; + ival=-1; + break; } - index.push_back(index[index.size()-1]+size); - - - iter=next_iter; + } + if (ival!=-1) + { + value.push_back(ival); + size++; + } } - + idep=index[index.size()-1]+size; + index.push_back(idep); + iter=next_iter; + } array=new MEDPARTITIONER::MEDSKYLINEARRAY(index,value); - - cout<< "end of graph creation"<0"); + using std::cout; + using std::endl; + + if (MyGlobals::_verbose>10) cout<<"proc "< 0")); MEDPARTITIONER::MEDSKYLINEARRAY* array=0; int* edgeweights=0; - cout<<"Building cell graph"; + //cout<<"Building cell graph... "; // if ( _domain_selector ) // buildCellGraphParallel(array,edgeweights); // else - buildCellGraph(array,edgeweights); + buildCellGraph(array,edgeweights); //cvwat09 + //MPI_Barrier(MPI_COMM_WORLD); + //cout<<"proc "<10) cout<<"METISGraph"<10) cout<<"SCOTCHGraph"<setVerticesWeights(user_vertices_weights); - cout<<"Partitioning graph"; - cellGraph->partGraph(nbdomain,options_string,_domain_selector); - - + if (MyGlobals::_is0verbose>10) cout<<"partitioning graph on "<partGraph(nbdomain, options_string, _domain_selector); //cvwat10 - cout<<"Building new topology"; + if (MyGlobals::_is0verbose>10) cout<<"building new topology"<11) cout<<"proc "<nbCells())); //cellGraph is a shared pointer - Topology* topology = new ParallelTopology (cellGraph, nbdomain, getMeshDimension()); + Topology* topology = new ParallelTopology (cellGraph, getTopology(), nbdomain, getMeshDimension()); // if (array!=0) delete array; delete cellGraph; @@ -960,9 +1724,248 @@ void MESHCollection::setDomainNames(const std::string& name) { for (int i=0; i<_topology->nbDomain(); i++) { - ostringstream oss; + std::ostringstream oss; oss<isMyDomain(i)) _mesh[i]->setName(oss.str().c_str()); } } + +ParaMEDMEM::DataArrayDouble* MESHCollection::getField(std::string descriptionField, int iold) +//getField look for and read it if not done, and assume decrRef() in ~MESHCollection; +//something like MEDCouplingFieldDouble *f2=MEDLoader::ReadFieldCell(name.c_str(),f1->getMesh()->getName(),0,f1->getName(),0,1); + { + int rank=MyGlobals::_rank; + string tag="ioldFieldDouble="+intToStr(iold); + string descriptionIold=descriptionField+serializeFromString(tag); + if (_mapDataArrayDouble.find(descriptionIold)!=_mapDataArrayDouble.end()) + { + if (MyGlobals::_verbose>300) cout<<"proc "<reprZip()<200) cout<<"proc "<10) + cout<<"proc "<getArray(); + //to know names of components + vector browse=browseFieldDouble(f2); + //done yet + //double time=f2->getTime(IT,DT); + //browse.push_back("time="+doubleToStr(time)); + string localFieldInformation=descriptionIold+serializeFromVectorOfString(browse); + if (MyGlobals::_verbose>10) cout<<"proc "<incrRef(); //free field, keep res + f2->decrRef(); + _mapDataArrayDouble[descriptionIold]=res; + + //duplicate it! because f2->decRef!! + //DataArrayDouble* res=f2->getArray()->deepCpy(); + //f2->decrRef(); + //cout<reprZip()< r2; + //from allgatherv then vector(procs) of serialised vector(fields) of vector(description) data + for (int i=0; i<_fieldDescriptions.size(); i++) + { + vector r1=deserializeToVectorOfString(_fieldDescriptions[i]); + for (int i=0; i& inodesFace,vector< int >& inodesCell) +{ + int ires=0; + int nbok=inodesFace.size(); + for (int i=0; inbDomain(); inew++) + { + if (isParallelMode() && _domain_selector->isMyDomain(inew)) + { + if (MyGlobals::_verbose>200) + std::cout<<"proc "<getNumberOfCells()< nodeIds; + //cout<<"proc "<getReverseNodalConnectivity(revNodalCel,revNodalIndxCel); + int *revC=revNodalCel->getPointer(); + int *revIndxC=revNodalIndxCel->getPointer(); + + vector< int > faceOnCell; + vector< int > faceNotOnCell; + int nbface=mfac->getNumberOfCells(); + for (int iface=0; iface inodesFace; + mfac->getNodeIdsOfCell(iface, inodesFace); + int nbnodFace=inodesFace.size(); + //set inodesFace in mcel + for (int i=0; i inodesCell; + mcel->getNodeIdsOfCell(icel, inodesCell); + ok=isFaceOncell(inodesFace, inodesCell); + if (ok) break; + } + if (ok) + { + faceOnCell.push_back(iface); + //if (MyGlobals::_is0verbose) cout<<"face on cell "<decrRef(); + revNodalIndxCel->decrRef(); + + string cle; + cle=cle1ToStr("filterFaceOnCell",inew); + _mapDataArrayInt[cle]=createDataArrayIntFromVector(faceOnCell); + cle=cle1ToStr("filterNotFaceOnCell",inew); + _mapDataArrayInt[cle]=createDataArrayIntFromVector(faceNotOnCell); + + /*ParaMEDMEM::DataArrayInt* index=ParaMEDMEM::DataArrayInt::New(); + ParaMEDMEM::DataArrayInt* revConn=ParaMEDMEM::DataArrayInt::New(); + _mesh[idomain]->getReverseNodalConnectivity(revConn,index); + int* index_ptr=index->getPointer();*/ + + /*if (MyGlobals::_is0verbose) + { + cout<<"proc "<nbDomain(); inew++) + { + if (isParallelMode() && _domain_selector->isMyDomain(inew)) + { + if (MyGlobals::_verbose>1) std::cout<<"proc "<getNumberOfCells()<buildDescendingConnectivity(desc,descIndx,revDesc,revDescIndx); + revDesc->decrRef(); + desc->decrRef(); + descIndx->decrRef(); + int nbOfCells=meshDM1->getNumberOfCells(); + const int *revDescIndxC=revDescIndx->getConstPointer(); + std::vector boundaryCells; + for(int i=0; idecrRef(); + bool keepCoords=true; + MEDCouplingUMesh *ret=(MEDCouplingUMesh *)meshDM1->buildPartOfMySelf(&boundaryCells[0],&boundaryCells[0]+boundaryCells.size(),keepCoords); + meshDM1->decrRef(); + //don't know what to do with result yet.. + //_faceMesh[inew]->decrRef(); + //_faceMesh[inew]=ret; + } + } +} +*/ + diff --git a/src/MEDPartitioner/MEDPARTITIONER_MESHCollection.hxx b/src/MEDPartitioner/MEDPARTITIONER_MESHCollection.hxx index 331d33339..e30a9b639 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_MESHCollection.hxx +++ b/src/MEDPartitioner/MEDPARTITIONER_MESHCollection.hxx @@ -22,6 +22,8 @@ #include "MEDPARTITIONER.hxx" #include "MEDPARTITIONER_Graph.hxx" +#include "MEDCouplingUMesh.hxx" + //#include "MEDPARTITIONER_FaceModel.hxx" //#include "boost/shared_ptr.hpp" #include @@ -89,62 +91,40 @@ namespace MEDPARTITIONER //creation of a user specified partition Topology* createPartition(const int* partition); - - // //retrieving list of types -// void getTypeList(int* cell_list,int nb_cells,MED_EN::medEntityMesh entity, -// MED_EN::medGeometryElement* type_list) const ; - -// //getting list of coordinates -// void getCoordinates(int* node_list,int nb_nodes, double* coordinates) const ; - -// //getting connectivities -// void getNodeConnectivity( const int* cell_list,int nb_cells,MED_EN::medEntityMesh,MED_EN::medGeometryElement type, int* type_connectivity) const ; -// void getPolygonNodeConnectivity(const int* cell_list,int nb_cells,MED_EN::medEntityMesh entity, -// vector& type_connectivity, vector& connectivity_index) const; -// void getPolyhedraNodeConnectivity(const int* cell_list,int nb_cells,MED_EN::medEntityMesh entity, -// vector& type_connectivity, vector& connectivity_index, vector& face_connectivity_index) const; - -// void getFaceConnectivity( const int* cell_list,int nb_cells,MED_EN::medEntityMesh,MED_EN::medGeometryElement type, int* type_connectivity) const ; - -// //void getFaceConnectivity( const int* cell_list,int nb_cells,MED_EN::medGeometryElement type, int* type_connectivity) const ; - -// //getting mesh dimension + + //getting mesh dimension int getMeshDimension() const ; -// //getting space dimension -// int getSpaceDimension() const ; - -// //getting system of coordinates -// std::string getSystem() const; + //getting a reference to mesh vector + std::vector& getMesh(); + std::vector& getFaceMesh(); + std::vector >& getGroupMeshes(); -// //getting name of the mesh -// std::string getMeshName() const; - -// //return constituent entity -// MED_EN::medEntityMesh getSubEntity() const; - -// //getting a reference to mesh vector - std::vector& getMesh() ; - std::vector& getFaceMesh() ; - std::vector >&getGroupMeshes(); - ParaMEDMEM::MEDCouplingUMesh* getMesh(int idomain) const; ParaMEDMEM::MEDCouplingUMesh* getFaceMesh(int idomain); std::vector& getGroupMeshes(int idomain); std::vector& getCellFamilyIds() {return _cellFamilyIds;} std::vector& getFaceFamilyIds() {return _faceFamilyIds;} - - std::map& getFamilyInfo(){return _familyInfo;} - std::map >& getGroupInfo(){return _groupInfo;} - -// //getting a reference to connect zones vector + + std::map& getMapDataArrayInt() {return _mapDataArrayInt;} + std::map& getMapDataArrayDouble() {return _mapDataArrayDouble;} + + std::map& getFamilyInfo() {return _familyInfo;} + std::map >& getGroupInfo() {return _groupInfo;} + + ParaMEDMEM::DataArrayDouble* getField(std::string descriptionField, int iold); + std::vector& getFieldDescriptions() {return _fieldDescriptions;} + void prepareFieldDescriptions(); + void filterFaceOnCell(); + + //getting a reference to connect zones vector std::vector& getCZ(); //getting a pointer to topology Topology* getTopology() const ; ParaDomainSelector* getParaDomainSelector() const{return _domain_selector;} - //settig a new topology + //settig a new topology void setTopology(Topology* topology); //getting/setting the name of the global mesh (as opposed @@ -158,48 +138,66 @@ namespace MEDPARTITIONER void setDescription(const std::string& name) { _description=name;} //creates the node mapping between an old collection and the present one - void createNodeMapping( MESHCollection& initialCollection, std::multimap,std::pair >& nodeMapping); + void createNodeMapping(MESHCollection& initialCollection, + std::multimap,std::pair >& nodeMapping); - void castCellMeshes(MESHCollection& initialCollection, std::vector > >& new2oldIds); + void castCellMeshes(MESHCollection& initialCollection, + std::vector > >& new2oldIds); + //creates faces on the new collection - void castFaceMeshes( MESHCollection& initialCollection,const std::multimap,std::pair >& nodeMapping); + void castFaceMeshes(MESHCollection& initialCollection, + const std::multimap, std::pair >& nodeMapping, + std::vector > >& new2oldIds); - //creates faces on the new collection - void castMeshes(std::vector& meshCastFrom,std::vector& meshCastTo, MESHCollection& initialCollection,const std::multimap,std::pair >& nodeMapping, std::vector > >& old2newIds); - private: - - void castIntField(std::vector& meshesCastFrom,std::vector& meshesCastTo, std::vector& arrayFrom, std::vector& arrayTo); + void castIntField2(std::vector& meshesCastFrom, + std::vector& meshesCastTo, + std::vector& arrayFrom, + std::string nameArrayTo); + + void castAllFields(MESHCollection& initialCollection, + std::string nameArrayTo); void findCommonDistantNodes(std::vector > >& commonDistantNodes); -void remapIntField(const ParaMEDMEM::MEDCouplingUMesh& sourceMesh, - const ParaMEDMEM::MEDCouplingUMesh& targetMesh, - const int* fromArray, - int* toArray); + void remapIntField(const ParaMEDMEM::MEDCouplingUMesh& sourceMesh, + const ParaMEDMEM::MEDCouplingUMesh& targetMesh, + const int* fromArray, + int* toArray); + + void remapIntField2(int inew, int iold, + const ParaMEDMEM::MEDCouplingUMesh& sourceMesh, + const ParaMEDMEM::MEDCouplingUMesh& targetMesh, + const int* fromArray, + std::string nameArrayTo); + + void remapDoubleField3(int inew, int iold, + ParaMEDMEM::DataArrayDouble* fromArray, + std::string nameArrayTo, + std::string descriptionField); //!link to mesh_collection topology - Topology* _topology; + Topology* _topology; //!control over topology - bool _owns_topology; + bool _owns_topology; //!link to graph - // Graph* _cell_graph; + //Graph* _cell_graph; //! Driver for read/write operations - MESHCollectionDriver* _driver; + MESHCollectionDriver* _driver; //! Parallelizer - mark of parallel execution mode - ParaDomainSelector* _domain_selector; + ParaDomainSelector* _domain_selector; //!links to meshes - std::vector _mesh; - std::vector _faceMesh; + std::vector _mesh; + std::vector _faceMesh; - //!index of a non empty mesh within _mesh (in parallel mode all of meshes can be empty) - int _i_non_empty_mesh; + //!index of a non empty mesh within _mesh (in parallel mode all of meshes can be empty) + int _i_non_empty_mesh; //!links to connectzones std::vector _connect_zones; @@ -207,34 +205,41 @@ void remapIntField(const ParaMEDMEM::MEDCouplingUMesh& sourceMesh, //!family ids storages std::vector _cellFamilyIds; std::vector _faceFamilyIds; - + + //!DataArrayInt* storages + std::map _mapDataArrayInt; + //!DataArrayDouble* storages + std::map _mapDataArrayDouble; + + std::vector _fieldDescriptions; //fields to be partitioned + //!group family conversion - std::map _familyInfo; + std::map _familyInfo; std::map > _groupInfo; //!list of groups that are not to be splitted - std::vector _indivisible_regions; + std::vector _indivisible_regions; //!name of global mesh - std::string _name; + std::string _name; //!description of global mesh - std::string _description; + std::string _description; //! specifies the driver associated to the collection - DriverType _driver_type; + DriverType _driver_type; /*! flag specifying that the splitter should create boundary constituent entity so that they are written in joints*/ - bool _subdomain_boundary_creates; + bool _subdomain_boundary_creates; /*! flag specifying that families must be preserved by the splitting*/ - bool _family_splitting; + bool _family_splitting; /*! flag specifying that groups must be created on all domains, even if they are empty*/ - bool _create_empty_groups; + bool _create_empty_groups; JointFinder* _joint_finder; }; diff --git a/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionDriver.cxx b/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionDriver.cxx index 2de4dc7b6..78b1e5edf 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionDriver.cxx +++ b/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionDriver.cxx @@ -31,9 +31,10 @@ #include #include "MEDCouplingUMesh.hxx" +#include "MEDCouplingFieldDouble.hxx" #include "MEDLoader.hxx" #include "MEDFileMesh.hxx" -#include "MEDMEM_Exception.hxx" + extern "C" { #include "med.h" } @@ -42,8 +43,10 @@ extern "C" { #include "MEDPARTITIONER_MESHCollectionDriver.hxx" #include "MEDPARTITIONER_MESHCollection.hxx" #include "MEDPARTITIONER_ParaDomainSelector.hxx" +#include "MEDPARTITIONER_utils.hxx" using namespace MEDPARTITIONER; +using namespace std; //template inclusion //#include "MEDPARTITIONER_MESHCollectionDriver.H" @@ -78,11 +81,9 @@ MESHCollectionDriver::MESHCollectionDriver(MESHCollection* collection):_collecti * */ int MESHCollectionDriver::readSeq(const char* filename, const char* meshname) { - //const char* LOC = "MEDPARTITIONER::MESHCollectionDriver::readSeq()"; - // BEGIN_OF_MED(LOC); - - _filename.resize(1); - _filename[0]=string(filename); + cout<<"readSeq"<getCZ()).clear(); + /*cvw vector cellglobal,nodeglobal,faceglobal; cellglobal.resize(1); nodeglobal.resize(1); @@ -122,11 +124,12 @@ int MESHCollectionDriver::readSeq(const char* filename, const char* meshname) //connectzone argument is 0 ParallelTopology* aPT = new ParallelTopology ((_collection->getMesh()), (_collection->getCZ()), cellglobal, nodeglobal, faceglobal); + */ + + ParallelTopology* aPT = new ParallelTopology((_collection->getMesh())); _collection->setTopology(aPT); _collection->setName(meshname); _collection->setDomainNames(meshname); - - // END_OF_MED(LOC); return 0; } @@ -137,35 +140,141 @@ int MESHCollectionDriver::readSeq(const char* filename, const char* meshname) */ //================================================================================ - -void MESHCollectionDriver::readSubdomain(vector& cellglobal, +void MESHCollectionDriver::readSubdomain(vector& cellglobal, //cvwat03 vector& faceglobal, vector& nodeglobal, int idomain) { - string meshname=_meshname[idomain]; - string file=_filename[idomain]; + string meshname=MyGlobals::_meshNames[idomain]; + string file=MyGlobals::_fileNames[idomain]; - cout << "Reading "<<_meshname[idomain]<<" in "<<_filename[idomain]<getMesh())[idomain]=mfm->getLevel0Mesh(false); - (_collection->getFaceMesh())[idomain]=mfm->getLevelM1Mesh(false); + vector nonEmpty=mfm->getNonEmptyLevels(); + + try + { + (_collection->getMesh())[idomain]=mfm->getLevel0Mesh(false); + //reading families groups + ParaMEDMEM::DataArrayInt* cellIds(mfm->getFamilyFieldAtLevel(0)->deepCpy()); + (_collection->getCellFamilyIds())[idomain]=cellIds; + } + catch(...) + { + (_collection->getMesh())[idomain]=createEmptyMEDCouplingUMesh(); // or 0 if you want tests; + ParaMEDMEM::DataArrayInt* empty=ParaMEDMEM::DataArrayInt::New(); + empty->alloc(0,1); + (_collection->getCellFamilyIds())[idomain]=empty; + cout<<"\nNO Level0Mesh (Cells)\n"; + } + try + { + if (nonEmpty.size()>1 && nonEmpty[1]==-1) + { + (_collection->getFaceMesh())[idomain]=mfm->getLevelM1Mesh(false); + //reading families groups + ParaMEDMEM::DataArrayInt* faceIds(mfm->getFamilyFieldAtLevel(-1)->deepCpy()); + (_collection->getFaceFamilyIds())[idomain]=faceIds; + } + else + { + throw "no faces"; + } + } + catch(...) + { + //ParaMEDMEM::MEDCouplingUMesh *umesh=ParaMEDMEM::MEDCouplingUMesh::New(); //empty one + //umesh->setMeshDimension(3); + //umesh->allocateCells(0); + //int nb=umesh->getNumberOfCells(); //no use if no allocateCells(0)! because thrown exception + //cout<<"\nempty mesh"<getFaceMesh())[idomain]=createEmptyMEDCouplingUMesh(); // or 0 if you want test; + ParaMEDMEM::DataArrayInt* empty=ParaMEDMEM::DataArrayInt::New(); + (_collection->getFaceFamilyIds())[idomain]=empty; + if (MyGlobals::_verbose>10) cout<<"proc "<getFamilyInfo()=mfm->getFamilyInfo(); + _collection->getGroupInfo()=mfm->getGroupInfo(); + + mfm->decrRef(); + + vector localInformation; + string str; + localInformation.push_back(str+"ioldDomain="+intToStr(idomain)); + localInformation.push_back(str+"meshName="+meshname); + MyGlobals::_generalInformations.push_back(serializeFromVectorOfString(localInformation)); + vector localFields=browseAllFieldsOnMesh(file, meshname, idomain); //cvwat07 + if (localFields.size()>0) + MyGlobals::_fieldDescriptions.push_back(serializeFromVectorOfString(localFields)); + //cout<< "End Reading "<getFamilyFieldAtLevel(0)->deepCpy()); - ParaMEDMEM::DataArrayInt* faceIds(mfm->getFamilyFieldAtLevel(-1)->deepCpy()); - (_collection->getCellFamilyIds())[idomain]=cellIds; - (_collection->getFaceFamilyIds())[idomain]=faceIds; +void MESHCollectionDriver::readSubdomain(int idomain) +{ + string meshname=MyGlobals::_meshNames[idomain]; + string file=MyGlobals::_fileNames[idomain]; + //cout << "Reading "< nonEmpty=mfm->getNonEmptyLevels(); + + try + { + (_collection->getMesh())[idomain]=mfm->getLevel0Mesh(false); + //reading families groups + ParaMEDMEM::DataArrayInt* cellIds(mfm->getFamilyFieldAtLevel(0)->deepCpy()); + (_collection->getCellFamilyIds())[idomain]=cellIds; + } + catch(...) + { + (_collection->getMesh())[idomain]=createEmptyMEDCouplingUMesh(); // or 0 if you want tests; + ParaMEDMEM::DataArrayInt* empty=ParaMEDMEM::DataArrayInt::New(); + empty->alloc(0,1); + (_collection->getCellFamilyIds())[idomain]=empty; + cout<<"\nNO Level0Mesh (Cells)\n"; + } + try + { + if (nonEmpty.size()>1 && nonEmpty[1]==-1) + { + (_collection->getFaceMesh())[idomain]=mfm->getLevelM1Mesh(false); + //reading families groups + ParaMEDMEM::DataArrayInt* faceIds(mfm->getFamilyFieldAtLevel(-1)->deepCpy()); + (_collection->getFaceFamilyIds())[idomain]=faceIds; + } + else + { + throw "no faces"; + } + } + catch(...) + { + (_collection->getFaceMesh())[idomain]=createEmptyMEDCouplingUMesh(); // or 0 if you want test; + ParaMEDMEM::DataArrayInt* empty=ParaMEDMEM::DataArrayInt::New(); + (_collection->getFaceFamilyIds())[idomain]=empty; + if (MyGlobals::_verbose>10) cout<<"proc "<getFamilyInfo()=mfm->getFamilyInfo(); _collection->getGroupInfo()=mfm->getGroupInfo(); - cout <<"End of Read"<decrRef(); + + vector localInformation; + string str; + localInformation.push_back(str+"ioldDomain="+intToStr(idomain)); + localInformation.push_back(str+"meshName="+meshname); + MyGlobals::_generalInformations.push_back(serializeFromVectorOfString(localInformation)); + vector localFields=browseAllFieldsOnMesh(file, meshname, idomain); //cvwat07 + if (localFields.size()>0) + MyGlobals::_fieldDescriptions.push_back(serializeFromVectorOfString(localFields)); + //cout<< "End Reading "< meshes; ParaMEDMEM::MEDCouplingUMesh* cellMesh=_collection->getMesh(idomain); - ParaMEDMEM::MEDCouplingUMesh*faceMesh =_collection->getFaceMesh(idomain); + ParaMEDMEM::MEDCouplingUMesh* faceMesh=_collection->getFaceMesh(idomain); + ParaMEDMEM::MEDCouplingUMesh* faceMeshFilter=0; + string finalMeshName=extractFromDescription(MyGlobals::_generalInformations[0], "finalMeshName="); + string cleFilter=cle1ToStr("filterFaceOnCell",idomain); + DataArrayInt* filter=0; + if (_collection->getMapDataArrayInt().find(cleFilter)!=_collection->getMapDataArrayInt().end()) + { + filter=_collection->getMapDataArrayInt().find(cleFilter)->second; + int* index=filter->getPointer(); + faceMeshFilter=(MEDCouplingUMesh *) faceMesh->buildPartOfMySelf(index,index+filter->getNbOfElems(),true); + faceMesh=faceMeshFilter; + } + cellMesh->setName(finalMeshName.c_str()); meshes.push_back(cellMesh); - // faceMesh->zipCoords(); + + //cellMesh->zipCoords(); + //faceMesh->zipCoords(); + faceMesh->checkCoherency(); - faceMesh->tryToShareSameCoordsPermute(*cellMesh,1e-10); - meshes.push_back(faceMesh); - MEDLoader::WriteUMeshes(distfilename.c_str(), meshes,true); - ParaMEDMEM::MEDFileUMesh* mfm=ParaMEDMEM::MEDFileUMesh::New(distfilename.c_str(),_collection->getMesh(idomain)->getName()); - mfm->setFamilyFieldArr(-1,(_collection->getFaceFamilyIds())[idomain]); + if (faceMesh->getNumberOfCells()>0) + { + faceMesh->tryToShareSameCoordsPermute(*cellMesh, 1e-10); + meshes.push_back(faceMesh); + } + + /*do not work + ParaMEDMEM::MEDFileUMesh* mfm2=ParaMEDMEM::MEDFileUMesh::New(); + MEDFileUMesh* mfm2 = static_cast(cellMesh->getMeshes()->getMeshAtPos(0)); + MEDFileUMesh* mfm2 = ParaMEDMEM::MEDFileUMesh::New(cellMesh); + string fname="FUM_"+distfilename; + mfm2->setMeshAtLevel(0, cellMesh ); + mfm2->setMeshAtLevel(-1, faceMesh ); + mfm2->write(fname.c_str(),0); + mfm2->decrRef(); + */ + + ParaMEDMEM::MEDCouplingUMesh* boundaryMesh=0; + //ParaMEDMEM::MEDCouplingUMesh* boundaryMesh1=0; + //ParaMEDMEM::MEDCouplingUMesh* finalboundaryMesh=0; + if (MyGlobals::_creates_boundary_faces>0) + { + //try to write Boundary meshes + bool keepCoords=false; //TODO or true + boundaryMesh=(MEDCouplingUMesh *) cellMesh->buildBoundaryMesh(keepCoords); + boundaryMesh->setName("boundaryMesh"); + //cout<<"boundaryMesh "<getNumberOfCells()<checkCoherency(); + //boundaryMesh->tryToShareSameCoordsPermute(*cellMesh, 1e-10); + //meshes.push_back(boundaryMesh); + //string boundary="boundary_"+distfilename; + + /*try to find joint do no work + int rang=MyGlobals::_rank; + if (rang==1) (_collection->getParaDomainSelector())->sendMesh(*(boundaryMesh),0); + if (rang==0) + { + (_collection->getParaDomainSelector())->recvMesh(boundaryMesh1,1); + //vector meshes; + //vector corr; + //meshes.push_back(boundaryMesh); + //meshes.push_back(boundaryMesh1); + //need share the same coords + //boundaryMesh1->tryToShareSameCoordsPermute(*boundaryMesh, 1e-10); + //finalboundaryMesh=MEDCouplingUMesh::FuseUMeshesOnSameCoords(meshes,2, corr); + //boundaryMesh=finalboundaryMesh; + + boundaryMesh->zipCoords(); + boundaryMesh1->zipCoords(); + finalboundaryMesh=MEDCouplingUMesh::MergeUMeshes(boundaryMesh,boundaryMesh1); + DataArrayInt* commonNodes=0; + commonNodes=finalboundaryMesh->zipCoordsTraducer(); + boundaryMesh=finalboundaryMesh; + cout<<"zipcoords"<repr()<decrRef(); + + + if (boundaryMesh!=0) + { + //doing that testMesh becomes second mesh sorted by alphabetical order of name + MEDLoader::WriteUMesh(distfilename.c_str(), boundaryMesh, false); + boundaryMesh->decrRef(); + } + + //cout<<"familyInfo :\n"<getFamilyInfo())<getGroupInfo())<getMesh(idomain)->getName()); + + /*example of adding new family + (_collection->getFamilyInfo())["FaceNotOnCell"]=-500; + vector FaceNotOnCell; + FaceNotOnCell.push_back("FaceNotOnCell"); + (_collection->getGroupInfo())["FaceNotOnCell"]=FaceNotOnCell; + */ + mfm->setFamilyInfo(_collection->getFamilyInfo()); mfm->setGroupInfo(_collection->getGroupInfo()); + + //cvwat08 + //without filter mfm->setFamilyFieldArr(-1,(_collection->getFaceFamilyIds())[idomain]); + + string cle=cle1ToStr("faceFamily_toArray",idomain); + if (_collection->getMapDataArrayInt().find(cle)!=_collection->getMapDataArrayInt().end()) + { + DataArrayInt* fam=_collection->getMapDataArrayInt().find(cle)->second; + DataArrayInt* famFilter=0; + if (filter!=0) + { + int* index=filter->getPointer(); + int nbTuples=filter->getNbOfElems(); + //not the good one...buildPartOfMySelf do not exist for DataArray + //Filter=fam->renumberAndReduce(index, filter->getNbOfElems()); + famFilter=DataArrayInt::New(); + famFilter->alloc(nbTuples,1); + int* pfamFilter=famFilter->getPointer(); + int* pfam=fam->getPointer(); + for (int i=0; isetFamilyFieldArr(-1,fam); + famFilter->decrRef(); + } + //cout<<"proc "<setFamilyFieldArr(-1,fam); + // if (famFilter!=0) famFilter->decrRef(); + } + + /*example visualisation of filter + if (_collection->getMapDataArrayInt().find(cle)!=_collection->getMapDataArrayInt().end()) + { + DataArrayInt* fam=_collection->getMapDataArrayInt().find(cle)->second; + string cle2=cle1ToStr("filterNotFaceOnCell",idomain); + if (_collection->getMapDataArrayInt().find(cle2)!=_collection->getMapDataArrayInt().end()) + { + DataArrayInt* filter=_collection->getMapDataArrayInt().find(cle2)->second; + int* index=filter->getPointer(); + int* pfam=fam->getPointer(); + for (int i=0; igetNbOfElems(); i++) pfam[index[i]]=-500; + } + mfm->setFamilyFieldArr(-1,fam); + //mfm->setFamilyFieldArr(-1,_collection->getMapDataArrayInt().find(cle)->second); + } + */ + + cle=cle1ToStr("cellFamily_toArray",idomain); + if (_collection->getMapDataArrayInt().find(cle)!=_collection->getMapDataArrayInt().end()) + mfm->setFamilyFieldArr(0,_collection->getMapDataArrayInt().find(cle)->second); + mfm->write(distfilename.c_str(),0); + cle="/inewFieldDouble="+intToStr(idomain)+"/"; + + map::iterator it; + int nbfFieldFound=0; + for (it=_collection->getMapDataArrayDouble().begin() ; it!=_collection->getMapDataArrayDouble().end(); it++) + { + string desc=(*it).first; + size_t found=desc.find(cle); + if (found==string::npos) continue; + if (MyGlobals::_verbose>20) cout<<"proc "<setName(fieldName.c_str()); + field->setMesh(mfm->getLevel0Mesh(false)); + DataArrayDouble* da=(*it).second; + + //get information for components etc.. + vector r1; + r1=selectTagsInVectorOfString(MyGlobals::_generalInformations,"fieldName="+fieldName); + r1=selectTagsInVectorOfString(r1,"typeField="+intToStr(typeField)); + r1=selectTagsInVectorOfString(r1,"DT="+intToStr(DT)); + r1=selectTagsInVectorOfString(r1,"IT="+intToStr(IT)); + //not saved in file? field->setDescription(extractFromDescription(r1[0], "fieldDescription=").c_str()); + int nbc=strToInt(extractFromDescription(r1[0], "nbComponents=")); + //double time=strToDouble(extractFromDescription(r1[0], "time=")); + if (nbc==da->getNumberOfComponents()) + { + for (int i=0; isetInfoOnComponent(i,extractFromDescription(r1[0], "componentInfo"+intToStr(i)+"=").c_str()); + } + else + { + cerr<<"Problem On field "<getNumberOfComponents()<setArray(da); + field->setTime(time,DT,IT); + field->checkCoherency(); + try + { + MEDLoader::WriteField(distfilename.c_str(),field,false); + //if entityName=="MED_NODE_ELEMENT" + //AN INTERP_KERNEL::EXCEPTION HAS BEEN THROWN : Not implemented other profile fitting from already written mesh for fields than on NODES and on CELLS.********** + //modification MEDLoader.cxx done + } + catch(INTERP_KERNEL::Exception& e) + { + //cout trying rewrite all data, only one field defined + string tmp,newName=distfilename; + tmp+="_"+fieldName+"_"+intToStr(nbfFieldFound)+".med"; + newName.replace(newName.find(".med"),4,tmp); + cout<<"WARNING : writeMedFile : new file name with only one field :"<decrRef(); - // writeSubdomain(idomain, nbdomains, distfilename.c_str(), domainSelector); + } + +/* +void writeFieldNodeCellTryingToFitExistingMesh(const char *fileName, const ParaMEDMEM::MEDCouplingFieldDouble *f) +{ + med_int numdt,numo; + med_float dt; + int nbComp=f->getNumberOfComponents(); + med_idt fid=appendFieldSimpleAtt(fileName,f,numdt,numo,dt); + std::list split; + prepareCellFieldDoubleForWriting(f,thisMeshCellIdsPerType,split); + const double *pt=f->getArray()->getConstPointer(); + int number=0; + for(std::list::const_iterator iter=split.begin();iter!