netgen/libsrc/meshing/parallelmesh.cpp
Joachim Schoeberl bfc7e7772f polish
2014-04-28 07:09:39 +00:00

1527 lines
36 KiB
C++

#ifdef PARALLEL
#include <meshing.hpp>
#include "paralleltop.hpp"
// #define METIS4
#ifdef METIS
namespace metis {
extern "C" {
#include <metis.h>
#if METIS_VER_MAJOR >= 5
#define METIS5
typedef idx_t idxtype;
#else
#define METIS4
typedef idxtype idx_t;
#endif
}
}
using namespace metis;
#endif
namespace netgen
{
template <>
inline MPI_Datatype MyGetMPIType<PointIndex> ( )
{ return MPI_INT; }
void Mesh :: SendRecvMesh ()
{
if (id == 0)
PrintMessage (1, "Send/Receive mesh");
{
// distribute global information
int nelglob, nseglob, nvglob;
if (id == 0)
{
paralleltop -> SetNV (GetNV());
paralleltop -> SetNE (GetNE());
paralleltop -> SetNSegm (GetNSeg());
paralleltop -> SetNSE (GetNSE());
nelglob = GetNE();
nseglob = GetNSE();
nvglob = GetNV();
}
MyMPI_Bcast (dimension);
MyMPI_Bcast (nelglob);
MyMPI_Bcast (nseglob);
MyMPI_Bcast (nvglob);
}
{
// distribute number of local elements
if (id == 0)
{
Array<int> num_els_on_proc(ntasks);
num_els_on_proc = 0;
for (ElementIndex ei = 0; ei < GetNE(); ei++)
num_els_on_proc[(*this)[ei].GetPartition()]++;
MPI_Scatter (&num_els_on_proc[0], 1, MPI_INT,
MPI_IN_PLACE, -1, MPI_INT, 0, MPI_COMM_WORLD);
}
else
{
int nelloc;
MPI_Scatter (NULL, 0, MPI_INT,
&nelloc, 1, MPI_INT, 0, MPI_COMM_WORLD);
paralleltop -> SetNE (nelloc);
}
}
if (id == 0)
SendMesh ();
else
ReceiveParallelMesh();
paralleltop -> UpdateCoarseGrid();
}
void Mesh :: SendMesh () const
{
Array<MPI_Request> sendrequests;
PrintMessage ( 3, "Sending vertices");
Array<int> num_els_on_proc(ntasks);
num_els_on_proc = 0;
for (ElementIndex ei = 0; ei < GetNE(); ei++)
num_els_on_proc[(*this)[ei].GetPartition()]++;
TABLE<ElementIndex> els_of_proc (num_els_on_proc);
for (ElementIndex ei = 0; ei < GetNE(); ei++)
els_of_proc.Add ( (*this)[ei].GetPartition(), ei);
Array<int> num_sels_on_proc(ntasks);
num_sels_on_proc = 0;
for (SurfaceElementIndex ei = 0; ei < GetNSE(); ei++)
num_sels_on_proc[(*this)[ei].GetPartition()]++;
TABLE<SurfaceElementIndex> sels_of_proc (num_sels_on_proc);
for (SurfaceElementIndex ei = 0; ei < GetNSE(); ei++)
sels_of_proc.Add ( (*this)[ei].GetPartition(), ei);
Array<int> num_segs_on_proc(ntasks);
num_segs_on_proc = 0;
for (SegmentIndex ei = 0; ei < GetNSeg(); ei++)
num_segs_on_proc[(*this)[ei].GetPartition()]++;
TABLE<SegmentIndex> segs_of_proc (num_segs_on_proc);
for (SegmentIndex ei = 0; ei < GetNSeg(); ei++)
segs_of_proc.Add ( (*this)[ei].GetPartition(), ei);
Array<int, PointIndex::BASE> vert_flag (GetNV());
Array<int, PointIndex::BASE> num_procs_on_vert (GetNV());
Array<int> num_verts_on_proc (ntasks);
num_verts_on_proc = 0;
num_procs_on_vert = 0;
vert_flag = -1;
for (int dest = 1; dest < ntasks; dest++)
{
FlatArray<ElementIndex> els = els_of_proc[dest];
for (int hi = 0; hi < els.Size(); hi++)
{
const Element & el = (*this) [ els[hi] ];
for (int i = 0; i < el.GetNP(); i++)
{
PointIndex epi = el[i];
if (vert_flag[epi] < dest)
{
vert_flag[epi] = dest;
num_verts_on_proc[dest]++;
num_procs_on_vert[epi]++;
paralleltop -> SetDistantPNum (dest, epi);
}
}
}
FlatArray<SurfaceElementIndex> sels = sels_of_proc[dest];
for (int hi = 0; hi < sels.Size(); hi++)
{
const Element2d & el = (*this) [ sels[hi] ];
for (int i = 0; i < el.GetNP(); i++)
{
PointIndex epi = el[i];
if (vert_flag[epi] < dest)
{
vert_flag[epi] = dest;
num_verts_on_proc[dest]++;
num_procs_on_vert[epi]++;
paralleltop -> SetDistantPNum (dest, epi);
}
}
}
FlatArray<SegmentIndex> segs = segs_of_proc[dest];
for (int hi = 0; hi < segs.Size(); hi++)
{
const Segment & el = (*this) [segs[hi]];
for (int i = 0; i < 2; i++)
{
PointIndex epi = el[i];
if (vert_flag[epi] < dest)
{
vert_flag[epi] = dest;
num_verts_on_proc[dest]++;
num_procs_on_vert[epi]++;
paralleltop -> SetDistantPNum (dest, epi);
}
}
}
}
TABLE<PointIndex> verts_of_proc (num_verts_on_proc);
TABLE<int, PointIndex::BASE> procs_of_vert (num_procs_on_vert);
TABLE<int, PointIndex::BASE> loc_num_of_vert (num_procs_on_vert);
