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Merge branch 'gitlab_mpi_builds' into metis_pic

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This commit is contained in:
Lukas 2019-04-17 16:53:47 +02:00
commit 59c4ec78d3
16 changed files with 141 additions and 26 deletions
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22
.gitlab-ci.yml
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@ -87,6 +87,16 @@ build_ubuntu:
- docker commit `cat netgen_${CI_BUILD_REF_NAME}_${UBUNTU_VERSION}.id` netgen_${CI_BUILD_REF_NAME}_installed:${UBUNTU_VERSION}
- rm netgen_${CI_BUILD_REF_NAME}_${UBUNTU_VERSION}.id
build_ubuntu_mpi:
<<: *ubuntu
stage: build
script:
- docker build -t netgen_mpi_${CI_BUILD_REF_NAME}:${UBUNTU_VERSION} -f tests/dockerfile_mpi .
- rm -f netgen_mpi_${CI_BUILD_REF_NAME}_$UBUNTU_VERSION.id_mpi
- docker run --cidfile netgen_mpi_${CI_BUILD_REF_NAME}_${UBUNTU_VERSION}.id -e CCACHE_DIR=/ccache -v /mnt/ccache:/ccache netgen_mpi_${CI_BUILD_REF_NAME}:${UBUNTU_VERSION} bash /root/src/netgen/tests/build_mpi.sh
- docker commit `cat netgen_mpi_${CI_BUILD_REF_NAME}_${UBUNTU_VERSION}.id` netgen_mpi_${CI_BUILD_REF_NAME}_installed:${UBUNTU_VERSION}
- rm netgen_mpi_${CI_BUILD_REF_NAME}_${UBUNTU_VERSION}.id
test_ubuntu:
<<: *ubuntu
stage: test
@ -98,6 +108,17 @@ test_ubuntu:
netgen_${CI_BUILD_REF_NAME}_installed:${UBUNTU_VERSION}
bash -c 'cd /root/build/netgen && make test_netgen ARGS="-V"'
test_ubuntu_mpi:
<<: *ubuntu
stage: test
script:
- >-
docker run
-e NETGENDIR=/opt/netgen/bin
-e PYTHONPATH=/opt/netgen/lib/python3/dist-packages
netgen_mpi_${CI_BUILD_REF_NAME}_installed:${UBUNTU_VERSION}
bash -c 'cd /root/build/netgen && make test_netgen ARGS="-V"'
# cpp guideline checks
test_guidelines:
<<: *ubuntu
@ -125,6 +146,7 @@ cleanup_ubuntu:
when: always
allow_failure: true
############################################
# MacOSX
############################################

4
libsrc/csg/CMakeLists.txt
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@ -12,7 +12,9 @@ if(APPLE)
endif(APPLE)
target_link_libraries(csg PUBLIC mesh ${PYTHON_LIBRARIES})
install( TARGETS csg ${NG_INSTALL_DIR})
if(NOT WIN32)
install( TARGETS csg ${NG_INSTALL_DIR})
endif(NOT WIN32)
target_link_libraries(csg PUBLIC ngcore)

4
libsrc/geom2d/CMakeLists.txt
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@ -5,7 +5,9 @@ if(APPLE)
endif(APPLE)
target_link_libraries(geom2d mesh ${PYTHON_LIBRARIES})
install( TARGETS geom2d ${NG_INSTALL_DIR})
if(NOT WIN32)
install( TARGETS geom2d ${NG_INSTALL_DIR})
endif(NOT WIN32)
target_link_libraries(geom2d ngcore)

4
libsrc/interface/CMakeLists.txt
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@ -9,7 +9,9 @@ add_library(interface ${NG_LIB_TYPE}
target_link_libraries(interface mesh csg geom2d)
target_link_libraries(interface visual)
install( TARGETS interface ${NG_INSTALL_DIR})
if(NOT WIN32)
install( TARGETS interface ${NG_INSTALL_DIR})
endif(NOT WIN32)
install(FILES
writeuser.hpp

1
libsrc/interface/readuser.cpp
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@ -260,6 +260,7 @@ namespace netgen
Point3d pmin, pmax;
mesh.ComputeNVertices();
mesh.RebuildSurfaceElementLists();
mesh.GetBox (pmin, pmax);
cout << "bounding-box = " << pmin << "-" << pmax << endl;
}

4
libsrc/meshing/CMakeLists.txt
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@ -24,7 +24,9 @@ endif(APPLE)
target_link_libraries( mesh PUBLIC ngcore PRIVATE gprim la gen )
target_link_libraries( mesh PUBLIC ${ZLIB_LIBRARIES} ${MPI_CXX_LIBRARIES} ${PYTHON_LIBRARIES} ${METIS_LIBRARY})
install( TARGETS mesh ${NG_INSTALL_DIR})
if(NOT WIN32)
install( TARGETS mesh ${NG_INSTALL_DIR})
endif(NOT WIN32)
install(FILES
adfront2.hpp adfront3.hpp basegeom.hpp bcfunctions.hpp bisect.hpp