=split.end();iter++) + { + INTERP_KERNEL::AutoPtr nommaa=MEDLoaderBase::buildEmptyString(MED_NAME_SIZE); + MEDLoaderBase::safeStrCpy(f->getMesh()->getName(),MED_NAME_SIZE,nommaa,MEDLoader::_TOO_LONG_STR); + INTERP_KERNEL::AutoPtr profileName=MEDLoaderBase::buildEmptyString(MED_NAME_SIZE); + std::ostringstream oss; oss << "Pfl" << f->getName() << "_" << number++; + MEDLoaderBase::safeStrCpy(oss.str().c_str(),MED_NAME_SIZE,profileName,MEDLoader::_TOO_LONG_STR); + const std::vector& ids=(*iter).getCellIdPerType(); + int *profile=new int [ids.size()]; + std::transform(ids.begin(),ids.end(),profile,std::bind2nd(std::plus(),1)); + MEDprofileWr(fid,profileName,ids.size(),profile); + delete [] profile; + MEDfieldValueWithProfileWr(fid,f->getName(),numdt,numo,dt,MED_NODE_CELL,typmai3[(int)(*iter).getType()],MED_COMPACT_PFLMODE,profileName, + MED_NO_LOCALIZATION,MED_FULL_INTERLACE,MED_ALL_CONSTITUENT,(*iter).getNbOfTuple(),(const unsigned char*)pt); + pt+=(*iter).getNbOfTuple()*nbComp; + } + MEDfileClose(fid); +}*/ + diff --git a/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionDriver.hxx b/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionDriver.hxx index 01502b62b..53ec045db 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionDriver.hxx +++ b/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionDriver.hxx @@ -20,6 +20,8 @@ #define MEDPARTITIONER_MESHCOLLECTIONDRIVER_HXX_ #include "MEDPARTITIONER.hxx" + +#include #include namespace MEDPARTITIONER @@ -38,45 +40,21 @@ namespace MEDPARTITIONER int readSeq(const char*,const char*); virtual void write(const char*, ParaDomainSelector* sel=0)=0; -// virtual void readFields (vector *>& filenames, char* fieldname, -// int itnumber, int ordernumber) =0; -// virtual void readFields (vector *>& filenames, char* fieldname, -// int itnumber, int ordernumber) =0; -// virtual void writeFields(vector *>& filenames, char* fieldname)=0; -// virtual void writeFields(vector *>& filenames, char* fieldname)=0; - -// void readFileStruct(vector & field_names,vector& iternumber,vector & ordernumber,vector & types); - -// int getFieldType(const std::string& fieldname); -// // void exportFamily(vector,MED_EN::medEntityMesh, const string& name); - -// void readLoc2GlobCellConnect(int idomain, const set& loc_domains, ParaDomainSelector* ds, -// vector & loc2glob_corr); - -// int readMeshDimension() const; protected: - void readSubdomain(vector& cellglobal, - vector& faceglobal, - vector& nodeglobal, int idomain); + void readSubdomain(std::vector& cellglobal, + std::vector& faceglobal, + std::vector& nodeglobal, int idomain); + void readSubdomain(int idomain); void writeMedFile(int idomain, const std::string& distfilename); -// void writeElementJoint(medEntityMesh entity , -// int icz, -// int idomain, -// int idistant, -// char* mesh_name, -// char* joint_name, -// med_2_3::med_idt fid ); -// void jointSort(int* elems, int nbelems, bool is_first); - - MESHCollection* _collection; - std::vector _filename; - std::vector _meshname; + //to Globals + //std::vector _filename; + //std::vector _meshname; }; diff --git a/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionMedAsciiDriver.cxx b/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionMedAsciiDriver.cxx index 222bc87eb..515b1f8ec 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionMedAsciiDriver.cxx +++ b/src/MEDPartitioner/MEDPARTITIONER_MESHCollectionMedAsciiDriver.cxx @@ -30,8 +30,6 @@ #include #include -//Debug macros -#include "MEDMEM_Exception.hxx" #include "MEDCouplingUMesh.hxx" #include "MEDLoader.hxx" @@ -42,8 +40,10 @@ #include "MEDPARTITIONER_MESHCollection.hxx" #include "MEDPARTITIONER_MESHCollectionMedAsciiDriver.hxx" #include "MEDPARTITIONER_ParaDomainSelector.hxx" +#include "MEDPARTITIONER_utils.hxx" using namespace MEDPARTITIONER; +using namespace std; //template inclusion //#include "MEDPARTITIONER_MESHCollectionMedAsciiDriver.H" @@ -62,21 +62,17 @@ MESHCollectionMedAsciiDriver::MESHCollectionMedAsciiDriver(MESHCollection* colle int MESHCollectionMedAsciiDriver::read(const char* filename, ParaDomainSelector* domainSelector) { - - //ditributed meshes + //distributed meshes vector cellglobal; vector nodeglobal; vector faceglobal; - int nbdomain; // reading ascii master file - try{ + try + { ifstream asciiinput(filename); - - if (!asciiinput) - throw INTERP_KERNEL::Exception("MEDPARTITIONER read - Master File does not exist"); - + if (!asciiinput) throw INTERP_KERNEL::Exception(LOCALIZED("Master ASCII File does not exist")); char charbuffer[512]; asciiinput.getline(charbuffer,512); @@ -87,20 +83,18 @@ int MESHCollectionMedAsciiDriver::read(const char* filename, ParaDomainSelector* //reading number of domains nbdomain=atoi(charbuffer); - cout << "nb domain "<>nbdomain; - _filename.resize(nbdomain); - _meshname.resize(nbdomain); + MyGlobals::_fileNames.resize(nbdomain); + MyGlobals::_meshNames.resize(nbdomain); (_collection->getMesh()).resize(nbdomain); cellglobal.resize(nbdomain); nodeglobal.resize(nbdomain); faceglobal.resize(nbdomain); - if (nbdomain == 0) - throw INTERP_KERNEL::Exception("Empty ASCII master file"); + if (nbdomain == 0) throw INTERP_KERNEL::Exception(LOCALIZED("Empty ASCII master file")); for (int i=0; i> mesh >> idomain >> MyGlobals::_meshNames[i] >> host >> MyGlobals::_fileNames[i]; - asciiinput >> mesh >> idomain >> _meshname[i] >> host >> _filename[i]; - - //Setting the name of the global mesh (which is the same - //for all the subdomains) + //Setting the name of the global mesh (which should be is the same for all the subdomains) if (i==0) _collection->setName(mesh); if (idomain!=i+1) { - cerr<<"Error : domain must be written from 1 to N in asciifile descriptor"<isMyDomain(i)) readSubdomain(cellglobal,faceglobal,nodeglobal, i); @@ -128,8 +120,7 @@ int MESHCollectionMedAsciiDriver::read(const char* filename, ParaDomainSelector* }//of try catch(...) { - cerr << "I/O error reading parallel MED file"<getMesh().size(); - _filename.resize(nbdomains); + int nbdomains=_collection->getMesh().size(); + vector filenames; + filenames.resize(nbdomains); //loop on the domains - for (int idomain=0; idomainisMyDomain( idomain ) ) { if ( !_collection->getMesh()[idomain]->getNumberOfCells()==0 ) continue;//empty domain - MEDLoader::WriteUMesh(distfilename.c_str(),(_collection->getMesh())[idomain],true); - // writeSubdomain(idomain, nbdomains, distfilename.c_str(), domainSelector); } } @@ -186,15 +169,14 @@ void MESHCollectionMedAsciiDriver::write(const char* filename, ParaDomainSelecto if ( !domainSelector || domainSelector->rank() == 0 ) { ofstream file(filename); + file << "#MED Fichier V 2.3"<<" "<getMesh().size()<<" "<getMesh().size()<<" "<getName() <<" "<< idomain+1 << " " << (_collection->getMesh())[idomain]->getName() << " localhost " - << _filename[idomain] << " "< -#include "MEDMEM_Utilities.hxx" -#include "MEDMEM_Exception.hxx" //MEDSPLITTER includes #include "MEDCouplingUMesh.hxx" #include "MEDLoader.hxx" @@ -42,8 +40,10 @@ #include "MEDPARTITIONER_MESHCollection.hxx" #include "MEDPARTITIONER_MESHCollectionMedXMLDriver.hxx" #include "MEDPARTITIONER_ParaDomainSelector.hxx" +#include "MEDPARTITIONER_utils.hxx" using namespace MEDPARTITIONER; +using namespace std; //template inclusion //#include "MEDPARTITIONER_MESHCollectionMedXMLDriver.H" @@ -76,13 +76,11 @@ MESHCollectionMedXMLDriver::MESHCollectionMedXMLDriver(MESHCollection* collectio int MESHCollectionMedXMLDriver::read(const char* filename, ParaDomainSelector* domainSelector) { - const char* LOC = "MEDPARTITIONER::MESHCollectionDriver::read()"; - BEGIN_OF_MED(LOC); - - //ditributed meshes + //distributed meshes //cvwat02 + /*cvw vector cellglobal; vector nodeglobal; - vector faceglobal; + vector faceglobal;*/ int nbdomain; @@ -90,13 +88,11 @@ int MESHCollectionMedXMLDriver::read(const char* filename, ParaDomainSelector* d // reading ascii master file try{ - MESSAGE_MED("Start reading"); - // Setting up the XML tree corresponding to filename xmlDocPtr master_doc=xmlParseFile(filename); - if (!master_doc) - throw MEDMEM::MEDEXCEPTION("MEDPARTITIONER XML read - Master File does not exist o r is not compliant with XML scheme"); + if (!master_doc) + throw INTERP_KERNEL::Exception(LOCALIZED("XML Master File does not exist or is not compliant with XML scheme")); //////////////////// //number of domains @@ -104,7 +100,7 @@ int MESHCollectionMedXMLDriver::read(const char* filename, ParaDomainSelector* d xmlXPathContextPtr xpathCtx = xmlXPathNewContext(master_doc); xmlXPathObjectPtr xpathObj = xmlXPathEvalExpression(BAD_CAST "//splitting/subdomain", xpathCtx); if (xpathObj==0 || xpathObj->nodesetval->nodeNr ==0) - throw MEDMEM::MEDEXCEPTION("MEDPARTITIONER read - XML Master File does not contain /MED/splitting/subdomain node"); + throw INTERP_KERNEL::Exception(LOCALIZED("XML Master File does not contain /MED/splitting/subdomain node")); /* as subdomain has only one property which is "number" * it suffices to take the content of its first child */ @@ -114,40 +110,43 @@ int MESHCollectionMedXMLDriver::read(const char* filename, ParaDomainSelector* d ////////////////// //mesh name ////////////////// + xmlXPathFreeObject(xpathObj); xpathObj = xmlXPathEvalExpression(BAD_CAST "//content/mesh", xpathCtx); if (xpathObj==0 || xpathObj->nodesetval->nodeNr ==0) - throw MEDMEM::MEDEXCEPTION("MEDPARTITIONER read - XML Master File does not contain /MED/content/mesh node"); + throw INTERP_KERNEL::Exception(LOCALIZED("XML Master File does not contain /MED/content/mesh node")); _collection->setName( (const char*)xpathObj->nodesetval->nodeTab[0]->properties->children->content); - cout << "nb domain " << nbdomain << endl; - _filename.resize(nbdomain); - _meshname.resize(nbdomain); + //cout << "nb domain " << nbdomain << endl; + MyGlobals::_fileNames.resize(nbdomain); + MyGlobals::_meshNames.resize(nbdomain); (_collection->getMesh()).resize(nbdomain); (_collection->getFaceMesh()).resize(nbdomain); (_collection->getCellFamilyIds()).resize(nbdomain); (_collection->getFaceFamilyIds()).resize(nbdomain); + /*cvw cellglobal.resize(nbdomain); nodeglobal.resize(nbdomain); faceglobal.resize(nbdomain); - + */ // retrieving the node which contains the file names const char filechar[]="//files/subfile"; + xmlXPathFreeObject(xpathObj); xpathObj = xmlXPathEvalExpression(BAD_CAST filechar, xpathCtx); if (xpathObj==0 || xpathObj->nodesetval->nodeNr ==0) - throw MEDMEM::MEDEXCEPTION("MEDPARTITIONER read - XML Master File does not contain /MED/files/subfile nodes"); + throw INTERP_KERNEL::Exception(LOCALIZED("XML Master File does not contain /MED/files/subfile nodes")); int nbfiles = xpathObj->nodesetval ->nodeNr; for (int i=0; inodesetval ==0) - throw MEDMEM::MEDEXCEPTION("MED XML reader : Error retrieving file name "); - _filename[i]=(const char*)xpathObjfilename->nodesetval->nodeTab[0]->children->content; + throw INTERP_KERNEL::Exception(LOCALIZED("Error retrieving a file name from subfile of XML Master File")); + MyGlobals::_fileNames[i]=(const char*)xpathObjfilename->nodesetval->nodeTab[0]->children->content; //////////////////////////////// //reading the local mesh names @@ -169,13 +168,13 @@ int MESHCollectionMedXMLDriver::read(const char* filename, ParaDomainSelector* d xmlXPathObjectPtr xpathMeshObj = xmlXPathEvalExpression(BAD_CAST mesh_search_string.str().c_str(),xpathCtx); if (xpathMeshObj->nodesetval ==0) - throw MEDMEM::MEDEXCEPTION("MED XML reader : Error retrieving mesh name "); - _meshname[i]=(const char*)xpathMeshObj->nodesetval->nodeTab[0]->children->content; + throw INTERP_KERNEL::Exception(LOCALIZED("Error retrieving mesh name from chunk of XML Master File")); + MyGlobals::_meshNames[i]=(const char*)xpathMeshObj->nodesetval->nodeTab[0]->children->content; if ( !domainSelector || domainSelector->isMyDomain(i)) - readSubdomain(cellglobal, faceglobal, nodeglobal, i); + readSubdomain(i); //cvwat03 + //cvw readSubdomain(cellglobal, faceglobal, nodeglobal, i); //cvwat03 xmlXPathFreeObject(xpathObjfilename); - xmlXPathFreeObject(xpathMeshObj); }//loop on domains @@ -184,26 +183,34 @@ int MESHCollectionMedXMLDriver::read(const char* filename, ParaDomainSelector* d xmlXPathFreeContext(xpathCtx); xmlFreeDoc(master_doc); - MESSAGE_MED("end of read"); }//of try catch(...) { - throw MEDMEM::MEDEXCEPTION("I/O error reading parallel MED file"); + throw INTERP_KERNEL::Exception(LOCALIZED("I/O error reading parallel MED file")); } + + ParallelTopology* aPT = new ParallelTopology(_collection->getMesh()); //creation of topology from mesh and connect zones + if ( _collection->isParallelMode() ) + { + //to know nb of cells on each proc to compute global cell ids from locally global + domainSelector->gatherNbOf(_collection->getMesh()); + } + /*cvw ParallelTopology* aPT = new ParallelTopology ((_collection->getMesh()), (_collection->getCZ()), cellglobal, nodeglobal, faceglobal); + */ _collection->setTopology(aPT); _collection->setDomainNames(_collection->getName()); + /*cvw for (int i=0; igetName().c_str()); int nbdomains= _collection->getMesh().size(); - _filename.resize(nbdomains); + //vector filenames; + //filenames.resize(nbdomains); //loop on the domains + string finalMeshName=extractFromDescription(MyGlobals::_generalInformations[0], "finalMeshName="); for (int idomain=nbdomains-1; idomain>=0;idomain--) { string distfilename; - ostringstream suffix; - suffix << filename<< idomain+1 <<".med"; - + suffix<isMyDomain( idomain ) ) - { - if ( (_collection->getMesh())[idomain]->getNumberOfCells()==0 ) continue;//empty domain - writeMedFile(idomain,distfilename); + { + if ( (_collection->getMesh())[idomain]->getNumberOfCells()==0 ) continue; //empty domain + if (MyGlobals::_verbose>1) + cout<<"proc "<rank()<<" : writeMedFile "<getMesh())[idomain]->getNumberOfCells()<<" cells" + << " "<<(_collection->getFaceMesh())[idomain]->getNumberOfCells()<<" faces" + << " "<<(_collection->getMesh())[idomain]->getNumberOfNodes()<<" nodes"<getMesh())[idomain]->getName()); - } + if (domainSelector->rank()==0) + { + //updating the ascii description file + node = xmlNewChild(file_node, 0, BAD_CAST "subfile",0); + sprintf (buff,"%d",idomain+1); + xmlNewProp(node, BAD_CAST "id", BAD_CAST buff); + xmlNewChild(node,0,BAD_CAST "name",BAD_CAST distfilename.c_str()); + xmlNewChild(node,0,BAD_CAST "machine",BAD_CAST "localhost"); + + node = xmlNewChild(mesh_node,0, BAD_CAST "chunk",0); + xmlNewProp(node, BAD_CAST "subdomain", BAD_CAST buff); + xmlNewChild(node,0,BAD_CAST "name", BAD_CAST finalMeshName.c_str()); + //xmlNewChild(node,0,BAD_CAST "name", BAD_CAST (_collection->getMesh())[idomain]->getName()); + } + } + + //create the ascii description file + if (domainSelector->rank()==0) + { + string myfile(filename); + myfile.append(".xml"); + _master_filename=myfile; + if ( !domainSelector || domainSelector->rank() == 0 ) + xmlSaveFormatFileEnc(myfile.c_str(), master_doc, "UTF-8", 1); + //xmlFreeDoc(master_doc); + //xmlCleanupParser(); } - string myfile(filename); - myfile.append(".xml"); - _master_filename=myfile; - if ( !domainSelector || domainSelector->rank() == 0 ) - xmlSaveFormatFileEnc(myfile.c_str(), master_doc, "UTF-8", 1); xmlFreeDoc(master_doc); xmlCleanupParser(); - - END_OF_MED(LOC); - } diff --git a/src/MEDPartitioner/MEDPARTITIONER_METISGraph.cxx b/src/MEDPartitioner/MEDPARTITIONER_METISGraph.cxx index f0c7d100e..84731f495 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_METISGraph.cxx +++ b/src/MEDPartitioner/MEDPARTITIONER_METISGraph.cxx @@ -25,7 +25,11 @@ extern "C" { } #include "MEDPARTITIONER_METISGraph.hxx" #include "MEDPARTITIONER_ParaDomainSelector.hxx" -#include "MEDMEM_Exception.hxx" +#include "MEDPARTITIONER_utils.hxx" +#include "InterpKernelException.hxx" + +#include + using namespace MEDPARTITIONER; METISGraph::METISGraph():Graph() @@ -41,61 +45,149 @@ METISGraph::~METISGraph() { } -void METISGraph::partGraph(int ndomain, - const std::string& options_string, +void METISGraph::partGraph(int ndomain, //cvwat10 + const std::string& options_string, ParaDomainSelector* parallelizer) { + using std::vector; + vector ran,vx,va; //for randomize + + if (MyGlobals::_verbose>10) cout<<"proc "<getNumberOf(); - + int n=_graph->getNumberOf(); //graph int * xadj=const_cast(_graph->getIndex()); - int * adjncy = const_cast(_graph->getValue()); + int * adjncy=const_cast(_graph->getValue()); //constraints int * vwgt=_cellweight; int * adjwgt=_edgeweight; int wgtflag=(_edgeweight!=0)?1:0+(_cellweight!