vert_flag = -1;
for (int dest = 1; dest < ntasks; dest++)
{
FlatArray<ElementIndex> els = els_of_proc[dest];
for (int hi = 0; hi < els.Size(); hi++)
{
const Element & el = (*this) [ els[hi] ];
for (int i = 0; i < el.GetNP(); i++)
{
PointIndex epi = el[i];
if (vert_flag[epi] < dest)
{
vert_flag[epi] = dest;
procs_of_vert.Add (epi, dest);
}
}
}
FlatArray<SurfaceElementIndex> sels = sels_of_proc[dest];
for (int hi = 0; hi < sels.Size(); hi++)
{
const Element2d & el = (*this) [ sels[hi] ];
for (int i = 0; i < el.GetNP(); i++)
{
PointIndex epi = el[i];
if (vert_flag[epi] < dest)
{
vert_flag[epi] = dest;
procs_of_vert.Add (epi, dest);
}
}
}
FlatArray<SegmentIndex> segs = segs_of_proc[dest];
for (int hi = 0; hi < segs.Size(); hi++)
{
const Segment & el = (*this) [ segs[hi] ];
for (int i = 0; i < 2; i++)
{
PointIndex epi = el[i];
if (vert_flag[epi] < dest)
{
vert_flag[epi] = dest;
procs_of_vert.Add (epi, dest);
}
}
}
}
for (int vert = 1; vert <= GetNP(); vert++ )
{
FlatArray<int> procs = procs_of_vert[vert];
for (int j = 0; j < procs.Size(); j++)
{
int dest = procs[j];
verts_of_proc.Add (dest, vert);
loc_num_of_vert.Add (vert, verts_of_proc[dest].Size());
}
}
for (int dest = 1; dest < ntasks; dest++)
{
FlatArray<PointIndex> verts = verts_of_proc[dest];
sendrequests.Append (MyMPI_ISend (verts, dest, MPI_TAG_MESH+1));
MPI_Datatype mptype = MeshPoint::MyGetMPIType();
int numv = verts.Size();
MPI_Datatype newtype;
Array<int> blocklen (numv);
blocklen = 1;
MPI_Type_indexed (numv, &blocklen[0],
reinterpret_cast<int*> (&verts[0]),
mptype, &newtype);
MPI_Type_commit (&newtype);
MPI_Request request;
MPI_Isend( &points[0], 1, newtype, dest, MPI_TAG_MESH+1, MPI_COMM_WORLD, &request);
sendrequests.Append (request);
}
Array<int> num_distpnums(ntasks);
num_distpnums = 0;
for (int vert = 1; vert <= GetNP(); vert++)
{
FlatArray<int> procs = procs_of_vert[vert];
for (int j = 0; j < procs.Size(); j++)
num_distpnums[procs[j]] += 3 * (procs.Size()-1);
}
TABLE<int> distpnums (num_distpnums);
for (int vert = 1; vert <= GetNP(); vert++)
{
FlatArray<int> procs = procs_of_vert[vert];
for (int j = 0; j < procs.Size(); j++)
for (int k = 0; k < procs.Size(); k++)
if (j != k)
{
distpnums.Add (procs[j], loc_num_of_vert[vert][j]);
distpnums.Add (procs[j], procs_of_vert[vert][k]);
distpnums.Add (procs[j], loc_num_of_vert[vert][k]);
}
}
for ( int dest = 1; dest < ntasks; dest ++ )
sendrequests.Append (MyMPI_ISend (distpnums[dest], dest, MPI_TAG_MESH+1));
PrintMessage ( 3, "Sending elements" );
Array<int> elarraysize (ntasks);
elarraysize = 0;
for ( int ei = 1; ei <= GetNE(); ei++)
{
const Element & el = VolumeElement (ei);
int dest = el.GetPartition();
elarraysize[dest] += 3 + el.GetNP();
}
TABLE<int> elementarrays(elarraysize);
for (int ei = 1; ei <= GetNE(); ei++)
{
const Element & el = VolumeElement (ei);
int dest = el.GetPartition();
elementarrays.Add (dest, ei);
elementarrays.Add (dest, el.GetIndex());
elementarrays.Add (dest, el.GetNP());
for (int i = 0; i < el.GetNP(); i++)
elementarrays.Add (dest, el[i]);
}
for (int dest = 1; dest < ntasks; dest ++ )
sendrequests.Append (MyMPI_ISend (elementarrays[dest], dest, MPI_TAG_MESH+2));
PrintMessage ( 3, "Sending Face Descriptors" );
Array<double> fddata (6 * GetNFD());
for (int fdi = 1; fdi <= GetNFD(); fdi++)
{
fddata[6*fdi-6] = GetFaceDescriptor(fdi).SurfNr();
fddata[6*fdi-5] = GetFaceDescriptor(fdi).DomainIn();
fddata[6*fdi-4] = GetFaceDescriptor(fdi).DomainOut();
fddata[6*fdi-3] = GetFaceDescriptor(fdi).BCProperty();
fddata[6*fdi-2] = GetFaceDescriptor(fdi).domin_singular;
fddata[6*fdi-1] = GetFaceDescriptor(fdi).domout_singular;
}
for (int dest = 1; dest < ntasks; dest++)
sendrequests.Append (MyMPI_ISend (fddata, dest, MPI_TAG_MESH+3));
PrintMessage ( 3, "Sending Surface elements" );
Array <int> nlocsel(ntasks), bufsize(ntasks);
nlocsel = 0;
bufsize = 1;
for (int sei = 1; sei <= GetNSE(); sei++ )
{
const Element2d & sel = SurfaceElement (sei);
int dest = sel.GetPartition();
nlocsel[dest] ++;
bufsize[dest] += 4 + 2*sel.GetNP();
