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Merge branch 'mpi_fixes' into 'master'

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Mpi fixes

See merge request jschoeberl/netgen!134
This commit is contained in:
Joachim Schöberl 2019-02-25 23:15:41 +00:00
commit fa1353dd07
5 changed files with 156 additions and 87 deletions
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49
libsrc/interface/nginterface.cpp
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@ -157,15 +157,15 @@ void Ng_LoadMesh (const char * filename, ngcore::NgMPI_Comm comm)
SetGlobalMesh (mesh);
// make string from rest of file (for geometry info!)
if(!ng_geometry) {
stringstream geom_part;
geom_part << infile->rdbuf();
string geom_part_string = geom_part.str();
strs = geom_part_string.size();
// buf = new char[strs];
buf.SetSize(strs);
memcpy(&buf[0], geom_part_string.c_str(), strs*sizeof(char));
}
// (this might be empty, in which case we take the global ng_geometry)
stringstream geom_part;
geom_part << infile->rdbuf();
string geom_part_string = geom_part.str();
strs = geom_part_string.size();
// buf = new char[strs];
buf.SetSize(strs);
memcpy(&buf[0], geom_part_string.c_str(), strs*sizeof(char));
delete infile;
if (ntasks > 1)
@ -238,32 +238,23 @@ void Ng_LoadMesh (const char * filename, ngcore::NgMPI_Comm comm)
mesh->SendRecvMesh();
}
if(!ng_geometry && ntasks>1) {
if(ntasks>1) {
#ifdef PARALLEL
/** Scatter the geometry-string (no dummy-implementation in mpi_interface) **/
MyMPI_Bcast(buf, comm);
int strs = buf.Size();
MyMPI_Bcast(strs, comm);
if(strs>0)
MyMPI_Bcast(buf, comm);
#endif
}
if(!ng_geometry) {
infile = new istringstream(string((const char*)&buf[0], (size_t)strs));
// delete[] buf;
for (int i = 0; i < geometryregister.Size(); i++)
{
NetgenGeometry * hgeom = geometryregister[i]->LoadFromMeshFile (*infile);
if (hgeom)
{
ng_geometry.reset (hgeom);
mesh->SetGeometry(ng_geometry);
break;
}
}
shared_ptr<NetgenGeometry> geo;
if(buf.Size()) { // if we had geom-info in the file, take it
istringstream geom_infile(string((const char*)&buf[0], buf.Size()));
geo = geometryregister.LoadFromMeshFile(geom_infile);
}
/** Dummy Geometry if we still could not find any geometry info! **/
// if (!ng_geometry)
// ng_geometry = make_shared<NetgenGeometry>();
if(ng_geometry)
mesh->SetGeometry(ng_geometry);
if(geo!=nullptr) mesh->SetGeometry(geo);
else if(ng_geometry!=nullptr) mesh->SetGeometry(ng_geometry);
}
void Ng_LoadMeshFromString (const char * mesh_as_string)

3
libsrc/meshing/clusters.cpp
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@ -26,6 +26,9 @@ namespace netgen
const MeshTopology & top = mesh.GetTopology();
auto id = this->mesh.GetCommunicator().Rank();
auto ntasks = this->mesh.GetCommunicator().Size();
bool hasedges = top.HasEdges();
bool hasfaces = top.HasFaces();