=0)?2:0; - //base 0 or 1 int base=0; - //ndomain - int nparts = ndomain; - + int nparts=ndomain; //options - int options[5]={0,0,0,0,0}; - + /* + (0=default_option,option,random_seed) see defs.h + #define PMV3_OPTION_DBGLVL 1 + #define PMV3_OPTION_SEED 2 + #define PMV3_OPTION_IPART 3 + #define PMV3_OPTION_PSR 3 + seems no changes int options[4]={1,0,33,0}; //test for a random seed of 33 + */ + int options[4]={0,0,0,0}; // output parameters int edgecut; - int* partition = new int[n]; + int* partition=new int[n]; - cout << "ParMETIS : n="<10) cout<<"proc "<100) + cout<<"proc "<getProcVtxdist(); + MPI_Comm comm=MPI_COMM_WORLD; + try + { + if (MyGlobals::_verbose>200) + { + cout<<"proc "<0) + { + cout<<"\nproc "<1000) + { + cout<<"\n -cell "<imaxx) imaxx=ilg; + } + cout<<"\nproc "<10) + cout<<"proc "< index(n+1); - std::vector value(n); + + vector index(n+1); + vector value(n); index[0]=0; - for (int i=0; i0 && MyGlobals::_atomize==0) //there is randomize { - index[i+1]=index[i]+1; - value[i]=partition[i]; + if (MyGlobals::_is0verbose>100) cout<<"randomize"< + namespace MEDPARTITIONER { class MEDSKYLINEARRAY; class MEDPARTITIONER_EXPORT METISGraph:public Graph diff --git a/src/MEDPartitioner/MEDPARTITIONER_ParaDomainSelector.cxx b/src/MEDPartitioner/MEDPARTITIONER_ParaDomainSelector.cxx index 9c1a29202..199d545e2 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_ParaDomainSelector.cxx +++ b/src/MEDPartitioner/MEDPARTITIONER_ParaDomainSelector.cxx @@ -21,11 +21,11 @@ // Author : Edward AGAPOV (eap) #include "MEDCouplingUMesh.hxx" - #include "MEDPARTITIONER_ParaDomainSelector.hxx" - #include "MEDPARTITIONER_UserGraph.hxx" +#include "MEDPARTITIONER_utils.hxx" +#include #include #ifdef HAVE_MPI2 @@ -36,9 +36,9 @@ #include #endif -using namespace MEDPARTITIONER; -using namespace MED_EN; +//using namespace MED_EN; using namespace std; +using namespace MEDPARTITIONER; //================================================================================ /*! @@ -77,8 +77,7 @@ ParaDomainSelector::~ParaDomainSelector() bool ParaDomainSelector::isOnDifferentHosts() const { evaluateMemory(); - if ( _world_size < 2 ) - return false; + if ( _world_size < 2 ) return false; #ifdef HAVE_MPI2 char name_here[ MPI_MAX_PROCESSOR_NAME+1 ], name_there[ MPI_MAX_PROCESSOR_NAME+1 ]; @@ -93,7 +92,18 @@ bool ParaDomainSelector::isOnDifferentHosts() const MPI_Sendrecv((void*)&name_here[0], MPI_MAX_PROCESSOR_NAME, MPI_CHAR, next_proc, tag, (void*)&name_there[0], MPI_MAX_PROCESSOR_NAME, MPI_CHAR, prev_proc, tag, MPI_COMM_WORLD, &status); - return string(name_here) != string(name_there); + + //cout<<"proc "<& domain_meshes) +void ParaDomainSelector::gatherNbOf(const vector& domain_meshes) { evaluateMemory(); - // get nb of elems of each domain mesh - int nb_domains = domain_meshes.size(); - vector nb_elems( nb_domains, 0 ); - for ( int i = 0; i < nb_domains; ++i ) + int nb_domains=domain_meshes.size(); + //cout<<"proc "< nb_elems(nb_domains*2, 0); //NumberOfCells & NumberOfNodes + for (int i=0; igetNumberOfCells(); - + { + nb_elems[i*2] = domain_meshes[i]->getNumberOfCells(); + nb_elems[i*2+1] = domain_meshes[i]->getNumberOfNodes(); + } // receive nb of elems from other procs - vector all_nb_elems( nb_domains ); + vector all_nb_elems( nb_domains*2 ); #ifdef HAVE_MPI2 - MPI_Allreduce((void*)&nb_elems[0], (void*)&all_nb_elems[0], nb_domains, + MPI_Allreduce((void*)&nb_elems[0], (void*)&all_nb_elems[0], nb_domains*2, MPI_INT, MPI_SUM, MPI_COMM_WORLD); #endif - int total_nb = std::accumulate( all_nb_elems.begin(), all_nb_elems.end(), 0 ); - - vector& elem_shift_by_domain = _cell_shift_by_domain; - - // fill elem_shift_by_domain - - vector< int > ordered_nbs, domain_order( nb_domains ); - ordered_nbs.push_back(0); - for ( int iproc = 0; iproc < nbProcs(); ++iproc ) - for ( int idomain = 0; idomain < nb_domains; ++idomain ) - if ( getProcessorID( idomain ) == iproc ) + int total_nb_cells=0, total_nb_nodes=0; + for (int i=0; i10) + cout<<"totalNbCells "<& cell_shift_by_domain=_cell_shift_by_domain; + vector& node_shift_by_domain=_node_shift_by_domain; + vector& face_shift_by_domain=_face_shift_by_domain; + + vector< int > ordered_nbs_cell, ordered_nbs_node, domain_order(nb_domains); + ordered_nbs_cell.push_back(0); + ordered_nbs_node.push_back(0); + for (int iproc=0; iproc300) + { + cout<<"proc "<200) + { + cout<<"proc "<0 ) - throw INTERP_KERNEL::Exception("invalid nb of cell pairs"); + throw INTERP_KERNEL::Exception(LOCALIZED("invalid nb of cell pairs")); } //================================================================================ @@ -433,8 +472,7 @@ int ParaDomainSelector::getFisrtGlobalIdOfSubentity( int loc_domain, int dist_do int id = total_nb_faces + 1; if ( _nb_cell_pairs_by_joint.empty() ) - throw INTERP_KERNEL::Exception("MEDPARTITIONER::ParaDomainSelector::getFisrtGlobalIdOfSubentity(), " - "gatherNbCellPairs() must be called before"); + throw INTERP_KERNEL::Exception(LOCALIZED("gatherNbCellPairs() must be called before")); int joint_id = jointId( loc_domain, dist_domain ); for ( int j = 0; j < joint_id; ++j ) id += _nb_cell_pairs_by_joint[ j ]; @@ -475,7 +513,7 @@ int ParaDomainSelector::jointId( int local_domain, int distant_domain ) const { evaluateMemory(); if (_nb_result_domains < 0) - throw INTERP_KERNEL::Exception("ParaDomainSelector::jointId(): setNbDomains() must be called before()"); + throw INTERP_KERNEL::Exception(LOCALIZED("setNbDomains() must be called before")); if ( local_domain < distant_domain ) swap( local_domain, distant_domain ); @@ -533,8 +571,7 @@ Sends content of \a mesh to processor \a target. To be used with \a recvMesh met void ParaDomainSelector::sendMesh(const ParaMEDMEM::MEDCouplingUMesh& mesh, int target) const { - - + if (MyGlobals::_verbose>600) cout<<"proc "<<_rank<<" : sendMesh '"< tinyInfoLocal; @@ -543,54 +580,59 @@ void ParaDomainSelector::sendMesh(const ParaMEDMEM::MEDCouplingUMesh& mesh, int //Getting tiny info of local mesh to allow the distant proc to initialize and allocate //the transmitted mesh. mesh.getTinySerializationInformation(tinyInfoLocalD,tinyInfoLocal,tinyInfoLocalS); + //cout<<"sendMesh getTinySerializationInformation "<0) //no sends if empty + { + ParaMEDMEM::DataArrayInt *v1Local=0; + ParaMEDMEM::DataArrayDouble *v2Local=0; + //serialization of local mesh to send data to distant proc. + mesh.serialize(v1Local,v2Local); + int nbLocalElems=0; + int* ptLocal=0; + if(v1Local) //cvw if empty getNbOfElems() is 1! { - nbLocalElems=v1Local->getNbOfElems(); + nbLocalElems=v1Local->getNbOfElems(); //cvw if empty be 1! ptLocal=v1Local->getPointer(); } - #ifdef HAVE_MPI2 - MPI_Send(ptLocal, nbLocalElems, MPI_INT, - target, 1111, MPI_COMM_WORLD); - #endif - double *ptLocal2=0; - if(v2Local) +#ifdef HAVE_MPI2 + MPI_Send(ptLocal, nbLocalElems, MPI_INT, target, 1111, MPI_COMM_WORLD); +#endif + int nbLocalElems2=0; + double *ptLocal2=0; + if(v2Local) //cvw if empty be 0! { - nbLocalElems=v2Local->getNbOfElems(); + nbLocalElems2=v2Local->getNbOfElems(); ptLocal2=v2Local->getPointer(); } #ifdef HAVE_MPI2 - MPI_Send(ptLocal2, nbLocalElems, MPI_DOUBLE, - target, 1110, MPI_COMM_WORLD); + MPI_Send(ptLocal2, nbLocalElems2, MPI_DOUBLE, target, 1110, MPI_COMM_WORLD); #endif - if(v1Local) - v1Local->decrRef(); - if(v2Local) - v2Local->decrRef(); - + if(v1Local) v1Local->decrRef(); + if(v2Local) v2Local->decrRef(); + } + else + { + //cout<<"sendMesh empty Mesh cvw3344 "< tinyInfoDistant; @@ -601,7 +643,7 @@ void ParaDomainSelector::recvMesh(ParaMEDMEM::MEDCouplingUMesh*& mesh, int sourc #ifdef HAVE_MPI2 MPI_Status status; int tinyVecSize; - MPI_Recv(&tinyVecSize, 1, MPI_INT,source,1113,MPI_COMM_WORLD, &status); + MPI_Recv(&tinyVecSize, 1, MPI_INT, source, 1113, MPI_COMM_WORLD, &status); tinyInfoDistant.resize(tinyVecSize); #endif std::fill(tinyInfoDistant.begin(),tinyInfoDistant.end(),0); @@ -609,103 +651,50 @@ void ParaDomainSelector::recvMesh(ParaMEDMEM::MEDCouplingUMesh*& mesh, int sourc #ifdef HAVE_MPI2 MPI_Recv(&tinyInfoDistant[0], tinyVecSize, MPI_INT,source,1112,MPI_COMM_WORLD, &status); #endif - ParaMEDMEM::DataArrayInt *v1Distant=ParaMEDMEM::DataArrayInt::New(); - ParaMEDMEM::DataArrayDouble *v2Distant=ParaMEDMEM::DataArrayDouble::New(); - //Building the right instance of copy of distant mesh. - ParaMEDMEM::MEDCouplingPointSet *distant_mesh_tmp=ParaMEDMEM::MEDCouplingPointSet::BuildInstanceFromMeshType((ParaMEDMEM::MEDCouplingMeshType)tinyInfoDistant[0]); - std::vector unusedTinyDistantSts; - mesh=dynamic_cast (distant_mesh_tmp); + //there was tinyInfoLocal.push_back(mesh.getNumberOfCells()); + int NumberOfCells=tinyInfoDistant[tinyVecSize-1]; + //cout<<"recvMesh NumberOfCells "<0) + { + ParaMEDMEM::DataArrayInt *v1Distant=ParaMEDMEM::DataArrayInt::New(); + ParaMEDMEM::DataArrayDouble *v2Distant=ParaMEDMEM::DataArrayDouble::New(); + //Building the right instance of copy of distant mesh. + ParaMEDMEM::MEDCouplingPointSet *distant_mesh_tmp= + ParaMEDMEM::MEDCouplingPointSet::BuildInstanceFromMeshType( + (ParaMEDMEM::MEDCouplingMeshType) tinyInfoDistant[0]); + std::vector unusedTinyDistantSts; + mesh=dynamic_cast (distant_mesh_tmp); - mesh->resizeForUnserialization(tinyInfoDistant,v1Distant,v2Distant,unusedTinyDistantSts); - int nbDistElem=0; - int *ptDist=0; - if(v1Distant) + mesh->resizeForUnserialization(tinyInfoDistant,v1Distant,v2Distant,unusedTinyDistantSts); + int nbDistElem=0; + int *ptDist=0; + if(v1Distant) { nbDistElem=v1Distant->getNbOfElems(); ptDist=v1Distant->getPointer(); } #ifdef HAVE_MPI2 - MPI_Recv(ptDist, nbDistElem, MPI_INT, - source,1111, - MPI_COMM_WORLD, &status); + MPI_Recv(ptDist, nbDistElem, MPI_INT, source,1111, MPI_COMM_WORLD, &status); #endif - int nbLocalElems=0; - double *ptDist2=0; - nbDistElem=0; - if(v2Distant) + double *ptDist2=0; + nbDistElem=0; + if(v2Distant) { nbDistElem=v2Distant->getNbOfElems(); ptDist2=v2Distant->getPointer(); } #ifdef HAVE_MPI2 - MPI_Recv(ptDist2, nbDistElem, MPI_DOUBLE,source, 1110, MPI_COMM_WORLD, &status); -#endif - // - //finish unserialization - mesh->unserialization(tinyInfoDistantD,tinyInfoDistant,v1Distant,v2Distant,unusedTinyDistantSts); - - if(v1Distant) - v1Distant->decrRef(); - if(v2Distant) - v2Distant->decrRef(); - -} -/*! -Sends content of \a vec to processor \a target. To be used with \a recvDoubleVec method. -\param vec vector to be sent -\param target processor id of the target -*/ -void ParaDomainSelector::sendDoubleVec(const std::vector& vec, int target)const -{ - int size=vec.size(); -#ifdef HAVE_MPI2 - MPI_Send(&size,1,MPI_INT,target,1211, MPI_COMM_WORLD); - MPI_Send(const_cast(&vec[0]), size,MPI_DOUBLE, target, 1212, MPI_COMM_WORLD); -#endif -} -/*! Receives messages from proc \a source to fill vector vec. -To be used with \a sendDoubleVec method. - -\param vec vector that is filled -\param source processor id of the incoming messages - */ -void ParaDomainSelector::recvDoubleVec(std::vector& vec, int source)const -{ - int size; -#ifdef HAVE_MPI2 - MPI_Status status; - MPI_Recv(&size,1,MPI_INT,source,1211, MPI_COMM_WORLD, &status); - vec.resize(size); - MPI_Recv(&vec[0],size,MPI_DOUBLE,source, 1212, MPI_COMM_WORLD,&status); -#endif -} -/*! -Sends content of \a vec to processor \a target. To be used with \a recvIntVec method. -\param vec vector to be sent -\param target processor id of the target -*/ -void ParaDomainSelector::sendIntVec(const std::vector& vec, int target)const -{ - int size=vec.size(); -#ifdef HAVE_MPI2 - MPI_Send(&size,1,MPI_INT,target,1211, MPI_COMM_WORLD); - MPI_Send(const_cast(&vec[0]), size,MPI_INT, target, 1212, MPI_COMM_WORLD); -#endif -} -/*! Receives messages from proc \a source to fill vector vec. -To be used with \a sendIntVec method. - -\param vec vector that is filled -\param source processor id of the incoming messages - */ -void ParaDomainSelector::recvIntVec(std::vector& vec, int source)const -{ - int size; -#ifdef HAVE_MPI2 - MPI_Status status; - MPI_Recv(&size,1,MPI_INT,source,1211, MPI_COMM_WORLD, &status); - vec.resize(size); - MPI_Recv(&vec[0],size,MPI_INT,source, 1212, MPI_COMM_WORLD,&status); + MPI_Recv(ptDist2, nbDistElem, MPI_DOUBLE,source, 1110, MPI_COMM_WORLD, &status); #endif + //finish unserialization + mesh->unserialization(tinyInfoDistantD,tinyInfoDistant,v1Distant,v2Distant,unusedTinyDistantSts); + if(v1Distant) v1Distant->decrRef(); + if(v2Distant) v2Distant->decrRef(); + } + else + { + mesh=createEmptyMEDCouplingUMesh(); + } + if (MyGlobals::_verbose>600) cout<<"proc "<<_rank<<" : recvMesh '"<getName()<<"' size "<getNumberOfCells()<<" from "< - #include #include @@ -47,62 +45,54 @@ namespace MEDPARTITIONER */ class MEDPARTITIONER_EXPORT ParaDomainSelector { + public: ParaDomainSelector(bool mesure_memory=false); ~ParaDomainSelector(); - //!< return processor rank + // return processor rank int rank() const { return _rank; } - - //!< return number of processors + // return number of processors int nbProcs() const { return _world_size; } - // Return true if is running on different hosts bool isOnDifferentHosts() const; - // Return true if the domain with domainIndex is to be loaded on this proc bool isMyDomain(int domainIndex) const; - // Return processor id where the domain with domainIndex resides int getProcessorID(int domainIndex) const; - - - //!< Set nb of required domains. (Used to sort joints via jointId()) + //Set nb of required domains. (Used to sort joints via jointId()) void setNbDomains(int nb) { _nb_result_domains = nb; } - // Return identifier for a joint int jointId( int local_domain, int distant_domain ) const; + + int getNbTotalCells() { return _cell_shift_by_domain.back(); } + int getNbTotalNodes() { return _node_shift_by_domain.back(); }; + int getNbTotalFaces() { return _face_shift_by_domain.back(); }; // Return domain order - //int getDomianOrder(int domainIndex, int nb_domains) const; - - - // Collect nb of entities on procs and return total nb - int gatherNbOf( - //MED_EN::medEntityMesh entity, -const std::vector& domain_meshes); + //int getDomainOrder(int domainIndex, int nb_domains) const; + // Collect nb of entities on procs + void gatherNbOf(const std::vector& domain_meshes); + // Return distribution of the graph vertices among the processors - int* getNbVertOfProcs() const; - - // Return nb of cells on processors with lower rank - int getProcShift() const; + int* getProcVtxdist() const; + // Return nb of nodes on processors with lower rank + int getProcNodeShift() const; // Return nb of cells in domains with lower index - int getDomainShift(int domainIndex) const; - + int getDomainCellShift(int domainIndex) const; + // Return nb of nodes in domains with lower index + int getDomainNodeShift(int domainIndex) const; // Gather graphs from all processors into one std::auto_ptr gatherGraph(const Graph* graph) const; - // Set nb of cell/cell pairs in a joint between domains void setNbCellPairs( int nb_cell_pairs, int dist_domain, int loc_domain ); - // Gather size of each proc/proc joint void gatherNbCellPairs(); - // Return nb of cell/cell pairs in a joint between domains on different procs int getNbCellPairs( int dist_domain, int loc_domain ) const; @@ -111,11 +101,9 @@ const std::vector& domain_meshes); // Return the first global id of sub-entity for the joint int getFisrtGlobalIdOfSubentity( int loc_domain, int dist_domain ) const; - // Send-receive local ids of joint faces int* exchangeSubentityIds( int loc_domain, int dist_domain, const std::vector& loc_ids_here ) const; - // Return time passed from construction in seconds double getPassedTime() const; @@ -123,35 +111,25 @@ const std::vector& domain_meshes); int evaluateMemory() const; void sendMesh(const ParaMEDMEM::MEDCouplingUMesh& mesh, int target) const; - void recvMesh(ParaMEDMEM::MEDCouplingUMesh*& mesh, int source) const; - - void sendDoubleVec(const std::vector& vec, int target) const; - - void recvDoubleVec(std::vector& vec, int source) const; - - void sendIntVec(const std::vector& vec, int target) const; - void recvIntVec(std::vector& vec, int source) const; - + private: int _rank, _world_size; // my rank and nb of processors - int _nb_result_domains; // required nb of domains //int _total_nb_faces; // nb of faces in the whole mesh without proc/proc joint faces std::vector< int > _nb_cell_pairs_by_joint; - std::vector< int > _nb_vert_of_procs; // graph vertices std::vector< int > _cell_shift_by_domain; + std::vector< int > _node_shift_by_domain; std::vector< int > _face_shift_by_domain; double _init_time; bool _mesure_memory; int _init_memory, _max_memory; }; - } #endif diff --git a/src/MEDPartitioner/MEDPARTITIONER_ParallelTopology.cxx b/src/MEDPartitioner/MEDPARTITIONER_ParallelTopology.cxx index 010ef4fd3..42055958f 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_ParallelTopology.cxx +++ b/src/MEDPartitioner/MEDPARTITIONER_ParallelTopology.cxx @@ -19,6 +19,7 @@ #include #include #include +#include #include "InterpKernelHashMap.hxx" #include "MEDPARTITIONER_MESHCollection.hxx" @@ -28,29 +29,111 @@ #include "MEDPARTITIONER_ConnectZone.hxx" #include "MEDCouplingUMesh.hxx" -#include "MEDMEM_Exception.hxx" -#include "MEDMEM_Utilities.hxx" +#include "MEDPARTITIONER_utils.hxx" -#ifndef WNT -using namespace __gnu_cxx; -#else -using namespace std; +#ifdef HAVE_MPI2 +#include #endif using namespace MEDPARTITIONER; +using namespace std; //empty constructor ParallelTopology::ParallelTopology():_nb_domain(0),_mesh_dimension(0) {} +//!constructing topology according to mesh collection without global numerotation (use setGlobalNumerotation later) +ParallelTopology::ParallelTopology(const vector& meshes) +{ + _nb_domain=meshes.size(); + _nb_cells.resize(_nb_domain); + _nb_nodes.resize(_nb_domain); + // _nb_faces.resize(_nb_domain); + + if (MyGlobals::_is0verbose>100) cout<<"new ParallelTopology\n"; + _loc_to_glob.resize(0); //precaution, need gatherNbOf() setGlobalNumerotation() + _node_loc_to_glob.resize(0); //precaution, need gatherNbOf() setGlobalNumerotation() + //_face_loc_to_glob.resize(_nb_domain); + _mesh_dimension = -1; + bool parallel_mode = false; + for (int idomain=0; !parallel_mode && idomain<_nb_domain; idomain++) + parallel_mode = (!meshes[idomain]); + + if (MyGlobals::_is0verbose>20 && !parallel_mode) cout<<"WARNING : ParallelTopology contructor without parallel_mode"<getMeshDimension(); + } + else + { + if (_mesh_dimension!