}
TABLE<int> selbuf(bufsize);
for (int dest = 1; dest < ntasks; dest++ )
selbuf.Add (dest, nlocsel[dest]);
for (int sei = 1; sei <= GetNSE(); sei ++ )
{
const Element2d & sel = SurfaceElement (sei);
int dest = sel.GetPartition();
selbuf.Add (dest, sei);
selbuf.Add (dest, sel.GetIndex());
// selbuf.Add (dest, 0);
selbuf.Add (dest, sel.GetNP());
for ( int ii = 1; ii <= sel.GetNP(); ii++)
{
selbuf.Add (dest, sel.PNum(ii));
selbuf.Add (dest, sel.GeomInfoPi(ii).trignum);
}
}
for (int dest = 1; dest < ntasks; dest++)
sendrequests.Append (MyMPI_ISend(selbuf[dest], dest, MPI_TAG_MESH+4));
PrintMessage ( 3, "Sending Edge Segments");
Array <int> nloc(ntasks);
nloc = 0;
bufsize = 1;
for (int i = 1; i <= GetNSeg(); i++ )
{
const Segment & seg = LineSegment (i);
int dest = seg.GetPartition();
nloc[dest] ++;
bufsize[dest] += 14;
}
TABLE<double> segm_buf(bufsize);
/*
for (int dest = 1; dest < ntasks; dest++ )
segm_buf.Add (dest, nloc[dest]);
*/
for (int i = 1; i <= GetNSeg(); i++ )
{
const Segment & seg = LineSegment (i);
int dest = seg.GetPartition();
segm_buf.Add (dest, i);
segm_buf.Add (dest, seg.si);
segm_buf.Add (dest, seg.pnums[0]);
segm_buf.Add (dest, seg.pnums[1]);
segm_buf.Add (dest, seg.geominfo[0].trignum);
segm_buf.Add (dest, seg.geominfo[1].trignum);
segm_buf.Add (dest, seg.surfnr1);
segm_buf.Add (dest, seg.surfnr2);
segm_buf.Add (dest, seg.edgenr);
segm_buf.Add (dest, seg.epgeominfo[0].dist);
segm_buf.Add (dest, seg.epgeominfo[1].edgenr);
segm_buf.Add (dest, seg.epgeominfo[1].dist);
segm_buf.Add (dest, seg.singedge_right);
segm_buf.Add (dest, seg.singedge_left);
}
for (int dest = 1; dest < ntasks; dest++)
sendrequests.Append (MyMPI_ISend(segm_buf[dest], dest, MPI_TAG_MESH+5));
/*
Array <int> nlocseg(ntasks), segi(ntasks);
for ( int i = 0; i < ntasks; i++)
{
nlocseg[i] = 0;
bufsize[i] = 0;
segi[i] = 0;
}
for (int segi = 1; segi <= GetNSeg(); segi ++ )
{
Array<int> volels;
const MeshTopology & topol = GetTopology();
topol . GetSegmentSurfaceElements ( segi, volels );
for (int j = 0; j < volels.Size(); j++)
{
int ei = volels[j];
if ( ei > 0 && ei <= GetNSE() )
{
const Element2d & el = SurfaceElement (ei);
int dest = el.GetPartition();
nlocseg[dest] ++;
bufsize[dest] += 14;
}
}
}
TABLE<double> segmbuf(bufsize);
for ( int ls=1; ls <= GetNSeg(); ls++)
{
Array<int> volels;
GetTopology().GetSegmentSurfaceElements ( ls, volels );
const Segment & seg = LineSegment (ls);
for (int j = 0; j < volels.Size(); j++)
{
int ei = volels[j];
if ( ei > 0 && ei <= GetNSE() )
{
const Element2d & el = SurfaceElement (ei);
int dest = el.GetPartition();
if ( dest > 0 )
{
segmbuf.Add (dest, ls);
segmbuf.Add (dest, seg.si);
segmbuf.Add (dest, seg.pnums[0]);
segmbuf.Add (dest, seg.pnums[1]);
segmbuf.Add (dest, seg.geominfo[0].trignum);
segmbuf.Add (dest, seg.geominfo[1].trignum);
segmbuf.Add (dest, seg.surfnr1);
segmbuf.Add (dest, seg.surfnr2);
segmbuf.Add (dest, seg.edgenr);
segmbuf.Add (dest, seg.epgeominfo[0].dist);
segmbuf.Add (dest, seg.epgeominfo[1].edgenr);
segmbuf.Add (dest, seg.epgeominfo[1].dist);
segmbuf.Add (dest, seg.singedge_right);
segmbuf.Add (dest, seg.singedge_left);
segi[dest] += 14;
}
// paralleltop -> SetDistantSegm ( dest, ls, int ( segi[dest] / 14 ) );
}
}
}
for ( int dest = 1; dest < ntasks; dest++)
sendrequests.Append (MyMPI_ISend(segmbuf[dest], dest, MPI_TAG_MESH+5));
*/
PrintMessage ( 3, "now wait ...");
MPI_Waitall (sendrequests.Size(), &sendrequests[0], MPI_STATUS_IGNORE);
MPI_Barrier(MPI_COMM_WORLD);
}
// slaves receive the mesh from the master
void Mesh :: ReceiveParallelMesh ( )
{
int timer = NgProfiler::CreateTimer ("ReceiveParallelMesh");
int timer_pts = NgProfiler::CreateTimer ("Receive points");
int timer_els = NgProfiler::CreateTimer ("Receive elements");
int timer_sels = NgProfiler::CreateTimer ("Receive surface elements");
NgProfiler::RegionTimer reg(timer);
// string st;
// receive vertices
NgProfiler::StartTimer (timer_pts);
Array<int> verts;
MyMPI_Recv (verts, 0, MPI_TAG_MESH+1);
int numvert = verts.Size();
paralleltop -> SetNV (numvert);