8
libsrc/meshing/parallelmesh.cpp
View File

@ -702,7 +702,7 @@ namespace netgen
Array<int> bcname_sizes(nbcs);
int tot_bcsize = 0;
for(int k=0;k<nbcs;k++) {
bcname_sizes[k] = bcnames[k]->size();
bcname_sizes[k] = (bcnames[k]!=NULL) ? bcnames[k]->size() : 0;
tot_bcsize += bcname_sizes[k];
}
char compiled_bcnames[tot_bcsize];
@ -722,7 +722,7 @@ namespace netgen
Array<int> mat_sizes(nmats);
int tot_matsize = 0;
for(int k=0;k<nmats;k++) {
mat_sizes[k] = materials[k]->size();
mat_sizes[k] = (materials[k]!=NULL) ? materials[k]->size() : 0;
tot_matsize += mat_sizes[k];
}
char compiled_mats[tot_matsize];
@ -965,7 +965,7 @@ namespace netgen
SetNBCNames(nbcs);
int cnt = 0;
for(int k=0;k<nbcs;k++) {
SetBCName(k, string(&compiled_bcnames[cnt], bcs[k]));
if(bcs[k]>0) SetBCName(k, string(&compiled_bcnames[cnt], bcs[k]));
cnt += bcs[k];
}
@ -983,7 +983,7 @@ namespace netgen
materials.SetSize(nmats);
for(int k=0;k<nmats;k++) {
// setmaterial is 1-based ...
SetMaterial(k+1, string(&compiled_mats[cnt], matsz[k]));
if(matsz[k]>0) SetMaterial(k+1, string(&compiled_mats[cnt], matsz[k]));
cnt += matsz[k];
}