=meshes[idomain]->getMeshDimension()) + throw INTERP_KERNEL::Exception(LOCALIZED("meshes dimensions incompatible")); + } + _nb_cells[idomain]=meshes[idomain]->getNumberOfCells(); + _nb_nodes[idomain]=meshes[idomain]->getNumberOfNodes(); + //note: in parallel mode _nb_cells and _nb_nodes are not complete now, needs gatherNbOf() + } +} + +//!constructing _loc_to_glob etc by default, needs gatherNbOf() done +void ParallelTopology::setGlobalNumerotationDefault(ParaDomainSelector* domainSelector) +{ + if (MyGlobals::_is0verbose>100) cout<<"setGlobalNumerotationDefault on "<<_nb_domain<<" domains\n"; + if (_loc_to_glob.size()!=0) throw INTERP_KERNEL::Exception(LOCALIZED("a global numerotation is done yet")); + _loc_to_glob.resize(_nb_domain); + _node_loc_to_glob.resize(_nb_domain); + + //warning because _nb_cells[idomain] is 0 if not my domain(s) + //we set loc_to_glob etc.. only for my domain(s) + if (MyGlobals::_is0verbose>500) cout<<"(c)idomain|ilocalCell|iglobalCell"<getDomainCellShift(idomain); + for (int i=0; i<_nb_cells[idomain]; i++) + { + int global=domainCellShift+i ; + _glob_to_loc.insert(make_pair(global,make_pair(idomain,i))); + _loc_to_glob[idomain][i]=global; + if (MyGlobals::_verbose>500) cout<<"c"<500) MPI_Barrier(MPI_COMM_WORLD); + if (MyGlobals::_is0verbose>500) cout<500) cout<<"(n)idomain|ilocalNode|iglobalNode"<getDomainNodeShift(idomain); + for (int i=0; i<_nb_nodes[idomain]; i++) + { + int global=domainNodeShift+i ; + _node_glob_to_loc.insert(make_pair(global,make_pair(idomain,i))); + _node_loc_to_glob[idomain][i]=global; + if (MyGlobals::_verbose>500) cout<<"n"<500) MPI_Barrier(MPI_COMM_WORLD); + if (MyGlobals::_is0verbose>500) cout<getNbTotalCells(); + _nb_total_nodes=domainSelector->getNbTotalNodes(); + _nb_total_faces=domainSelector->getNbTotalFaces(); + if (MyGlobals::_is0verbose>200) cout<<"globalNumerotation default done meshDimension "<<_mesh_dimension<<" nbTotalCells "<<_nb_total_cells<<" nbTotalNodes "<<_nb_total_nodes<& meshes, const vector& cz, vector& cellglobal, vector& nodeglobal, - vector& faceglobal):_nb_domain(meshes.size())/*,_mesh_dimension(meshes[0]->getMeshDimension())*/ + vector& faceglobal) { - + _nb_domain=meshes.size(); int index_global=0; int index_node_global=0; int index_face_global=0; @@ -58,24 +141,20 @@ ParallelTopology::ParallelTopology(const vector& _nb_cells.resize(_nb_domain); _nb_nodes.resize(_nb_domain); // _nb_faces.resize(_nb_domain); - + _loc_to_glob.resize(_nb_domain); _node_loc_to_glob.resize(_nb_domain); // _face_loc_to_glob.resize(_nb_domain); - //MED_EN::medEntityMesh constituent_entity; - bool parallel_mode = false; for (int idomain=0; !parallel_mode && idomain<_nb_domain; idomain++) parallel_mode = (!meshes[idomain]); for (int idomain=0; idomain<_nb_domain; idomain++) { - if ( !meshes[idomain] ) - continue; + if ( !meshes[idomain] ) continue; _mesh_dimension = meshes[idomain]->getMeshDimension(); - //constituent_entity = (_mesh_dimension == 3 ? MED_EN::MED_FACE : MED_EN::MED_EDGE ); - + //creating cell maps _nb_cells[idomain]=meshes[idomain]->getNumberOfCells(); // cout << "Nb cells (domain "<& if (cellglobal[idomain]==0 || parallel_mode) { - MESSAGE_MED("Creating global numbering"); + //int cellDomainShift=_cell_shift_by_domain[idomain]; //creating global numbering from scratch for (int i=0; i<_nb_cells[idomain]; i++) { - - _glob_to_loc.insert(make_pair(index_global,make_pair(idomain,i+1))); - _loc_to_glob[idomain][i]=index_global; - // cout<<"glob:"< ("<& } _nb_total_nodes=meshes[idomain]->getNumberOfNodes(); _nb_nodes[0]=_nb_total_nodes; - - MESSAGE_MED ("nb total cells "<< _nb_total_cells); - MESSAGE_MED("nb total nodes "<< _nb_total_nodes); return; } @@ -185,19 +260,68 @@ ParallelTopology::ParallelTopology(const vector& _nb_total_cells=index_global; _nb_total_nodes=index_node_global; _nb_total_faces=index_face_global; - SCRUTE_MED(_nb_total_cells); - SCRUTE_MED(_nb_total_faces); - SCRUTE_MED(_nb_total_nodes); - } //!constructing ParallelTopology from an old topology and a graph -ParallelTopology::ParallelTopology(Graph* graph, int nb_domain, int mesh_dimension): - _nb_domain(nb_domain), - _nb_cells(graph->nbVertices()), - _mesh_dimension(mesh_dimension) +ParallelTopology::ParallelTopology(Graph* graph, Topology* oldTopology, int nb_domain, int mesh_dimension) { + + _nb_domain=nb_domain; + //cvw !!whatisit! _nb_cells=graph->nbVertices(); + _mesh_dimension=mesh_dimension; + + if (MyGlobals::_verbose>200) + cout<<"proc "<nbDomain()<<" newNbDomain "<<_nb_domain<getPart(); //all cells for this proc (may be more domains) + _nb_total_cells=graph->nbVertices(); //all cells for this proc (may be more domains) + if (MyGlobals::_verbose>300) + cout<<"proc "<nbDomain(); iold++) + { + int ioldNbCell=oldTopology->getCellNumber(iold); + //cout<<"proc "< globalids(ioldNbCell); + oldTopology->getCellList(iold, &globalids[0]); //unique global numerotation + for (int icell=0; icell300) + for (int idomain=0; idomain<_nb_domain; idomain++) + cout<<"proc "<nbVertices(); + _mesh_dimension=mesh_dimension; + + cout<<"proc "<nbDomain()<<" new nbDomain "<<_nb_domain<getPart(); + _nb_total_cells=graph->nbVertices(); - const int* part = graph-> getPart(); - _nb_total_cells= graph->nbVertices(); + cout<<"proc "< local_node = _node_glob_to_loc.find(node_list[i])->second; @@ -264,7 +388,7 @@ void ParallelTopology::convertGlobalNodeList(const int* node_list, int nbnode, i void ParallelTopology::convertGlobalNodeList(const int* node_list, int nbnode, int* local, int ip) { if (_node_glob_to_loc.empty()) - throw MEDMEM::MEDEXCEPTION("convertGlobalNodeList - Node mapping has not yet been built"); + throw INTERP_KERNEL::Exception(LOCALIZED("Node mapping has not yet been built")); for (int i=0; i< nbnode; i++) { @@ -288,7 +412,7 @@ void ParallelTopology::convertGlobalNodeList(const int* node_list, int nbnode, i void ParallelTopology::convertGlobalNodeListWithTwins(const int* node_list, int nbnode, int*& local, int*& ip,int*& full_array, int& size) { if (_node_glob_to_loc.empty()) - throw MEDMEM::MEDEXCEPTION("convertGlobalNodeList - Node mapping has not yet been built"); + throw INTERP_KERNEL::Exception(LOCALIZED("Node mapping has not yet been built")); size=0; for (int i=0; i< nbnode; i++) @@ -355,11 +479,21 @@ void ParallelTopology::convertGlobalFaceListWithTwins(const int* face_list, int //!to a distributed array with local cell numbers void ParallelTopology::convertGlobalCellList(const int* cell_list, int nbcell, int* local, int* ip) { - for (int i=0; i< nbcell; i++) + for (int i=0; i >::const_iterator iter = _glob_to_loc.find(cell_list[i]); INTERP_KERNEL::HashMap >::const_iterator iter = _glob_to_loc.find(cell_list[i]); - ip[i]=(iter->second).first; - local[i]=(iter->second).second; + if (iter == _glob_to_loc.end()) + { + cerr<<"proc "<second).first; //no domain + local[i]=(iter->second).second; //no local cell + //cout<<"proc "< >::const_iterator iter = _face_glob_to_loc.find(face_list[i]); if (iter == _face_glob_to_loc.end()) { - throw MED_EXCEPTION("convertGlobalFaceList - Face not found"); + throw INTERP_KERNEL::Exception(LOCALIZED("ParallelTopology::convertGlobalFaceList : Face not found")); } ip[i]=(iter->second).first; local[i]=(iter->second).second; @@ -404,8 +538,6 @@ void ParallelTopology::convertGlobalFaceList(const int* face_list, int nbface, i } } - - //replacing a table of global numbering with a table with local numberings // type_connectivity contains global connectivity for each type in input // type_connectivity contains local connectivity for each type in output @@ -421,17 +553,15 @@ void ParallelTopology::convertToLocal2ndVersion(int* nodes, int nbnodes, int ido { if ((it->second).first==idomain) nodes[inode]=(it->second).second; - } + } } } - //================================================================================ /*! * \brief Return max global face number */ //================================================================================ - int ParallelTopology::getMaxGlobalFace() const { int max = 0; diff --git a/src/MEDPartitioner/MEDPARTITIONER_ParallelTopology.hxx b/src/MEDPartitioner/MEDPARTITIONER_ParallelTopology.hxx index 3d6e7f418..72dbcc574 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_ParallelTopology.hxx +++ b/src/MEDPartitioner/MEDPARTITIONER_ParallelTopology.hxx @@ -24,7 +24,9 @@ #include "InterpKernelHashMap.hxx" #include "MEDPARTITIONER_Topology.hxx" +#include "MEDPARTITIONER_ParaDomainSelector.hxx" +/* namespace INTERP_KERNEL { template<> struct hash< std::pair > @@ -34,7 +36,7 @@ namespace INTERP_KERNEL return hash< int >()( x.first*1000000+x.second ); } }; -} +}*/ namespace MEDPARTITIONER { @@ -49,15 +51,19 @@ namespace MEDPARTITIONER { ParallelTopology(); + ParallelTopology(const std::vector&); ParallelTopology(const std::vector&, const std::vector&, std::vector&, std::vector&, std::vector&); - ParallelTopology(Graph* graph, int nbdomain, int mesh_dimension); + ParallelTopology(Graph* graph, Topology* oldTopology, int nbdomain, int mesh_dimension); ~ParallelTopology(); + + void setGlobalNumerotationDefault(ParaDomainSelector* domainSelector); + //!converts a list of global cell numbers //!to a distributed array with local cell numbers void convertGlobalNodeList(const int*, int,int*,int*); @@ -131,17 +137,17 @@ namespace MEDPARTITIONER { { return _nb_total_cells; } + int nbNodes() const - {return _nb_total_nodes;} + { + return _nb_total_nodes; + } inline int nbCells( int idomain) const { return _nb_cells[idomain]; } - - - //!retrieving number of nodes inline int getNodeNumber(int idomain) const { @@ -163,7 +169,7 @@ namespace MEDPARTITIONER { //!retrieving list of nodes in global numbers inline void getNodeList(int idomain, int* list) const { - for (int i=0; i<_nb_nodes[idomain];i++) + for (int i=0; i<_nb_nodes[idomain]; i++) list[i]=_node_loc_to_glob[idomain][i]; } @@ -172,6 +178,7 @@ namespace MEDPARTITIONER { { return _cell_loc_to_glob_fuse[idomain]; } + const std::vector & getFusedCellNumbers(int idomain) const { return _cell_loc_to_glob_fuse[idomain]; @@ -204,8 +211,6 @@ namespace MEDPARTITIONER { { for (int i=0; i<_nb_cells[idomain];i++) list[i]=_loc_to_glob[idomain][i]; - - } inline int getFaceNumber(int idomain) const @@ -258,6 +263,7 @@ namespace MEDPARTITIONER { } return -1; } + //!adding a face to the topology inline void appendFace(int idomain, int ilocal, int iglobal) { @@ -268,12 +274,9 @@ namespace MEDPARTITIONER { //return max global face number int getMaxGlobalFace() const; - private: - bool hasCellWithNodes( const MESHCollection&, int dom, const std::set& nodes ); - private: //!mapping global -> local typedef INTERP_KERNEL::HashMultiMap > TGlob2DomainLoc; @@ -291,30 +294,20 @@ namespace MEDPARTITIONER { std::vector > _cell_loc_to_glob_fuse; // glob nums after fusing std::vector > _face_loc_to_glob_fuse; // glob nums after fusing - //!mapping global -> local typedef INTERP_KERNEL::HashMultiMap > TGlob2LocsMap; TGlob2LocsMap _face_glob_to_loc; //!mapping local -> global std::vector > _face_loc_to_glob; - std::vector _nb_cells; - std::vector _nb_nodes; - std::vector _nb_faces; - int _nb_total_cells; - int _nb_total_nodes; - int _nb_total_faces; - int _nb_domain; - int _mesh_dimension; - }; diff --git a/src/MEDPartitioner/MEDPARTITIONER_SkyLineArray.cxx b/src/MEDPartitioner/MEDPARTITIONER_SkyLineArray.cxx index 20cfd4c50..3f0cf14fd 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_SkyLineArray.cxx +++ b/src/MEDPartitioner/MEDPARTITIONER_SkyLineArray.cxx @@ -21,7 +21,6 @@ // #include "MEDPARTITIONER_SkyLineArray.hxx" -#include "MEDMEM_Utilities.hxx" #include @@ -29,7 +28,7 @@ using namespace MEDPARTITIONER; MEDSKYLINEARRAY::MEDSKYLINEARRAY() { - MESSAGE_MED("Constructeur MEDSKYLINEARRAY sans parametre"); + //MESSAGE_MED("Constructeur MEDSKYLINEARRAY sans parametre"); } MEDSKYLINEARRAY::MEDSKYLINEARRAY(const MEDSKYLINEARRAY &myArray) @@ -40,7 +39,7 @@ MEDSKYLINEARRAY::MEDSKYLINEARRAY(const MEDSKYLINEARRAY &myArray) MEDSKYLINEARRAY::~MEDSKYLINEARRAY() { - MESSAGE_MED("Destructeur ~MEDSKYLINEARRAY"); + //MESSAGE_MED("Destructeur ~MEDSKYLINEARRAY"); //if (_index != NULL) delete [] _index; //if (_value != NULL) delete [] _value; diff --git a/src/MEDPartitioner/MEDPARTITIONER_SkyLineArray.hxx b/src/MEDPartitioner/MEDPARTITIONER_SkyLineArray.hxx index 21d6fffbc..d56fd94bb 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_SkyLineArray.hxx +++ b/src/MEDPartitioner/MEDPARTITIONER_SkyLineArray.hxx @@ -41,23 +41,21 @@ public : // Constructeur par recopie MEDSKYLINEARRAY( const MEDSKYLINEARRAY &myArray ); - // Avec ce constructeur la mémoire pour le tableau de valeur et le - // tableau d'index est réservée. Il suffit d'effectuer les séquences + // Avec ce constructeur la m�moire pour le tableau de valeur et le + // tableau d'index est r�serv�e. Il suffit d'effectuer les s�quences // d'appels suivantes pour initialiser le MEDSKYLINEARRAY - // 1) setIndex(index) puis fois setI(i,&listValeurN°I) avec i dans 1..count - // rem : listValeurN°I est dupliquée + // 1) setIndex(index) puis fois setI(i,&listValeurN�I) avec i dans 1..count + // rem : listValeurN�I est dupliqu�e // 2) appeler fois setIJ(i,j,valeur) avec i dans 1..count et avec j dans 1..count MEDSKYLINEARRAY( const std::vector& index, const std::vector& value ); - - ~MEDSKYLINEARRAY(); //void setMEDSKYLINEARRAY( const int count, const int