// INDEX_CLOSED_HASHTABLE<int> glob2loc_vert_ht (3*numvert+1);
INDEX_HASHTABLE<int> glob2loc_vert_ht (3*numvert+1);
for (int vert = 0; vert < numvert; vert++)
{
int globvert = verts[vert];
paralleltop->SetLoc2Glob_Vert ( vert+1, globvert );
glob2loc_vert_ht.Set (globvert, vert+1);
}
for (int i = 0; i < numvert; i++)
AddPoint (netgen::Point<3> (0,0,0));
MPI_Datatype mptype = MeshPoint::MyGetMPIType();
MPI_Status status;
MPI_Recv( &points[1], numvert, mptype, 0, MPI_TAG_MESH+1, MPI_COMM_WORLD, &status);
Array<int> dist_pnums;
MyMPI_Recv (dist_pnums, 0, MPI_TAG_MESH+1);
for (int hi = 0; hi < dist_pnums.Size(); hi += 3)
paralleltop ->
SetDistantPNum (dist_pnums[hi+1], dist_pnums[hi]); // , dist_pnums[hi+2]);
NgProfiler::StopTimer (timer_pts);
*testout << "got " << numvert << " vertices" << endl;
{
Element el;
Array<int> elarray;
MyMPI_Recv (elarray, 0, MPI_TAG_MESH+2);
NgProfiler::RegionTimer reg(timer_els);
for (int ind = 0, elnum = 1; ind < elarray.Size(); elnum++)
{
paralleltop->SetLoc2Glob_VolEl ( elnum, elarray[ind++]);
el.SetIndex(elarray[ind++]);
el.SetNP(elarray[ind++]);
for ( int j = 0; j < el.GetNP(); j++)
el[j] = glob2loc_vert_ht.Get (elarray[ind++]);
AddVolumeElement (el);
}
}
{
Array<double> fddata;
MyMPI_Recv (fddata, 0, MPI_TAG_MESH+3);
for (int i = 0; i < fddata.Size(); i += 6)
{
int faceind = AddFaceDescriptor
(FaceDescriptor(int(fddata[i]), int(fddata[i+1]), int(fddata[i+2]), 0));
GetFaceDescriptor(faceind).SetBCProperty (int(fddata[i+3]));
GetFaceDescriptor(faceind).domin_singular = fddata[i+4];
GetFaceDescriptor(faceind).domout_singular = fddata[i+5];
}
}
{
NgProfiler::RegionTimer reg(timer_sels);
Array<int> selbuf;
MyMPI_Recv ( selbuf, 0, MPI_TAG_MESH+4);
int ii = 0;
int sel = 0;
int nlocsel = selbuf[ii++];
paralleltop -> SetNSE ( nlocsel );
while (ii < selbuf.Size()-1)
{
int globsel = selbuf[ii++];
int faceind = selbuf[ii++];
//bool isghost = selbuf[ii++];
int nep = selbuf[ii++];
Element2d tri(nep);
tri.SetIndex(faceind);
for(int j = 1; j <= nep; j++)
{
tri.PNum(j) = glob2loc_vert_ht.Get (selbuf[ii++]);
tri.GeomInfoPi(j).trignum = selbuf[ii++];
}
paralleltop->SetLoc2Glob_SurfEl ( sel+1, globsel );
AddSurfaceElement (tri);
sel ++;
}
}
{
Array<double> segmbuf;
MyMPI_Recv ( segmbuf, 0, MPI_TAG_MESH+5);
Segment seg;
int globsegi;
int ii = 0;
int segi = 1;
int nsegloc = int ( segmbuf.Size() / 14 ) ;
paralleltop -> SetNSegm ( nsegloc );
while ( ii < segmbuf.Size() )
{
globsegi = int (segmbuf[ii++]);
seg.si = int (segmbuf[ii++]);
seg.pnums[0] = glob2loc_vert_ht.Get (int(segmbuf[ii++]));
seg.pnums[1] = glob2loc_vert_ht.Get (int(segmbuf[ii++]));
seg.geominfo[0].trignum = int( segmbuf[ii++] );
seg.geominfo[1].trignum = int ( segmbuf[ii++]);
seg.surfnr1 = int ( segmbuf[ii++]);
seg.surfnr2 = int ( segmbuf[ii++]);
seg.edgenr = int ( segmbuf[ii++]);
seg.epgeominfo[0].dist = segmbuf[ii++];
seg.epgeominfo[1].edgenr = int (segmbuf[ii++]);
seg.epgeominfo[1].dist = segmbuf[ii++];
seg.singedge_left = segmbuf[ii++];
seg.singedge_right = segmbuf[ii++];
seg.epgeominfo[0].edgenr = seg.epgeominfo[1].edgenr;
seg.domin = seg.surfnr1;
seg.domout = seg.surfnr2;
if ( seg.pnums[0] >0 && seg.pnums[1] > 0 )
{
paralleltop-> SetLoc2Glob_Segm ( segi, globsegi );
AddSegment (seg);
segi++;
}
}
}
MPI_Barrier(MPI_COMM_WORLD);
int timerloc = NgProfiler::CreateTimer ("Update local mesh");
int timerloc2 = NgProfiler::CreateTimer ("CalcSurfacesOfNode");
NgProfiler::RegionTimer regloc(timerloc);
stringstream str;
str << "p" << id << ": got " << GetNE() << " elements and "
<< GetNSE() << " surface elements";
cout << str.str() << endl;
// PrintMessage (2, "Got ", GetNE(), " elements and ", GetNSE(), " surface elements");
// PrintMessage (2, "Got ", GetNSE(), " surface elements");
NgProfiler::StartTimer (timerloc2);
CalcSurfacesOfNode ();
NgProfiler::StopTimer (timerloc2);
topology -> Update();
clusters -> Update();
// paralleltop -> UpdateCoarseGrid();
SetNextMajorTimeStamp();
}
// distribute the mesh to the slave processors
// call it only for the master !