181
libsrc/meshing/python_mesh.cpp
View File

@ -569,7 +569,7 @@ DLL_HEADER void ExportNetgenMeshing(py::module &m)
// cout << " rank " << MyMPI_GetId(comm) << " of " << MyMPI_GetNTasks(comm) << " called Distribute " << endl;
if(comm.Rank()==0) self->Distribute();
else self->SendRecvMesh();
return self;
return self;
}, py::arg("comm"))
.def("Receive", [](NgMPI_Comm comm) {
auto mesh = make_shared<Mesh>();
@ -578,66 +578,139 @@ DLL_HEADER void ExportNetgenMeshing(py::module &m)
return mesh;
})
.def("Load", FunctionPointer
([](Mesh & self, const string & filename)
([](shared_ptr<Mesh> self, const string & filename)
{
istream * infile;
NgMPI_Comm comm = self.GetCommunicator();
id = comm.Rank();
ntasks = comm.Size();
auto comm = self->GetCommunicator();
int id = comm.Rank();
int ntasks = comm.Size();
auto & mesh = self;
#ifdef PARALLEL
char* buf = nullptr;
int strs = 0;
if(id==0) {
#endif
if (filename.find(".vol.gz") != string::npos)
infile = new igzstream (filename.c_str());
else
infile = new ifstream (filename.c_str());
// ifstream input(filename);
#ifdef PARALLEL
//still inside id==0-bracket...
self.Load(*infile);
self.Distribute();
/** Copy the rest of the file into a string (for geometry) **/
stringstream geom_part;
geom_part << infile->rdbuf();
string geom_part_string = geom_part.str();
strs = geom_part_string.size();
buf = new char[strs];
memcpy(buf, geom_part_string.c_str(), strs*sizeof(char));
}
else {
self.SendRecvMesh();
{
ifstream infile(filename.c_str());
if(!infile.good())
throw NgException(string("Error opening file ") + filename);
}
/** Scatter the geometry-string **/
MPI_Bcast(&strs, 1, MPI_INT, 0, comm);
if(id!=0)
buf = new char[strs];
MPI_Bcast(buf, strs, MPI_CHAR, 0, comm);
if(id==0)
delete infile;
infile = new istringstream(string((const char*)buf, (size_t)strs));
delete[] buf;
#else
self.Load(*infile);
#endif
for (int i = 0; i < geometryregister.Size(); i++)
if ( filename.find(".vol") == string::npos )
{
NetgenGeometry * hgeom = geometryregister[i]->LoadFromMeshFile (*infile);
if (hgeom)
{
ng_geometry.reset (hgeom);
self.SetGeometry(ng_geometry);
break;
}
if(ntasks>1)
throw NgException("Not sure what to do with this?? Does this work with MPI??");
mesh->SetCommunicator(comm);
ReadFile(*mesh,filename.c_str());
//mesh->SetGlobalH (mparam.maxh);
//mesh->CalcLocalH();
return;
}
self.SetGeometry(ng_geometry);
delete infile;
istream * infile;
Array<char> buf; // for distributing geometry!
int strs;
if( id == 0) {
if (filename.substr (filename.length()-3, 3) == ".gz")
infile = new igzstream (filename.c_str());
else
infile = new ifstream (filename.c_str());
mesh -> Load(*infile);
// make string from rest of file (for geometry info!)
// (this might be empty, in which case we take the global ng_geometry)
stringstream geom_part;
geom_part << infile->rdbuf();
string geom_part_string = geom_part.str();
strs = geom_part_string.size();
// buf = new char[strs];
buf.SetSize(strs);
memcpy(&buf[0], geom_part_string.c_str(), strs*sizeof(char));
delete infile;
if (ntasks > 1)
{
char * weightsfilename = new char [filename.size()+1];
strcpy (weightsfilename, filename.c_str());
weightsfilename[strlen (weightsfilename)-3] = 'w';
weightsfilename[strlen (weightsfilename)-2] = 'e';
weightsfilename[strlen (weightsfilename)-1] = 'i';
ifstream weightsfile(weightsfilename);
delete [] weightsfilename;
if (!(weightsfile.good()))
{
// cout << "regular distribute" << endl;
mesh -> Distribute();
}
else
{
char str[20];
bool endfile = false;
int n, dummy;
Array<int> segment_weights;
Array<int> surface_weights;
Array<int> volume_weights;
while (weightsfile.good() && !endfile)
{
weightsfile >> str;
if (strcmp (str, "edgeweights") == 0)
{
weightsfile >> n;
segment_weights.SetSize(n);
for (int i = 0; i < n; i++)
weightsfile >> dummy >> segment_weights[i];
}
if (strcmp (str, "surfaceweights") == 0)
{
weightsfile >> n;
surface_weights.SetSize(n);
for (int i=0; i<n; i++)
weightsfile >> dummy >> surface_weights[i];
}
if (strcmp (str, "volumeweights") == 0)
{
weightsfile >> n;
volume_weights.SetSize(n);
for (int i=0; i<n; i++)
weightsfile >> dummy >> volume_weights[i];
}
if (strcmp (str, "endfile") == 0)
endfile = true;
}
mesh -> Distribute(volume_weights, surface_weights, segment_weights);
}
} // ntasks>1 end
} // id==0 end
else {
mesh->SendRecvMesh();
}
if(ntasks>1) {
#ifdef PARALLEL
/** Scatter the geometry-string (no dummy-implementation in mpi_interface) **/
int strs = buf.Size();
MyMPI_Bcast(strs, comm);
if(strs>0)
MyMPI_Bcast(buf, comm);
#endif
}
shared_ptr<NetgenGeometry> geo;
if(buf.Size()) { // if we had geom-info in the file, take it
istringstream geom_infile(string((const char*)&buf[0], buf.Size()));
geo = geometryregister.LoadFromMeshFile(geom_infile);
}
if(geo!=nullptr) mesh->SetGeometry(geo);
else if(ng_geometry!=nullptr) mesh->SetGeometry(ng_geometry);
}),py::call_guard<py::gil_scoped_release>())
// static_cast<void(Mesh::*)(const string & name)>(&Mesh::Load))
.def("Save", static_cast<void(Mesh::*)(const string & name)const>(&Mesh::Save),py::call_guard<py::gil_scoped_release>())

2
libsrc/meshing/topology.cpp
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@ -338,6 +338,8 @@ namespace netgen
// ParallelMeshTopology & paralleltop = mesh.GetParallelTopology();
#endif
auto id = this->mesh->GetCommunicator().Rank();
auto ntasks = this->mesh->GetCommunicator().Size();
if (timestamp > mesh->GetTimeStamp()) return;