length, int* index , int* value ) ; - inline int getNumberOf() const; - inline int getLength() const; - inline const int* getIndex() const; - inline const int* getValue() const; + inline int getNumberOf() const; + inline int getLength() const; + inline const int* getIndex() const; + inline const int* getValue() const; }; // --------------------------------------- diff --git a/src/MEDPartitioner/MEDPARTITIONER_Topology.hxx b/src/MEDPartitioner/MEDPARTITIONER_Topology.hxx index a38bdda02..d0821e7af 100644 --- a/src/MEDPartitioner/MEDPARTITIONER_Topology.hxx +++ b/src/MEDPartitioner/MEDPARTITIONER_Topology.hxx @@ -19,8 +19,6 @@ #ifndef MEDPARTITIONER_TOPOLOGY_HXX_ #define MEDPARTITIONER_TOPOLOGY_HXX_ -//#include "MEDMEM_define.hxx" - //#include "boost/shared_ptr.hpp" #include diff --git a/src/MEDPartitioner/MEDPARTITIONER_utils.cxx b/src/MEDPartitioner/MEDPARTITIONER_utils.cxx new file mode 100644 index 000000000..19843caba --- /dev/null +++ b/src/MEDPartitioner/MEDPARTITIONER_utils.cxx @@ -0,0 +1,1627 @@ +// Copyright (C) 2007-2010 CEA/DEN, EDF R&D +// +// This library is free software; you can redistribute it and/or +// modify it under the terms of the GNU Lesser General Public +// License as published by the Free Software Foundation; either +// version 2.1 of the License. +// +// This library is distributed in the hope that it will be useful, +// but WITHOUT ANY WARRANTY; without even the implied warranty of +// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +// Lesser General Public License for more details. +// +// You should have received a copy of the GNU Lesser General Public +// License along with this library; if not, write to the Free Software +// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +// +// See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com +// + +#include "MEDLoader.hxx" +#include "MEDLoaderBase.hxx" +#include "MEDFileUtilities.hxx" +#include "CellModel.hxx" +#include "MEDCouplingUMesh.hxx" +#include "MEDCouplingFieldDouble.hxx" +#include "MEDPARTITIONER_utils.hxx" +#include "InterpKernelException.hxx" +#include "MEDCouplingAutoRefCountObjectPtr.hxx" +#include "InterpKernelAutoPtr.hxx" + +#ifdef HAVE_MPI2 +#include +#endif + +#include +#include +#include +#include +#include + +using namespace std; +using namespace MEDPARTITIONER; + +int MEDPARTITIONER::MyGlobals::_verbose=0; +int MEDPARTITIONER::MyGlobals::_is0verbose=0; +int MEDPARTITIONER::MyGlobals::_rank=-1; +int MEDPARTITIONER::MyGlobals::_world_size=-1; +int MEDPARTITIONER::MyGlobals::_randomize=0; +int MEDPARTITIONER::MyGlobals::_atomize=0; +int MEDPARTITIONER::MyGlobals::_creates_boundary_faces=0; +vector MEDPARTITIONER::MyGlobals::_fileNames; +vector MEDPARTITIONER::MyGlobals::_meshNames; +vector MEDPARTITIONER::MyGlobals::_fieldDescriptions; +vector MEDPARTITIONER::MyGlobals::_generalInformations; + +string MEDPARTITIONER::trim(string& s, const string& drop) +{ + string r=s.erase(s.find_last_not_of(drop)+1); + return r.erase(0,r.find_first_not_of(drop)); +} + +string MEDPARTITIONER::intToStr(int i) +{ + ostringstream oss; + oss<>res; + return res; +} + +string MEDPARTITIONER::doubleToStr(double i) +{ + ostringstream oss; + oss<>res; + return res; +} + +bool MEDPARTITIONER::testArg(const char *arg, const char *argExpected, string& argValue) +{ + argValue=""; + int i; + for (i=0; i MEDPARTITIONER::createRandomSize(int size) +{ + vector res(size); + for (int i=0; i& ran, vector& vx, vector& va) +//randomize a xadj and adjncy, renumbering vertices belong rand. +//work only on one processor!!!! +{ + if (MyGlobals::_world_size>1) + { + cerr<<"randomizeAdj only on one proc!"< invran(size); + for (int i=0; i r=createRandomSize(size); + vector vx,va; + randomizeAdj(&xadj[0],&adjncy[0],r,vx,va); + for (int i=0; i& vec) +{ + if (vec.size()==0) return string(" NONE\n"); + ostringstream oss; + for (vector::const_iterator i=vec.begin(); i!=vec.end(); ++i) + oss<<" -> '"<<*i<<"'"<& vec, string sep) +{ + if (vec.size()==0) return string(" NONE\n"); + ostringstream oss; + for (vector::const_iterator i=vec.begin(); i!=vec.end(); ++i) + oss<& mymap) +{ + if (mymap.size()==0) return string(" NONE\n"); + ostringstream oss; + for (map::const_iterator i=mymap.begin(); i!=mymap.end(); ++i) + oss<<" -> ["<<(*i).first<<"]="<<(*i).second< >& mymap) +{ + if (mymap.size()==0) return string(" NONE\n"); + ostringstream oss; + for (map< string,vector >::const_iterator i=mymap.begin(); i!=mymap.end(); ++i) + oss<<" -> ["<<(*i).first<<"]="<& vec, string sep) +{ + if (vec.size()==0) return string(" NONE\n"); + ostringstream oss; + for (vector::const_iterator i=vec.begin(); i!=vec.end(); ++i) + { + oss<<" ->"; + oss< vec2=deserializeToVectorOfString(*i); + for (vector::const_iterator j=vec2.begin(); j!=vec2.end(); ++j) + oss<.push_back("toto") on serialized_FromVectorOfString_string +{ + ostringstream oss; + oss<& vec) +//a vector of string gives a string +{ + ostringstream oss; + for (vector::const_iterator i=vec.begin(); i!=vec.end(); ++i) + oss< MEDPARTITIONER::deserializeToVectorOfString(const string& str) +//a string gives a vector of string +{ + //vector res=new vector; + vector res; + size_t pos=0; + size_t posmax=str.size(); + if (posmax==0) return res; //empty vector + size_t length; + while (pos < posmax-6) //setw(5)+" " + { + istringstream iss(str.substr(pos,5)); + iss>>length; + //cout<<"length "< vec=deserializeToVectorOfString(fromStr); + vector res; + for (int i=0; i MEDPARTITIONER::vectorizeFromMapOfStringInt(const map& mymap) +//elements first and second of map give one elements in result vector of string +//converting formatted the int second as firsts characters ending at first slash +{ + vector res; + for (map::const_iterator i=mymap.begin(); i!=mymap.end(); ++i) + { + ostringstream oss; + oss<<(*i).second<<"/"<<(*i).first; + res.push_back(oss.str()); + } + return res; +} + +map MEDPARTITIONER::devectorizeToMapOfStringInt(const vector& vec) +//if existing identicals (first,second) in vector no problem, else Exception +{ + map res; + for (vector::const_iterator i=vec.begin(); i!=vec.end(); ++i) + { + size_t pos=0; + size_t posmax=(*i).size(); + size_t found=(*i).find('/'); //first slash + if ((found==string::npos) || (found<1)) + throw INTERP_KERNEL::Exception(LOCALIZED("Error aIntNumber/anyString is expected")); + int second; + istringstream iss((*i).substr(pos,found)); + iss>>second; + string first=(*i).substr(pos+found+1,posmax-found); + map::iterator it=res.find(first); + if (it!=res.end()) + if ((*it).second!=second) + throw INTERP_KERNEL::Exception(LOCALIZED("Error not the same map value")); + res[first]=second; + } + return res; +} + +vector MEDPARTITIONER::vectorizeFromMapOfStringVectorOfString(const map< string,vector >& mymap) +//elements first and second of map give one elements in result vector of string +//adding key map and length of second vector as first string in each serialized vector +//one serialized vector per key map +{ + vector res; + for (map< string,vector >::const_iterator i=mymap.begin(); i!=mymap.end(); ++i) + { + vector vs=(*i).second; //a vector of string; + ostringstream oss; + oss<<"Keymap/"<<(*i).first<<"/"<<(*i).second.size(); + vs.insert(vs.begin(), oss.str()); + res.push_back(serializeFromVectorOfString(vs)); + } + return res; +} + +map< string,vector > MEDPARTITIONER::devectorizeToMapOfStringVectorOfString(const vector& vec) +//if existing identicals keymap in vector no problem +//duplicates in second vector +{ + map< string,vector > res; + for (vector::const_iterator i=vec.begin(); i!=vec.end(); ++i) + { + vector vs=deserializeToVectorOfString(*i); + + string enTete=vs[0]; + size_t posmax=enTete.size(); + size_t foundKey=enTete.find("Keymap/"); + size_t foundSizeVector=enTete.find_last_of('/'); + if ((foundKey==string::npos) || (foundKey!=0) || ((foundKey+7)>=foundSizeVector)) + throw INTERP_KERNEL::Exception(LOCALIZED("Error Keymap/anyString/aIntNumber is expected")); + int sizeVector; + istringstream iss(enTete.substr(foundSizeVector+1,posmax-foundSizeVector)); + iss>>sizeVector; + string keymap=enTete.substr(foundKey+7,foundSizeVector-foundKey-7); + //cout< MEDPARTITIONER::recvVectorOfString(const int source) +//non conseille, interblocages, utiliser sendAndReceive +{ + throw INTERP_KERNEL::Exception(LOCALIZED("use sendAndReceiveVectorOfString please.")); + int recSize=0; + int tag=111000; + MPI_Status status; + MPI_Recv(&recSize, 1, MPI_INT, source, tag, MPI_COMM_WORLD, &status); + string recData(recSize,'x'); + MPI_Recv((void*)recData.data(), recSize, MPI_CHAR, 1, tag+100, MPI_COMM_WORLD, &status); + //cout<<"proc "< MEDPARTITIONER::sendAndReceiveVectorOfString(const vector& vec, const int source, const int target) +//not optimized but suffisant +//return empty vector if i am not target +{ + int rank=MyGlobals::_rank; + + /*for test + ostringstream oss; + oss<<"sendAndReceive from "< res; + return res; //empty one for other proc +} + +vector MEDPARTITIONER::allgathervVectorOfString(const vector& vec) +//strings NO need all same size!!!! +{ + int world_size=MyGlobals::_world_size; + string str=serializeFromVectorOfString(vec); + + /*for test + int rank=MyGlobals::_rank; + ostringstream oss; + oss<<"allgatherv from "< indexes(world_size); + int size=str.length(); + MPI_Allgather(&size, 1, MPI_INT, + &indexes[0], 1, MPI_INT, MPI_COMM_WORLD); + + /*{ + ostringstream oss; + for (int i=0; i disp(1,0); + for (int i=0; i deserial=deserializeToVectorOfString(recData); + if (MyGlobals::_verbose>1000) + { + cout<<"proc "<& vec, const int source, const int target) +//TODO + +string MEDPARTITIONER::cle1ToStr(string s, int inew) +{ + ostringstream oss; + oss<>inew; +} + +string MEDPARTITIONER::cle2ToStr(string s, int inew, int iold) +{ + ostringstream oss; + oss<>inew>>iold; +} + +string MEDPARTITIONER::extractFromDescription(string description,string tag) +{ + size_t found=description.find(tag); + if ((found==string::npos) || (found<1)) + { + cerr<<"ERROR : not found '"<alloc(v.size()/nbComponents,nbComponents); + std::copy(v.begin(),v.end(),p->getPointer()); + return p; +} + +ParaMEDMEM::DataArrayDouble* MEDPARTITIONER::createDataArrayDoubleFromVector(vector& v) +{ + ParaMEDMEM::DataArrayDouble* p=DataArrayDouble::New(); + p->alloc(v.size(),1); + std::copy(v.begin(),v.end(),p->getPointer()); + return p; +} + +vector MEDPARTITIONER::browseFieldDouble(const MEDCouplingFieldDouble* fd) +//quick almost human readable information on a field double +/* example done by fd->simpleRepr() : +FieldDouble with name : "VectorFieldOnCells" +Description of field is : "" +FieldDouble space discretization is : P0 +FieldDouble time discretization is : One time label. Time is defined by iteration=0 order=1 and time=2. +Time unit is : "" +FieldDouble nature of field is : NoNature +FieldDouble default array has 3 components and 30000 tuples. +FieldDouble default array has following info on components : "vx" "vy" "vz" +Mesh support information : +__________________________ +Unstructured mesh with name : "testMesh" +Description of mesh : "" +Time attached to the mesh [unit] : 0 [] +Iteration : -1 Order : -1 +Mesh dimension : 3 +Space dimension : 3 +Info attached on space dimension : "" "" "" +Number of nodes : 33201 +Number of cells : 30000 +Cell types present : NORM_HEXA8 +*/ +{ + vector res; + //res.push_back("fieldName="); res.back()+=fd->getName(); + //not saved in file? res.push_back("fieldDescription="); res.back()+=fd->getDescription(); + //ret << "FieldDouble space discretization is : " << _type->getStringRepr() << "\n"; + //ret << "FieldDouble time discretization is : " << _time_discr->getStringRepr() << "\n"; + //ret << "FieldDouble nature of field is : " << MEDCouplingNatureOfField::getRepr(_nature) << "\n"; + if (fd->getArray()) + { + int nb=fd->getArray()->getNumberOfComponents(); + res.push_back("nbComponents="); res.back()+=intToStr(nb); + //ret << "FieldDouble default array has " << nbOfCompo << " components and " << getArray()->getNumberOfTuples() << " tuples.\n"; + //ret << "FieldDouble default array has following info on components : "; + for (int i=0; igetInfoOnComponent(i) << "\" "; + res.push_back("componentInfo"); + res.back()+=intToStr(i)+"="+fd->getArray()->getInfoOnComponent(i); + } + } + else + { + res.push_back("nbComponents=0"); //unknown + } + return res; +} + +vector MEDPARTITIONER::browseAllFields(const string& myfile) +//quick almost human readable information on all fields in a .med file +{ + vector res; + vector meshNames=MEDLoader::GetMeshNames(myfile.c_str()); + + for (int i=0; i fieldNames= + MEDLoader::GetAllFieldNamesOnMesh(myfile.c_str(),meshNames[i].c_str()); + for (int j = 0; j < fieldNames.size(); j++) + { + vector< ParaMEDMEM::TypeOfField > typeFields= + MEDLoader::GetTypesOfField(myfile.c_str(), meshNames[i].c_str(), fieldNames[j].c_str()); + for (int k = 0; k < typeFields.size(); k++) + { + vector< pair< int, int > > its= + MEDLoader::GetFieldIterations(typeFields[k], myfile.c_str(), meshNames[i].c_str(), fieldNames[j].c_str()); + if (MyGlobals::_is0verbose>100) cout<<"fieldName "< resi; + resi.push_back("fileName="); resi.back()+=myfile; + resi.push_back("meshName="); resi.back()+=meshNames[i]; + resi.push_back("fieldName="); resi.back()+=fieldNames[j]; + resi.push_back("typeField="); resi.back()+=intToStr((int)typeFields[k]); + resi.push_back("DT="); resi.back()+=intToStr((int)its[m].first); + resi.push_back("IT="); resi.back()+=intToStr((int)its[m].second); + res.push_back(serializeFromVectorOfString(resi)); + } + } + } + } + return res; +} + +/* +vector MEDPARTITIONER::browseAllFieldsOnMesh(const string& myfile, const string& mymesh, int idomain) +//quick almost human readable information on all fields on a mesh in a .med file using MEDFILEBROWSER +{ + vector res; + vector meshNames; + meshNames.push_back(mymesh); + MEDMEM::MEDFILEBROWSER myMed(myfile); + for (int i=0; i MEDPARTITIONER::GetInfosOfField(const char *fileName, const char *meshName, int idomain) +{ +const int lggeom=10; +const med_geometry_type GEOMTYPE[lggeom]={ //MED_N_CELL_FIXED_GEO] = { + //MED_POINT1, + //MED_SEG2, + //MED_SEG3, + //MED_SEG4, + //MED_TRIA3, + //MED_QUAD4, + //MED_TRIA6, + //MED_TRIA7, + //MED_QUAD8, + //MED_QUAD9, + MED_TETRA4, + MED_PYRA5, + MED_PENTA6, + MED_HEXA8, + MED_OCTA12, + MED_TETRA10, + MED_PYRA13, + MED_PENTA15, + MED_HEXA20, + MED_HEXA27, + //MED_POLYGON, + //MED_POLYHEDRON +}; + +const char * const GEOMTYPENAME[lggeom]={ + //"MED_POINT1", + //"MED_SEG2", + //"MED_SEG3", + //"MED_SEG4", + //"MED_TRIA3", + //"MED_QUAD4", + //"MED_TRIA6", + //"MED_TRIA7", + //"MED_QUAD8", + //"MED_QUAD9", + "MED_TETRA4", + "MED_PYRA5", + "MED_PENTA6", + "MED_HEXA8", + "MED_OCTA12", + "MED_TETRA10", + "MED_PYRA13", + "MED_PENTA15", + "MED_HEXA20", + "MED_HEXA27", + //"MED_POLYGONE", + //"MED_POLYEDRE", +}; + + +const int lgentity=3; +const med_entity_type ENTITYTYPE[lgentity]={ //MED_N_ENTITY_TYPES+2]={ + //MED_UNDEF_ENTITY_TYPE, + MED_CELL, + //MED_DESCENDING_FACE, + //MED_DESCENDING_EDGE, + MED_NODE, + MED_NODE_ELEMENT, + //MED_STRUCT_ELEMENT, + //MED_UNDEF_ENTITY_TYPE +}; + +const char * const ENTITYTYPENAME[lgentity]={ //MED_N_ENTITY_TYPES+2]={ + //"MED_UNDEF_ENTITY_TYPE", + "MED_CELL", + //"MED_FACE", + //"MED_ARETE", + "MED_NODE", + "MED_NODE_ELEMENT", + //"MED_STRUCT_ELEMENT", + //"MED_UNDEF_ENTITY_TYPE" +}; + + vector