void Mesh :: Distribute ()
{
MPI_Comm_size(MPI_COMM_WORLD, &ntasks);
MPI_Comm_rank(MPI_COMM_WORLD, &id);
if (id != 0 || ntasks == 1 ) return;
#ifdef METIS
ParallelMetis ();
#else
for (ElementIndex ei = 0; ei < GetNE(); ei++)
(*this)[ei].SetPartition(ntasks * ei/GetNE() + 1);
#endif
/*
for (ElementIndex ei = 0; ei < GetNE(); ei++)
*testout << "el(" << ei << ") is in part " << (*this)[ei].GetPartition() << endl;
for (SurfaceElementIndex ei = 0; ei < GetNSE(); ei++)
*testout << "sel(" << int(ei) << ") is in part " << (*this)[ei].GetPartition() << endl;
*/
// MyMPI_SendCmd ("mesh");
SendRecvMesh ();
}
#ifdef METIS5
void Mesh :: ParallelMetis ( )
{
PrintMessage (3, "call metis 5 ...");
int timer = NgProfiler::CreateTimer ("Mesh::Partition");
NgProfiler::RegionTimer reg(timer);
idx_t ne = GetNE() + GetNSE() + GetNSeg();
idx_t nn = GetNP();
Array<idx_t> eptr, eind;
for (int i = 0; i < GetNE(); i++)
{
eptr.Append (eind.Size());
const Element & el = VolumeElement(i+1);
for (int j = 0; j < el.GetNP(); j++)
eind.Append (el[j]-1);
}
for (int i = 0; i < GetNSE(); i++)
{
eptr.Append (eind.Size());
const Element2d & el = SurfaceElement(i+1);
for (int j = 0; j < el.GetNP(); j++)
eind.Append (el[j]-1);
}
for (int i = 0; i < GetNSeg(); i++)
{
eptr.Append (eind.Size());
const Segment & el = LineSegment(i+1);
eind.Append (el[0]-1);
eind.Append (el[1]-1);
}
eptr.Append (eind.Size());
Array<idx_t> epart(ne), npart(nn);
int nparts = ntasks-1;
int edgecut;
int ncommon = 3;
METIS_PartMeshDual (&ne, &nn, &eptr[0], &eind[0], NULL, NULL, &ncommon, &nparts,
NULL, NULL,
&edgecut, &epart[0], &npart[0]);
/*
METIS_PartMeshNodal (&ne, &nn, &eptr[0], &eind[0], NULL, NULL, &nparts,
NULL, NULL,
&edgecut, &epart[0], &npart[0]);
*/
PrintMessage (3, "metis complete");
// cout << "done" << endl;
for (int i = 0; i < GetNE(); i++)
VolumeElement(i+1).SetPartition(epart[i] + 1);
for (int i = 0; i < GetNSE(); i++)
SurfaceElement(i+1).SetPartition(epart[i+GetNE()] + 1);
for (int i = 0; i < GetNSeg(); i++)
LineSegment(i+1).SetPartition(epart[i+GetNE()+GetNSE()] + 1);
if (GetDimension() == 3)
{
// surface elements attached to volume elements
Array<bool, PointIndex::BASE> boundarypoints (GetNP());
boundarypoints = false;
for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
{
const Element2d & el = (*this)[sei];
for (int j = 0; j < el.GetNP(); j++)
boundarypoints[el[j]] = true;
}
// Build Pnt2Element table, boundary points only
Array<int, PointIndex::BASE> cnt(GetNP());
cnt = 0;
for (ElementIndex ei = 0; ei < GetNE(); ei++)
{
const Element & el = (*this)[ei];
for (int j = 0; j < el.GetNP(); j++)
if (boundarypoints[el[j]])
cnt[el[j]]++;
}
TABLE<ElementIndex, PointIndex::BASE> pnt2el(cnt);
cnt = 0;
for (ElementIndex ei = 0; ei < GetNE(); ei++)
{
const Element & el = (*this)[ei];
for (int j = 0; j < el.GetNP(); j++)
if (boundarypoints[el[j]])
pnt2el.Add (el[j], ei);
}
for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
{
Element2d & sel = (*this)[sei];
PointIndex pi1 = sel[0];
FlatArray<ElementIndex> els = pnt2el[pi1];
sel.SetPartition (-1);
for (int j = 0; j < els.Size(); j++)
{
const Element & el = (*this)[els[j]];
bool hasall = true;
for (int k = 0; k < sel.GetNP(); k++)
{
bool haspi = false;
for (int l = 0; l < el.GetNP(); l++)
if (sel[k] == el[l])
haspi = true;
if (!haspi) hasall = false;
}
if (hasall)
{
sel.SetPartition (el.GetPartition());
break;
}
}
if (sel.GetPartition() == -1)
cerr << "no volume element found" << endl;
}
for (SegmentIndex si = 0; si < GetNSeg(); si++)
{
Segment & sel = (*this)[si];
PointIndex pi1 = sel[0];
FlatArray<ElementIndex> els = pnt2el[pi1];
sel.SetPartition (-1);
for (int j = 0; j < els.Size(); j++)
{
const Element & el = (*this)[els[j]];
bool haspi[9] = { false }; // max surfnp
for (int k = 0; k < 2; k++)
for (int l = 0; l < el.GetNP(); l++)
if (sel[k] == el[l])
haspi[k] = true;
bool hasall = true;
for (int k = 0; k < sel.GetNP(); k++)
if (!haspi[k]) hasall = false;
if (hasall)
{
sel.SetPartition (el.GetPartition());
break;
}
}
if (sel.GetPartition() == -1)
cerr << "no volume element found" << endl;
}
}
}
#endif
//========================== weights =================================================================
// distribute the mesh to the slave processors
// call it only for the master !
void Mesh :: Distribute (Array<int> & volume_weights , Array<int> & surface_weights, Array<int> & segment_weights)
{
MPI_Comm_size(MPI_COMM_WORLD, &ntasks);
MPI_Comm_rank(MPI_COMM_WORLD, &id);
if (id != 0 || ntasks == 1 ) return;
#ifdef METIS
ParallelMetis (volume_weights, surface_weights, segment_weights);
#else
for (ElementIndex ei = 0; ei < GetNE(); ei++)
(*this)[ei].SetPartition(ntasks * ei/GetNE() + 1);
#endif
/*
for (ElementIndex ei = 0; ei < GetNE(); ei++)
*testout << "el(" << ei << ") is in part " << (*this)[ei].GetPartition() << endl;
for (SurfaceElementIndex ei = 0; ei < GetNSE(); ei++)
*testout << "sel(" << int(ei) << ") is in part " << (*this)[ei].GetPartition() << endl;
*/
// MyMPI_SendCmd ("mesh");
SendRecvMesh ();
}
#ifdef METIS5
void Mesh :: ParallelMetis (Array<int> & volume_weights , Array<int> & surface_weights, Array<int> & segment_weights)
{
PrintMessage (3, "call metis 5 with weights ...");
// cout << "segment_weights " << segment_weights << endl;
// cout << "surface_weights " << surface_weights << endl;
// cout << "volume_weights " << volume_weights << endl;
int timer = NgProfiler::CreateTimer ("Mesh::Partition");
NgProfiler::RegionTimer reg(timer);
idx_t ne = GetNE() + GetNSE() + GetNSeg();
idx_t nn = GetNP();
Array<idx_t> eptr, eind , nwgt;
for (int i = 0; i < GetNE(); i++)
{
eptr.Append (eind.Size());
const Element & el = VolumeElement(i+1);
int ind = el.GetIndex();
if (volume_weights.Size()<ind)
nwgt.Append(0);
else
nwgt.Append (volume_weights[ind -1]);
for (int j = 0; j < el.GetNP(); j++)
eind.Append (el[j]-1);
}
for (int i = 0; i < GetNSE(); i++)
{
eptr.Append (eind.Size());
const Element2d & el = SurfaceElement(i+1);
int ind = el.GetIndex();
ind = GetFaceDescriptor(ind).BCProperty();
if (surface_weights.Size()<ind)
nwgt.Append(0);
else
nwgt.Append (surface_weights[ind -1]);
for (int j = 0; j < el.GetNP(); j++)
eind.Append (el[j]-1);
}
for (int i = 0; i < GetNSeg(); i++)
{
eptr.Append (eind.Size());
const Segment & el = LineSegment(i+1);
int ind = el.si;
if (segment_weights.Size()<ind)
nwgt.Append(0);
else
nwgt.Append (segment_weights[ind -1]);
eind.Append (el[0]);
eind.Append (el[1]);
}
eptr.Append (eind.Size());
Array<idx_t> epart(ne), npart(nn);
int nparts = ntasks-1;
int edgecut;
int ncommon = 3;
METIS_PartMeshDual (&ne, &nn, &eptr[0], &eind[0], &nwgt[0], NULL, &ncommon, &nparts,
NULL, NULL,
&edgecut, &epart[0], &npart[0]);
/*
METIS_PartMeshNodal (&ne, &nn, &eptr[0], &eind[0], NULL, NULL, &nparts,
NULL, NULL,
&edgecut, &epart[0], &npart[0]);
*/
PrintMessage (3, "metis complete");
// cout << "done" << endl;
for (int i = 0; i < GetNE(); i++)
VolumeElement(i+1).SetPartition(epart[i] + 1);
for (int i = 0; i < GetNSE(); i++)
SurfaceElement(i+1).SetPartition(epart[i+GetNE()] + 1);
for (int i = 0; i < GetNSeg(); i++)
LineSegment(i+1).SetPartition(epart[i+GetNE()+GetNSE()] + 1);
}
#endif
//===========================================================================================
#ifdef METIS4
void Mesh :: ParallelMetis ( )
{
int timer = NgProfiler::CreateTimer ("Mesh::Partition");
NgProfiler::RegionTimer reg(timer);
PrintMessage (3, "Metis called");
if (GetDimension() == 2)
{
PartDualHybridMesh2D ( ); // neloc );
return;
}
idx_t ne = GetNE();
idx_t nn = GetNP();
if (ntasks <= 2 || ne <= 1)
{
if (ntasks == 1) return;
for (int i=1; i<=ne; i++)
VolumeElement(i).SetPartition(1);
for (int i=1; i<=GetNSE(); i++)
SurfaceElement(i).SetPartition(1);
return;
}
bool uniform_els = true;
ELEMENT_TYPE elementtype = TET;
for (int el = 1; el <= GetNE(); el++)
if (VolumeElement(el).GetType() != elementtype)
{
uniform_els = false;
break;
}
if (!uniform_els)
{
PartHybridMesh ();
}
else
{
// uniform (TET) mesh, JS
int npe = VolumeElement(1).GetNP();
Array<idxtype> elmnts(ne*npe);
int etype;
if (elementtype == TET)
etype = 2;
else if (elementtype == HEX)
etype = 3;
for (int i=1; i<=ne; i++)
for (int j=1; j<=npe; j++)