res; + med_idt fid=MEDfileOpen(fileName,MED_ACC_RDONLY); + med_int nbFields=MEDnField(fid); + if (MyGlobals::_verbose>20) cout<<"on filename "< comp=new char[ncomp*MED_SNAME_SIZE+1]; + INTERP_KERNEL::AutoPtr unit=new char[ncomp*MED_SNAME_SIZE+1]; + INTERP_KERNEL::AutoPtr dt_unit=new char[MED_LNAME_SIZE+1]; + med_int nbPdt; + MEDfieldInfo(fid,i,nomcha,maa_ass,&localmesh,&typcha,comp,unit,dt_unit,&nbPdt); + std::string curFieldName=MEDLoaderBase::buildStringFromFortran(nomcha,MED_NAME_SIZE+1); + std::string curMeshName=MEDLoaderBase::buildStringFromFortran(maa_ass,MED_NAME_SIZE+1); + for (int k=1; k<=nbPdt; k++) + { + MEDfieldComputingStepInfo(fid,nomcha,k,&numdt,&numo,&dt); + if (MyGlobals::_verbose>20) + cout<<"on filename "<0) + { + if (MyGlobals::_verbose>20) + cout<<"on filename "< resi; + resi.push_back("idomain="); resi.back()+=intToStr(idomain); + resi.push_back("fileName="); resi.back()+=fileName; + resi.push_back("meshName="); resi.back()+=curMeshName; + resi.push_back("fieldName="); resi.back()+=curFieldName; + resi.push_back("typeField="); resi.back()+=intToStr((int)ON_NODES); + resi.push_back("typeData="); resi.back()+=intToStr((int)typcha); //6 for double? + resi.push_back("nbComponent="); resi.back()+=intToStr((int)ncomp); + resi.push_back("DT="); resi.back()+=intToStr((int)numdt); + resi.push_back("IT="); resi.back()+=intToStr((int)numo); + resi.push_back("time="); resi.back()+=doubleToStr(dt); + resi.push_back("entity="); resi.back()+=intToStr((int)enttype); + resi.push_back("entityName="); resi.back()+=ENTITYTYPENAME[ie]; + resi.push_back("nbOfVal="); resi.back()+=intToStr((int)nbOfVal); + resi.push_back("profilName="); resi.back()+=pflname; + resi.push_back("profileSize="); resi.back()+=intToStr((int)profilesize); + resi.push_back("nbPtGauss="); resi.back()+=intToStr((int)nbi); + res.push_back(serializeFromVectorOfString(resi)); + } + break; //on nodes no need to scute all geomtype + } + else + { + med_geometry_type mygeomtype=GEOMTYPE[j]; + med_int nbOfVal=MEDfieldnValueWithProfile(fid,nomcha,numdt,numo,enttype,mygeomtype,profileit, + MED_COMPACT_PFLMODE,pflname,&profilesize,locname,&nbi); + if (nbOfVal>0) + { + if (MyGlobals::_verbose>20) + cout<<"on filename "< resi; + resi.push_back("idomain="); resi.back()+=intToStr(idomain); + resi.push_back("fileName="); resi.back()+=fileName; + resi.push_back("meshName="); resi.back()+=curMeshName; + resi.push_back("fieldName="); resi.back()+=curFieldName; + resi.push_back("typeField="); resi.back()+=intToStr((int)typeField); + resi.push_back("typeData="); resi.back()+=intToStr((int)typcha); //6 for double? + resi.push_back("nbComponent="); resi.back()+=intToStr((int)ncomp); + resi.push_back("DT="); resi.back()+=intToStr((int)numdt); + resi.push_back("IT="); resi.back()+=intToStr((int)numo); + resi.push_back("time="); resi.back()+=doubleToStr(dt); + resi.push_back("entity="); resi.back()+=intToStr((int)enttype); + resi.push_back("entityName="); resi.back()+=ENTITYTYPENAME[ie]; + resi.push_back("geomType="); resi.back()+=intToStr((int)GEOMTYPE[j]); + resi.push_back("geomTypeName="); resi.back()+=GEOMTYPENAME[j]; + resi.push_back("nbOfVal="); resi.back()+=intToStr((int)nbOfVal); + resi.push_back("profilName="); resi.back()+=pflname; + resi.push_back("profileSize="); resi.back()+=intToStr((int)profilesize); + resi.push_back("nbPtGauss="); resi.back()+=intToStr((int)nbi); + if (typeField==-1) + { + cout<<"WARNING : unknown typeField for entity type "<10) cout<<"detected fields:\n"< MEDPARTITIONER::browseAllFieldsOnMesh(const string& myfile, const string& mymesh, int idomain) +//quick almost human readable information on all fields on a mesh in a .med file +{ + vector res=GetInfosOfField(myfile.c_str(),mymesh.c_str(),idomain); + return res; + + /*obsolete do no work on GetTypesOfField ON_GAUSS_NE + vector res; + vector meshNames; + meshNames.push_back(mymesh); + + for (int i=0; i fieldNames= + MEDLoader::GetAllFieldNamesOnMesh(myfile.c_str(),meshNames[i].c_str()); + for (int j=0; j typeFields= + MEDLoader::GetTypesOfField(myfile.c_str(), meshNames[i].c_str(), fieldNames[j].c_str()); + //if (MyGlobals::_is0verbose>100) cout<<"fieldName "< > its; + its=MEDLoader::GetFieldIterations(typeFields[k], myfile.c_str(), meshNames[i].c_str(), fieldNames[j].c_str()); + //if (typeFields[k]==ON_GAUSS_NE) its.push_back(make_pair(5,6)); + if (MyGlobals::_is0verbose>100) cout<<"fieldName "< resi; + resi.push_back("idomain="); resi.back()+=intToStr(idomain); + resi.push_back("fileName="); resi.back()+=myfile; + resi.push_back("meshName="); resi.back()+=meshNames[i]; + resi.push_back("fieldName="); resi.back()+=fieldNames[j]; + resi.push_back("typeField="); resi.back()+=intToStr((int)typeFields[k]); + resi.push_back("DT="); resi.back()+=intToStr((int)its[m].first); + resi.push_back("IT="); resi.back()+=intToStr((int)its[m].second); + //cout<<"browseAllFieldsOnMesh add "<& vec, int target) +{ + int tag = 111002; + int size=vec.size(); + if (MyGlobals::_verbose>1000) + cout<<"proc "< sendDoubleVec "<(&vec[0]), size, MPI_DOUBLE, target, tag+100, MPI_COMM_WORLD); +#endif +} + +/*! Receives messages from proc \a source to fill vector vec. +To be used with \a sendDoubleVec method. + +\param vec vector that is filled +\param source processor id of the incoming messages + */ +std::vector* MEDPARTITIONER::recvDoubleVec(int source) +{ + int tag = 111002; + int size; +#ifdef HAVE_MPI2 + MPI_Status status; + MPI_Recv(&size, 1, MPI_INT, source, tag, MPI_COMM_WORLD, &status); + if (MyGlobals::_verbose>1000) + cout<<"proc "<* vec=new std::vector; + vec->resize(size); + MPI_Recv(&vec[0], size, MPI_DOUBLE, source, tag+100, MPI_COMM_WORLD, &status); +#endif + return vec; +} + +void MEDPARTITIONER::recvDoubleVec(std::vector& vec, int source) +{ + int tag = 111002; + int size; +#ifdef HAVE_MPI2 + MPI_Status status; + MPI_Recv(&size, 1, MPI_INT, source, tag, MPI_COMM_WORLD, &status); + if (MyGlobals::_verbose>1000) + cout<<"proc "<& vec, int target) +{ + int tag = 111003; + int size=vec.size(); + if (MyGlobals::_verbose>1000) + cout<<"proc "< sendIntVec "<(&vec[0]), size,MPI_INT, target, tag+100, MPI_COMM_WORLD); +#endif +} + +/*! Receives messages from proc \a source to fill vector vec. +To be used with \a sendIntVec method. +\param vec vector that is filled +\param source processor id of the incoming messages + */ +std::vector* MEDPARTITIONER::recvIntVec(int source) +{ + int tag = 111003; + int size; +#ifdef HAVE_MPI2 + MPI_Status status; + MPI_Recv(&size, 1, MPI_INT, source, tag, MPI_COMM_WORLD, &status); + if (MyGlobals::_verbose>1000) + cout<<"proc "<* vec=new std::vector; + vec->resize(size); + MPI_Recv(&vec[0], size, MPI_INT, source, tag+100, MPI_COMM_WORLD, &status); +#endif + return vec; +} + +void MEDPARTITIONER::recvIntVec(std::vector& vec, int source) +{ + int tag = 111003; + int size; +#ifdef HAVE_MPI2 + MPI_Status status; + MPI_Recv(&size, 1, MPI_INT, source, tag, MPI_COMM_WORLD, &status); + if (MyGlobals::_verbose>1000) + cout<<"proc "<getNbOfElems(); + size[1]=da->getNumberOfTuples(); + size[2]=da->getNumberOfComponents(); + if (MyGlobals::_verbose>1000) + cout<<"proc "< sendDataArrayInt "<getPointer(); + MPI_Send(const_cast(&p[0]), size[0] ,MPI_INT, target, tag+100, MPI_COMM_WORLD); +#endif +} + +/*! Receives messages from proc \a source to fill dataArrayInt da. +To be used with \a sendIntVec method. +\param da dataArrayInt that is filled +\param source processor id of the incoming messages + */ +ParaMEDMEM::DataArrayInt* MEDPARTITIONER::recvDataArrayInt(int source) +//std::vector& vec, int source)const +{ + int tag = 111004; + int size[3]; +#ifdef HAVE_MPI2 + MPI_Status status; + MPI_Recv(size, 3, MPI_INT, source, tag, MPI_COMM_WORLD, &status); + if (MyGlobals::_verbose>1000) + cout<<"proc "<alloc(size[1],size[2]); + int * p=da->getPointer(); + MPI_Recv(const_cast(&p[0]), size[0], MPI_INT, source, tag+100, MPI_COMM_WORLD, &status); +#endif + return da; +} + +/*! +Sends content of \a dataArrayInt to processor \a target. +To be used with \a recvDataArrayDouble method. +\param da dataArray to be sent +\param target processor id of the target +*/ +void MEDPARTITIONER::sendDataArrayDouble(ParaMEDMEM::DataArrayDouble* da, int target) +{ + if (da==0) throw INTERP_KERNEL::Exception(LOCALIZED("Problem send DataArrayDouble* NULL")); + int tag = 111005; + int size[3]; + size[0]=da->getNbOfElems(); + size[1]=da->getNumberOfTuples(); + size[2]=da->getNumberOfComponents(); + if (MyGlobals::_verbose>1000) + cout<<"proc "< sendDataArrayDouble "<getPointer(); + MPI_Send(const_cast(&p[0]), size[0] ,MPI_DOUBLE, target, tag+100, MPI_COMM_WORLD); +#endif +} + +/*! Receives messages from proc \a source to fill dataArrayDouble da. +To be used with \a sendDoubleVec method. +\param da dataArrayDouble that is filled +\param source processor id of the incoming messages + */ +ParaMEDMEM::DataArrayDouble* MEDPARTITIONER::recvDataArrayDouble(int source) +//std::vector& vec, int source)const +{ + int tag = 111005; + int size[3]; +#ifdef HAVE_MPI2 + MPI_Status status; + MPI_Recv(size, 3, MPI_INT, source, tag, MPI_COMM_WORLD, &status); + if (MyGlobals::_verbose>1000) + cout<<"proc "<alloc(size[1],size[2]); + double * p=da->getPointer(); + MPI_Recv(const_cast(&p[0]), size[0], MPI_DOUBLE, source, tag+100, MPI_COMM_WORLD, &status); +#endif + return da; +} + +ParaMEDMEM::MEDCouplingUMesh* MEDPARTITIONER::createEmptyMEDCouplingUMesh() + //create empty MEDCouplingUMesh* dim 3 +{ + ParaMEDMEM::MEDCouplingUMesh* umesh=ParaMEDMEM::MEDCouplingUMesh::New(); + umesh->setMeshDimension(3); + umesh->allocateCells(0); + umesh->finishInsertingCells(); + ParaMEDMEM::DataArrayDouble *myCoords=ParaMEDMEM::DataArrayDouble::New(); + myCoords->alloc(0,3); + umesh->setCoords(myCoords); + umesh->setName("EMPTY"); + myCoords->decrRef(); + umesh->checkCoherency(); + return umesh; +} + +void MEDPARTITIONER::testVectorOfStringMPI() +{ + int rank=MyGlobals::_rank; + int world_size=MyGlobals::_world_size; + vector myVector; + ostringstream oss; + oss<<"hello from "< v0=deserializeToVectorOfString(s0); + cout<<"v0 is : a vector of size "< res=deserializeToVectorOfString(s0); + if (res.size()!=myVector.size()) + throw INTERP_KERNEL::Exception(LOCALIZED("Problem in (de)serialise VectorOfString incoherent sizes")); + for (int i=0; i res=sendAndReceiveVectorOfString(myVector, i, j); + if ((rank==j) && MyGlobals::_verbose>20) + cout<<"proc "< res=allgathervVectorOfString(myVector); + //sometimes for test + res=allgathervVectorOfString(myVector); + res=allgathervVectorOfString(myVector); + if (rank==0 && MyGlobals::_verbose>20) + cout<<"proc "< myMap; + myMap["one"]=1; + myMap["two"]=22; //a bug + myMap["three"]=3; + myMap["two"]=2; //last speaking override + + if (rank==0) + { + vector v2=vectorizeFromMapOfStringInt(myMap); + /* + cout<<"v2 is : a vector of size "< m3=devectorizeToMapOfStringInt(v2); + if (reprMapOfStringInt(m3)!=reprMapOfStringInt(myMap)) + throw INTERP_KERNEL::Exception(LOCALIZED("Problem in (de)vectorize MapOfStringInt")); + } + + vector v2=allgathervVectorOfString(vectorizeFromMapOfStringInt(myMap)); + if (rank==0 && MyGlobals::_verbose>20) + { + cout<<"v2 is : a vector of size "< m2=devectorizeToMapOfStringInt(v2); + cout<<"m2 is : a map of size "< myVector; + ostringstream oss; + oss<<"hello from "< > m2; + m2["first key"]=myVector; + m2["second key"]=myVector; + vector v2=vectorizeFromMapOfStringVectorOfString(m2); + map< string,vector > m3=devectorizeToMapOfStringVectorOfString(v2); + if (rank==0 && MyGlobals::_verbose>20) + cout<<"m2 is : a MapOfStringVectorOfString of size "< > m4; + m4["1rst key"]=myVector; + m4["2snd key"]=myVector; + vector v4=allgathervVectorOfString(vectorizeFromMapOfStringVectorOfString(m4)); + if (rank==0 && MyGlobals::_verbose>20) + { + map< string,vector > m5=devectorizeToMapOfStringVectorOfString(v4); + map< string,vector > m6=deleteDuplicatesInMapOfStringVectorOfString(m5); + cout<<"m5 is : a map of size "<alloc(nbOfTuples,numberOfComponents); + vector vals; + for (int j=0; jgetPointer()); + if (rank==0) sendDataArrayInt(send, 1); + if (rank==1) recv=recvDataArrayInt(0); + if (rank==1 && MyGlobals::_verbose>20) + { + cout<repr()<repr()<repr()!=recv->repr()) + throw INTERP_KERNEL::Exception(LOCALIZED("Problem in send&recv DataArrayInt")); + } + send->decrRef(); + if (rank==1) recv->decrRef(); + } + //double + { + ParaMEDMEM::DataArrayDouble* send=ParaMEDMEM::DataArrayDouble::New(); + ParaMEDMEM::DataArrayDouble* recv=0; + int nbOfTuples=5; + int numberOfComponents=3; + send->alloc(nbOfTuples,numberOfComponents); + vector vals; + for (int j=0; jgetPointer()); + if (rank==0) sendDataArrayDouble(send, 1); + if (rank==1) recv=recvDataArrayDouble(0); + if (rank==1 && MyGlobals::_verbose>20) + { + cout<repr()<repr()<repr()!=recv->repr()) + throw INTERP_KERNEL::Exception(LOCALIZED("Problem in send&recv DataArrayDouble")); + } + send->decrRef(); + if (rank==1) recv->decrRef(); + } + + if (MyGlobals::_verbose) cout<<"proc "< x, y; + int tag=111111; + MPI_Request requete0, requete1; + MPI_Status statut; + int ok=0; + string res; + if (rang==0) + { + x.resize(taille); + MPI_Ssend_init(&x[0], taille, MPI_INT, 1, tag, MPI_COMM_WORLD , &requete0); + for(int k=0; k cela peut prendre du temps + MPI_Start(&requete0); + //Traitement sequentiel independant de "x" + //... + MPI_Wait(&requete0, &statut); + //Traitement sequentiel impliquant une modification de "x" en memoire + //x=... + } + MPI_Request_free(&requete0); + } + else if (rang == 1) + { + y.resize(taille); + MPI_Recv_init(&y[0], taille, MPI_INT, 0, tag, MPI_COMM_WORLD , &requete1); + for(int k=0; k cela peut prendre du temps + MPI_Start(&requete1); + //Traitement sequentiel independant de "y" + //... + MPI_Wait(&requete1, &statut); + //Traitement sequentiel dependant de "y" + //...=f(y) + int nb=0; + for (int i=0; i9) + { + res="0K"; if (nb!=taille) res="KO"; + cout<1) + cout<<"resultat "<=wsize) next=0; + vector x, y; + tagbefo=111111+befo; + tagnext=111111+rang; + MPI_Request requete0, requete1; + MPI_Status statut1, statut2; + int ok=0; + string res; + //cout<<"ini|"< cela peut prendre du temps + MPI_Start(&requete0); + //Reception du gros message --> cela peut prendre du temps + for (int i=0; i9) + { + res="0K"+intToStr(rang); if (nb!=taille) res="KO"+intToStr(rang); + cout<1) + cout<<"resultat proc "<=rangMax) couleur=MPI_UNDEFINED; + cout<<"coul|"<MyGlobals::_world_size) wsize=MyGlobals::_world_size; + befo=rang-1; if (befo<0) befo=wsize-1; + next=rang+1; if (next>=wsize) next=0; + vector x, y; + tagbefo=111111+befo; + tagnext=111111+rang; + MPI_Request requete0, requete1; + MPI_Status statut1, statut2; + int ok=0; + string res; + + //cout<<"ini|"< cela peut prendre du temps + MPI_Start(&requete0); + //Reception du gros message --> cela peut prendre du temps + for (int i=0; i9) + { + res="0K"+intToStr(rang); if (nb!