elmnts[(i-1)*npe+(j-1)] = VolumeElement(i).PNum(j)-1;
int numflag = 0;
int nparts = ntasks-1;
int ncommon = 3;
int edgecut;
Array<idxtype> epart(ne), npart(nn);
// if ( ntasks == 1 )
// {
// (*this) = *mastermesh;
// nparts = 4;
// metis :: METIS_PartMeshDual (&ne, &nn, elmnts, &etype, &numflag, &nparts,
// &edgecut, epart, npart);
// cout << "done" << endl;
// cout << "edge-cut: " << edgecut << ", balance: " << metis :: ComputeElementBalance(ne, nparts, epart) << endl;
// for (int i=1; i<=ne; i++)
// {
// mastermesh->VolumeElement(i).SetPartition(epart[i-1]);
// }
// return;
// }
int timermetis = NgProfiler::CreateTimer ("Metis itself");
NgProfiler::StartTimer (timermetis);
#ifdef METIS4
cout << "call metis(4)_PartMeshDual ... " << flush;
METIS_PartMeshDual (&ne, &nn, &elmnts[0], &etype, &numflag, &nparts,
&edgecut, &epart[0], &npart[0]);
#else
cout << "call metis(5)_PartMeshDual ... " << endl;
// idx_t options[METIS_NOPTIONS];
Array<idx_t> eptr(ne+1);
for (int j = 0; j < ne+1; j++)
eptr[j] = 4*j;
METIS_PartMeshDual (&ne, &nn, &eptr[0], &elmnts[0], NULL, NULL, &ncommon, &nparts,
NULL, NULL,
&edgecut, &epart[0], &npart[0]);
#endif
NgProfiler::StopTimer (timermetis);
cout << "complete" << endl;
#ifdef METIS4
cout << "edge-cut: " << edgecut << ", balance: "
<< ComputeElementBalance(ne, nparts, &epart[0]) << endl;
#endif
// partition numbering by metis : 0 ... ntasks - 1
// we want: 1 ... ntasks
for (int i=1; i<=ne; i++)
VolumeElement(i).SetPartition(epart[i-1] + 1);
}
for (int sei = 1; sei <= GetNSE(); sei++ )
{
int ei1, ei2;
GetTopology().GetSurface2VolumeElement (sei, ei1, ei2);
Element2d & sel = SurfaceElement (sei);
for (int j = 0; j < 2; j++)
{
int ei = (j == 0) ? ei1 : ei2;
if ( ei > 0 && ei <= GetNE() )
{
sel.SetPartition (VolumeElement(ei).GetPartition());
break;
}
}
}
}
#endif
void Mesh :: PartHybridMesh ()
{
#ifdef METIS
int ne = GetNE();
int nn = GetNP();
int nedges = topology->GetNEdges();
idxtype *xadj, * adjacency, *v_weights = NULL, *e_weights = NULL;
int weightflag = 0;
int numflag = 0;
int nparts = ntasks - 1;
int options[5];
options[0] = 0;
int edgecut;
idxtype * part;
xadj = new idxtype[nn+1];
part = new idxtype[nn];
Array<int> cnt(nn+1);
cnt = 0;
for ( int edge = 1; edge <= nedges; edge++ )
{
int v1, v2;
topology->GetEdgeVertices ( edge, v1, v2);
cnt[v1-1] ++;
cnt[v2-1] ++;
}
xadj[0] = 0;
for ( int n = 1; n <= nn; n++ )
{
xadj[n] = idxtype(xadj[n-1] + cnt[n-1]);
}
adjacency = new idxtype[xadj[nn]];
cnt = 0;
for ( int edge = 1; edge <= nedges; edge++ )
{
int v1, v2;
topology->GetEdgeVertices ( edge, v1, v2);
adjacency[ xadj[v1-1] + cnt[v1-1] ] = v2-1;
adjacency[ xadj[v2-1] + cnt[v2-1] ] = v1-1;
cnt[v1-1]++;
cnt[v2-1]++;
}
for ( int vert = 0; vert < nn; vert++ )
{
FlatArray<int> array ( cnt[vert], &adjacency[ xadj[vert] ] );
BubbleSort(array);
}
#ifdef METIS4
METIS_PartGraphKway ( &nn, xadj, adjacency, v_weights, e_weights, &weightflag,
&numflag, &nparts, options, &edgecut, part );
#else
cout << "currently not supported (metis5), A" << endl;
#endif
Array<int> nodesinpart(ntasks);
for ( int el = 1; el <= ne; el++ )
{
Element & volel = VolumeElement(el);
nodesinpart = 0;
int el_np = volel.GetNP();
int partition = 0;
for ( int i = 0; i < el_np; i++ )
nodesinpart[ part[volel[i]-1]+1 ] ++;
for ( int i = 1; i < ntasks; i++ )
if ( nodesinpart[i] > nodesinpart[partition] )
partition = i;
volel.SetPartition(partition);
}
delete [] xadj;
delete [] part;
delete [] adjacency;
#else
cout << "parthybridmesh not available" << endl;
#endif
}
void Mesh :: PartDualHybridMesh ( ) // Array<int> & neloc )
{
#ifdef METIS
int ne = GetNE();
// int nn = GetNP();
// int nedges = topology->GetNEdges();
int nfaces = topology->GetNFaces();
idxtype *xadj, * adjacency, *v_weights = NULL, *e_weights = NULL;
int weightflag = 0;
// int numflag = 0;
int nparts = ntasks - 1;
int options[5];
options[0] = 0;
int edgecut;
idxtype * part;
Array<int, 0> facevolels1(nfaces), facevolels2(nfaces);
facevolels1 = -1;
facevolels2 = -1;
Array<int, 0> elfaces;
xadj = new idxtype[ne+1];
part = new idxtype[ne];
Array<int, 0> cnt(ne+1);
cnt = 0;
for ( int el=1; el <= ne; el++ )
{
Element volel = VolumeElement(el);
topology->GetElementFaces(el, elfaces);
for ( int i = 0; i < elfaces.Size(); i++ )
{
if ( facevolels1[elfaces[i]-1] == -1 )
facevolels1[elfaces[i]-1] = el;
else
{
facevolels2[elfaces[i]-1] = el;
cnt[facevolels1[elfaces[i]-1]-1]++;
cnt[facevolels2[elfaces[i]-1]-1]++;
}
}
}
xadj[0] = 0;
for ( int n = 1; n <= ne; n++ )
{
xadj[n] = idxtype(xadj[n-1] + cnt[n-1]);
}
adjacency = new idxtype[xadj[ne]];
cnt = 0;
for ( int face = 1; face <= nfaces; face++ )
{
int e1, e2;
e1 = facevolels1[face-1];
e2 = facevolels2[face-1];
if ( e2 == -1 ) continue;
adjacency[ xadj[e1-1] + cnt[e1-1] ] = e2-1;
adjacency[ xadj[e2-1] + cnt[e2-1] ] = e1-1;
cnt[e1-1]++;
cnt[e2-1]++;
}
for ( int el = 0; el < ne; el++ )
{
FlatArray<int> array ( cnt[el], &adjacency[ xadj[el] ] );
BubbleSort(array);
}
int timermetis = NgProfiler::CreateTimer ("Metis itself");
NgProfiler::StartTimer (timermetis);
#ifdef METIS4
METIS_PartGraphKway ( &ne, xadj, adjacency, v_weights, e_weights, &weightflag,
&numflag, &nparts, options, &edgecut, part );
#else
cout << "currently not supported (metis5), B" << endl;
#endif
NgProfiler::StopTimer (timermetis);
Array<int> nodesinpart(ntasks);
for ( int el = 1; el <= ne; el++ )
{
// Element & volel = VolumeElement(el);
nodesinpart = 0;
VolumeElement(el).SetPartition(part[el-1 ] + 1);
}
/*
for ( int i=1; i<=ne; i++)
{
neloc[ VolumeElement(i).GetPartition() ] ++;
}
*/
delete [] xadj;
delete [] part;
delete [] adjacency;
#else
cout << "partdualmesh not available" << endl;
#endif
}
void Mesh :: PartDualHybridMesh2D ( )
{
#ifdef METIS
int ne = GetNSE();
int nv = GetNV();
Array<idxtype> xadj(ne+1);
Array<idxtype> adjacency(ne*4);
// first, build the vertex 2 element table:
Array<int, PointIndex::BASE> cnt(nv);
cnt = 0;
for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
for (int j = 0; j < (*this)[sei].GetNP(); j++)
cnt[ (*this)[sei][j] ] ++;
TABLE<SurfaceElementIndex, PointIndex::BASE> vert2els(cnt);
for (SurfaceElementIndex sei = 0; sei < GetNSE(); sei++)
for (int j = 0; j < (*this)[sei].GetNP(); j++)
vert2els.Add ((*this)[sei][j], sei);
// find all neighbour elements
int cntnb = 0;
Array<int> marks(ne); // to visit each neighbour just once
marks = -1;
for (SurfaceElementIndex sei = 0; sei < ne; sei++)
{
xadj[sei] = cntnb;
for (int j = 0; j < (*this)[sei].GetNP(); j++)
{
PointIndex vnr = (*this)[sei][j];
// all elements with at least one common vertex
for (int k = 0; k < vert2els[vnr].Size(); k++)
{
SurfaceElementIndex sei2 = vert2els[vnr][k];
if (sei == sei2) continue;
if (marks[sei2] == sei) continue;
// neighbour, if two common vertices
int common = 0;
for (int m1 = 0; m1 < (*this)[sei].GetNP(); m1++)
for (int m2 = 0; m2 < (*this)[sei2].GetNP(); m2++)
if ( (*this)[sei][m1] == (*this)[sei2][m2])
common++;
if (common >= 2)
{
marks[sei2] = sei; // mark as visited
adjacency[cntnb++] = sei2;
}
}
}
}
xadj[ne] = cntnb;
idxtype *v_weights = NULL, *e_weights = NULL;
int weightflag = 0;
// int numflag = 0;
int nparts = ntasks - 1;
int edgecut;
Array<idxtype> part(ne);
for ( int el = 0; el < ne; el++ )
BubbleSort (adjacency.Range (xadj[el], xadj[el+1]));
#ifdef METIS4
int options[5];
options[0] = 0;
METIS_PartGraphKway ( &ne, &xadj[0], &adjacency[0], v_weights, e_weights, &weightflag,
&numflag, &nparts, options, &edgecut, &part[0] );
#else
idx_t ncon = 1;
METIS_PartGraphKway ( &ne, &ncon, &xadj[0], &adjacency[0],
v_weights, NULL, e_weights,
&nparts,
NULL, NULL, NULL,
&edgecut, &part[0] );
#endif
for (SurfaceElementIndex sei = 0; sei < ne; sei++)
(*this) [sei].SetPartition (part[sei]+1);
#else
cout << "partdualmesh not available" << endl;
#endif
}
}
#endif