=taille) res="KO"+intToStr(rang); + cout<1) + cout<<"resultat proc "< +#include +#include -namespace MEDPARTITIONER { - std::string trim(std::string& s,const std::string& drop = " ") - { - std::string r=s.erase(s.find_last_not_of(drop)+1); - return r.erase(0,r.find_first_not_of(drop)); - } +#ifdef LOCALIZED +#undef LOCALIZED +#endif + +#if defined(_DEBUG_) || defined(_DEBUG) +//# define LOCALIZED(message) #message , __FILE__ , __FUNCTION__ , __LINE__ +# define LOCALIZED(message) #message , __FUNCTION__ , __LINE__ +#else +# define LOCALIZED(message) #message +#endif + +namespace MEDPARTITIONER +{ + using namespace std; + using namespace ParaMEDMEM; + + string trim(string& s,const string& drop); + string intToStr(int i); + string doubleToStr(double i); + int strToInt(string s); + double strToDouble(string s); + bool testArg(const char *arg, const char *argExpected, string& argValue); + vector createRandomSize(int size); + void randomizeAdj(int* xadj, int* adjncy, vector& ran, vector& vx, vector& va); + void testRandomize(); + + string reprVectorOfString(const vector& vec); + string reprVectorOfString(const vector& vec, string sep); + string reprMapOfStringInt(const map& mymap); + string reprMapOfStringVectorOfString(const map< string,vector >& mymap); + string reprFieldDescriptions(const vector& vec, string sep); + + string serializeFromString(const string& s); + string serializeFromVectorOfString(const vector& vec); + vector deserializeToVectorOfString(const string& str); + string eraseTagSerialized(string fromStr, string tag); + + vector vectorizeFromMapOfStringInt(const map& mymap); + map devectorizeToMapOfStringInt(const vector& vec); + + vector vectorizeFromMapOfStringVectorOfString(const map< string,vector >& mymap); + map< string,vector > devectorizeToMapOfStringVectorOfString(const vector& vec); + + vector selectTagsInVectorOfString(const vector& vec, string tag); + vector deleteDuplicatesInVectorOfString(const vector& vec); + map< string,vector > deleteDuplicatesInMapOfStringVectorOfString(const map< string,vector >& mymap); + + string cle1ToStr(string s, int inew); + void cle1ToData(string cle, string& s, int& inew); + + string cle2ToStr(string s, int inew, int iold); + void cle2ToData(string cle, string& s, int& inew, int& iold); + + string extractFromDescription(string description, string tag); + void fieldDescriptionToData(string description, + int& idomain, string& fileName, string& meshName, string& fieldName, + int& typeField, int& DT, int& IT); + void fieldShortDescriptionToData(string description, + string& fieldName, int& typeField, int& entity, int& DT, int& IT); + + ParaMEDMEM::DataArrayInt* createDataArrayIntFromVector(vector& v); + ParaMEDMEM::DataArrayInt* createDataArrayIntFromVector(vector& v, int nbComponents); + ParaMEDMEM::DataArrayDouble* createDataArrayDoubleFromVector(vector& v); + void sendVectorOfString(const vector& vec, const int target); + vector recvVectorOfString(const int source); + //TODO void sendrecvVectorOfString(const vector& vec, const int source, const int target); + vector sendAndReceiveVectorOfString(const vector& vec, const int source, const int target); + vector allgathervVectorOfString(const vector& vec); + + vector browseFieldDouble(const MEDCouplingFieldDouble* fd); + vector browseAllFields(const string& myfile); + vector browseAllFieldsOnMesh(const string& myfile, const string& mymesh, int idomain); + vector GetInfosOfField(const char *fileName, const char *meshName, int idomain ); + + void sendDoubleVec(const std::vector& vec, int target); + std::vector* recvDoubleVec(int source); + void recvDoubleVec(std::vector& vec, int source); + + void sendIntVec(const std::vector& vec, int target); + std::vector* recvIntVec(int source); + void recvIntVec(std::vector& vec, int source); + + void sendDataArrayInt(ParaMEDMEM::DataArrayInt* da, int target); + ParaMEDMEM::DataArrayInt* recvDataArrayInt(int source); + void sendDataArrayDouble(ParaMEDMEM::DataArrayDouble* da, int target); + ParaMEDMEM::DataArrayDouble* recvDataArrayDouble(int source); + + ParaMEDMEM::MEDCouplingUMesh* createEmptyMEDCouplingUMesh(); + + void testVectorOfStringMPI(); + void testMapOfStringIntMPI(); + void testMapOfStringVectorOfStringMPI(); + void testDataArrayMPI(); + void testPersistantMpi0To1(int taille, int nb); + void testPersistantMpiRing(int taille, int nb); + void testPersistantMpiRingOnCommSplit(int taille, int nb); + + class MyGlobals + { + public : static int _verbose; //0 to 1000 over 200 is debug + public : static int _rank; + public : static int _world_size; + public : static int _randomize; + public : static int _atomize; + public : static int _creates_boundary_faces; + public : static int _is0verbose; //cout if rank 0 and verbose + public : static vector _fileNames; //on [iold] + public : static vector _meshNames; //on [iold] + public : static vector _fieldDescriptions; + //used for descriptions of components of fields for example... + public : static vector _generalInformations; + + }; + + /*int MyGlobals::_verbose=0; + int MyGlobals::_is0verbose=0; + int MyGlobals::_rank=-1; + int MyGlobals::_world_size=-1;*/ } #endif /*MEDPARTITIONER_UTILS_HXX_*/ diff --git a/src/MEDPartitioner/Makefile.am b/src/MEDPartitioner/Makefile.am index 56326d10e..c731db984 100644 --- a/src/MEDPartitioner/Makefile.am +++ b/src/MEDPartitioner/Makefile.am @@ -16,14 +16,14 @@ # # See http://www.salome-platform.org/ or email : webmaster.salome@opencascade.com # -# MED MEDMEM : MED files in memory +# MED : MED files in memory # include $(top_srcdir)/adm_local/unix/make_common_starter.am # this directory must be recompiled before Test folder if CPPUNIT_IS_OK - SUBDIRS=. + SUBDIRS=. Test endif lib_LTLIBRARIES= libmedpartitioner.la @@ -53,6 +53,7 @@ if MED_ENABLE_SCOTCH endif dist_libmedpartitioner_la_SOURCES= \ +MEDPARTITIONER_utils.cxx \ MEDPARTITIONER_MESHCollection.cxx \ MEDPARTITIONER_MESHCollectionDriver.cxx \ MEDPARTITIONER_MESHCollectionMedXMLDriver.cxx \ @@ -74,7 +75,6 @@ endif libmedpartitioner_la_CPPFLAGS= $(MPI_INCLUDES) $(MED2_INCLUDES) $(HDF5_INCLUDES) @CXXTMPDPTHFLAGS@ \ $(BOOST_CPPFLAGS) $(LIBXML_INCLUDES) \ - -I$(srcdir)/../MEDMEM -I$(srcdir)/../MEDWrapper/V2_1/Core \ -I$(srcdir)/../INTERP_KERNEL/Bases -I$(srcdir)/../MEDCoupling \ -I$(srcdir)/../MEDLoader -I$(srcdir)/../INTERP_KERNEL @@ -99,8 +99,10 @@ if MED_ENABLE_KERNEL libmedpartitioner_la_LDFLAGS+= ${KERNEL_LDFLAGS} -lSALOMELocalTrace endif +#libmedpartitioner_la_LDFLAGS+= $(MED2_LIBS) $(HDF5_LIBS) $(STDLIB) $(LIBXML_LIBS) $(MPI_LIBS) \ +# ../MEDMEM/libmedmem.la ../INTERP_KERNEL/libinterpkernel.la ../MEDCoupling/libmedcoupling.la ../MEDLoader/libmedloader.la libmedpartitioner_la_LDFLAGS+= $(MED2_LIBS) $(HDF5_LIBS) $(STDLIB) $(LIBXML_LIBS) $(MPI_LIBS) \ - ../MEDMEM/libmedmem.la ../INTERP_KERNEL/libinterpkernel.la ../MEDCoupling/libmedcoupling.la ../MEDLoader/libmedloader.la + ../INTERP_KERNEL/libinterpkernel.la ../MEDCoupling/libmedcoupling.la ../MEDLoader/libmedloader.la # Executables targets bin_PROGRAMS= medpartitioner diff --git a/src/MEDPartitioner/medpartitioner.cxx b/src/MEDPartitioner/medpartitioner.cxx index fa6c5de9c..572af0cc0 100644 --- a/src/MEDPartitioner/medpartitioner.cxx +++ b/src/MEDPartitioner/medpartitioner.cxx @@ -40,8 +40,6 @@ namespace po=boost::program_options; using namespace std; - - int main(int argc, char** argv) { #ifndef ENABLE_METIS @@ -67,10 +65,8 @@ int main(int argc, char** argv) int ndomains; #ifdef BOOST_PROGRAM_OPTIONS_LIB - // Use boost::program_options for command-line options parsing - - po::options_description desc("Available options"); + po::options_description desc("Available options of medpartitioner V1.0"); desc.add_options() ("help","produces this help message") ("mesh-only","prevents the splitter from creating the fields contained in the original file(s)") @@ -114,7 +110,7 @@ int main(int argc, char** argv) if (!vm.count("distributed") && !vm.count("meshname") ) { - cout << "MEDPARTITIONER : for a serial MED file, mesh name must be selected with --meshname=..."<createPartition(ndomains,MEDPARTITIONER::Graph::SCOTCH); - cout << "MEDPARTITIONER - creating new meshes"< +#include +#include +#include +#include +#include #ifdef HAVE_MPI2 #include #endif -#include - #ifdef BOOST_PROGRAM_OPTIONS_LIB #include namespace po=boost::program_options; #endif using namespace std; - - +using namespace MEDPARTITIONER; int main(int argc, char** argv) { @@ -56,272 +82,281 @@ int main(int argc, char** argv) // Defining options // by parsing the command line - //bool mesh_only = false; - //bool is_sequential = true; - bool xml_output_master=true; - bool creates_boundary_faces=false; + //bool xml_output_master=true; bool split_family=false; bool empty_groups=false; bool mesure_memory=false; + bool filter_face=true; string input; string output; string meshname; string library; int ndomains; - -#ifdef BOOST_PROGRAM_OPTIONS_LIB - - // Use boost::program_options for command-line options parsing - - po::options_description desc("Available options"); - desc.add_options() - ("help","produces this help message") - //("mesh-only","prevents the splitter from creating the fields contained in the original file(s)") - //("distributed","specifies that the input file is distributed") - ("input-file",po::value(),"name of the input MED file") - ("output-file",po::value(),"name of the resulting file") - //("meshname",po::value(),"name of the input mesh") + int help=0; + int test=0; + MPI_Init(&argc,&argv); + MPI_Comm_size(MPI_COMM_WORLD, &MyGlobals::_world_size); + MPI_Comm_rank(MPI_COMM_WORLD, &MyGlobals::_rank); + //cout<<"proc "< : name of the input .med file or .xml master file\n" + "\t--output-file= : name of the resulting file (without exension)\n" + "\t--ndomains= : number of subdomains in the output file, default is 1\n" #ifdef ENABLE_PARMETIS #ifdef ENABLE_PTSCOTCH - ("split-method",po::value(&library)->default_value("metis"),"name of the splitting library (metis,scotch)") + "\t--split-method= : name of the splitting library (metis/scotch), default is metis\n" #endif #endif - ("ndomains",po::value(&ndomains)->default_value(1),"number of subdomains in the output file") - ("plain-master","creates a plain masterfile instead of an XML file") - ("creates-boundary-faces","creates the necessary faces so that faces joints are created in the output files") - ("family-splitting","preserves the family names instead of focusing on the groups") - ("empty-groups","creates empty groups in zones that do not contain a group from the original domain") - ("dump-cpu-memory","dumps passed CPU time and maximal increase of used memory"); - - po::variables_map vm; - po::store(po::parse_command_line(argc,argv,desc),vm); - po::notify(vm); + "\t--creates-boundary-faces : creates boundary faces mesh in the output files\n" + //"\t--family-splitting : preserves the family names instead of focusing on the groups\n" + "\t--dump-cpu-memory : dumps passed CPU time and maximal increase of used memory\n" + //"\t--randomize= : random seed for other partitionning (only on one proc)\n" + //"\t--atomize : do the opposite of a good partitionner (only on one proc)\n" + ); - if (vm.count("help")) + if (argc<=1) help=1; + string value; + for (int i = 1; i < argc; i++) { - cout<(); - if (!vm.count("input-file") || !vm.count("output-file")) + if (MyGlobals::_randomize!=0 && MyGlobals::_world_size!=1) { - cout << "input-file and output-file names must be specified"<(); - output = vm["output-file"].as(); - -// if (vm.count("mesh-only")) -// mesh_only=true; - -// if (vm.count("distributed")) -// is_sequential=false; - -// if (is_sequential) -// meshname = vm["meshname"].as(); - - if (vm.count("plain-master")) - xml_output_master=false; - - if (vm.count("creates-boundary-faces")) - creates_boundary_faces=true; - - if (vm.count("split-families")) - split_family=true; - - if (vm.count("empty-groups")) - empty_groups=true; - - if (vm.count("dump-cpu-memory")) - mesure_memory=true; - -#else // BOOST_PROGRAM_OPTIONS_LIB - - // Primitive parsing of command-line options - - string desc ("Available options:\n" - "\t--help : produces this help message\n" - //"\t--mesh-only : do not create the fields contained in the original file(s)\n" - //"\t--distributed : specifies that the input file is distributed\n" - "\t--input-file= : name of the input MED file\n" - "\t--output-file= : name of the resulting file\n" - //"\t--meshname= : name of the input mesh (not used with --distributed option)\n" - "\t--ndomains= : number of subdomains in the output file, default is 1\n" + #ifdef ENABLE_PARMETIS -#ifdef ENABLE_PTSCOTCH - "\t--split-method= : name of the splitting library (metis/scotch), default is metis\n" +#ifndef ENABLE_PTSCOTCH + library = "metis"; #endif +#else + library = "scotch"; #endif - "\t--plain-master : creates a plain masterfile instead of an XML file\n" - "\t--creates-boundary-faces: creates the necessary faces so that faces joints are created in the output files\n" - "\t--family-splitting : preserves the family names instead of focusing on the groups\n" - "\t--dump-cpu-memory : dumps passed CPU time and maximal increase of used memory\n" - ); - - if (argc < 4) { - cout << desc.c_str() << endl; + + if (help==1) + { + if (MyGlobals::_rank==0) cout<0) cout<<"tests on "< 13) { // "--input-file=" - input = (argv[i] + 13); - cout << "\tinput-file = " << input << endl; // tmp - } - } - else if (strncmp(argv[i],"--o",3) == 0) { - if (strlen(argv[i]) > 14) { // "--output-file=" - output = (argv[i] + 14); - cout << "\toutput-file = " << output << endl; // tmp - } + // Loading the mesh collection + if (MyGlobals::_is0verbose) cout << "Reading input files "<setGlobalNumerotationDefault(collection.getParaDomainSelector()); + //int nbfiles=MyGlobals::_fileMedNames->size(); //nb domains + //to have unique valid fields names/pointers/descriptions for partitionning + collection.prepareFieldDescriptions(); + //int nbfields=collection.getFieldDescriptions().size(); //on all domains + //cout< 15) { // "--split-method=" - library = (argv[i] + 15); - cout << "\tsplit-method = " << library << endl; // tmp + + // Creating the graph and partitioning it + if (MyGlobals::_is0verbose) cout << "Computing partition "< new_topo; + if (library == "metis") //cvwat06 + new_topo.reset( collection.createPartition(ndomains,MEDPARTITIONER::Graph::METIS)); + else + new_topo.reset( collection.createPartition(ndomains,MEDPARTITIONER::Graph::SCOTCH)); + parallelizer.evaluateMemory(); + + // Creating a new mesh collection from the partitioning + if (MyGlobals::_is0verbose) cout << "Creating new meshes"< finalInformations; + vector r1,r2; + r1=allgathervVectorOfString(MyGlobals::_generalInformations); + //if (MyGlobals::_is0verbose>1000) cout << "generalInformations : \n"< 11) { // "--ndomains=" - ndomains = atoi(argv[i] + 11); - cout << "\tndomains = " << ndomains << endl; // tmp + + //see field info nbComponents & componentInfo (if fields present) + r2=selectTagsInVectorOfString(r1,"fieldName="); + r2=selectTagsInVectorOfString(r2,"nbComponents="); + //may be yes? or not? + for (int i=0; i0) cout<<"OK END"<< endl; + MPI_Finalize(); + return 0; } - -// if (is_sequential && meshname.empty()) { -// cout << "Mesh name must be given for sequential(not distributed) input file." << endl; -// cout << desc << endl; -// return 1; -// } - -#endif // BOOST_PROGRAM_OPTIONS_LIB - - - //testing whether it is possible to write a file at the specified location - string outputtest = output + ".testioms."; - ofstream testfile (outputtest.c_str()); - if (testfile.fail()) - { - cout << "MEDPARTITIONER : output-file directory does not exist or is in read-only access" << endl; + catch(const char *mess) + { + cerr<<"proc "<