32
libsrc/meshing/curvedelems.cpp
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@ -409,6 +409,15 @@ namespace netgen
static Array<shared_ptr<RecPol>> jacpols2;
void CurvedElements::buildJacPols()
{
if (!jacpols2.Size())
{
jacpols2.SetSize (100);
for (int i = 0; i < 100; i++)
jacpols2[i] = make_shared<JacobiRecPol> (100, i, 2);
}
}
// compute face bubbles up to order n, 0 < y, y-x < 1, x+y < 1
template <class Tx, class Ty, class Ts>
@ -540,7 +549,6 @@ namespace netgen
CurvedElements :: ~CurvedElements()
{
jacpols2.SetSize(0);
}
@ -719,13 +727,7 @@ namespace netgen
ComputeGaussRule (aorder+4, xi, weight); // on (0,1)
if (!jacpols2.Size())
{
jacpols2.SetSize (100);
for (int i = 0; i < 100; i++)
jacpols2[i] = make_shared<JacobiRecPol> (100, i, 2);
}
buildJacPols();
PrintMessage (3, "Curving edges");
if (mesh.GetDimension() == 3 || rational)
@ -2239,6 +2241,20 @@ namespace netgen
switch (el.GetType())
{
case TRIG6:
{
AutoDiff<2,T> lam3 = 1-x-y;
AutoDiff<2,T> lami[6] = { x * (2*x-1), y * (2*y-1), lam3 * (2*lam3-1),
4 * y * lam3, 4 * x * lam3, 4 * x * y };
for (int j = 0; j < 6; j++)
{
Point<3> p = mesh[el[j]];
for (int k = 0; k < DIM_SPACE; k++)
mapped_x[k] += p(k) * lami[j];
}
break;
}
case TRIG:
{
// if (info.order >= 2) return false; // not yet supported

3
libsrc/meshing/curvedelems.hpp
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@ -33,6 +33,7 @@ class CurvedElements
bool rational;
bool ishighorder;
void buildJacPols();
public:
DLL_HEADER CurvedElements (const Mesh & amesh);
@ -50,6 +51,8 @@ public:
virtual void DoArchive(Archive& ar)
{
if(ar.Input())
buildJacPols();
ar & edgeorder & faceorder & edgecoeffsindex & facecoeffsindex & edgecoeffs & facecoeffs
& edgeweight & order & rational & ishighorder;
}

6
libsrc/meshing/meshclass.cpp
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@ -90,6 +90,7 @@ namespace netgen
Mesh & Mesh :: operator= (const Mesh & mesh2)
{
dimension = mesh2.dimension;
points = mesh2.points;
// eltyps = mesh2.eltyps;
segments = mesh2.segments;
@ -1320,6 +1321,7 @@ namespace netgen
archive & segments;
archive & facedecoding;
archive & materials & bcnames & cd2names & cd3names;
archive & numvertices;
archive & *ident;
@ -4995,6 +4997,10 @@ namespace netgen
// netgen::Point<3> pmin = p - Vec<3> (pointtol, pointtol, pointtol);
// netgen::Point<3> pmax = p + Vec<3> (pointtol, pointtol, pointtol);
if ( (dimension == 2 && !GetNSE()) ||
(dimension == 3 && !GetNE() && !GetNSE()) )
return -1;
if (dimension == 2 || (dimension==3 && !GetNE() && GetNSE()))
{
int ne;

1
libsrc/meshing/meshtype.cpp
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@ -1140,6 +1140,7 @@ namespace netgen
default: break;
cerr << "Element::SetType unknown type " << int(typ) << endl;
}
is_curved = (np > 4);
}

7
libsrc/meshing/meshtype.hpp
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@ -765,11 +765,12 @@ namespace netgen
void DoArchive (Archive & ar)
{
short _np, _typ;
bool _curved;
if (ar.Output())
{ _np = np; _typ = typ; }
ar & _np & _typ & index;
{ _np = np; _typ = typ; _curved = is_curved; }
ar & _np & _typ & index & _curved;
if (ar.Input())
{ np = _np; typ = ELEMENT_TYPE(_typ); }
{ np = _np; typ = ELEMENT_TYPE(_typ); is_curved = _curved; }
for (size_t i = 0; i < np; i++)
ar & pnum[i];
}

32
libsrc/meshing/parallelmesh.cpp
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@ -745,6 +745,38 @@ namespace netgen
MPI_Barrier(comm);
PrintMessage( 3, "Clean up local memory");
auto & self = const_cast<Mesh&>(*this);
self.points = T_POINTS(0);
self.surfelements = T_SURFELEMENTS(0);
self.volelements = T_VOLELEMENTS(0);
self.segments = Array<Segment, 0, size_t>(0);
self.lockedpoints = Array<PointIndex>(0);
auto cleanup_ptr = [](auto & ptr) {
if (ptr != nullptr) {
delete ptr;
ptr = nullptr;
}
};
cleanup_ptr(self.boundaryedges);
cleanup_ptr(self.boundaryedges);
cleanup_ptr(self.segmentht);
cleanup_ptr(self.surfelementht);
self.openelements = Array<Element2d>(0);
self.opensegments = Array<Segment>(0);
self.numvertices = 0;
self.mlbetweennodes = Array<PointIndices<2>,PointIndex::BASE> (0);
self.mlparentelement = Array<int>(0);
self.mlparentsurfaceelement = Array<int>(0);
self.topology.Update();
self.curvedelems = new CurvedElements (self);
self.clusters = new AnisotropicClusters (self);
self.ident = new Identifications (self);
self.BuildElementSearchTree();
// const_cast<Mesh&>(*this).DeleteMesh();
PrintMessage( 3, "send mesh complete");
}

32
libsrc/meshing/python_mesh.cpp
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@ -17,6 +17,8 @@ namespace netgen
{
extern bool netgen_executable_started;
extern shared_ptr<NetgenGeometry> ng_geometry;
extern void Optimize2d (Mesh & mesh, MeshingParameters & mp);
#ifdef PARALLEL
/** we need allreduce in python-wrapped communicators **/
template <typename T>
@ -865,13 +867,20 @@ DLL_HEADER void ExportNetgenMeshing(py::module &m)
},
py::arg("mp")=NGDummyArgument(),py::call_guard<py::gil_scoped_release>())
.def ("OptimizeVolumeMesh", FunctionPointer
([](Mesh & self)
.def ("OptimizeVolumeMesh", [](Mesh & self)
{
MeshingParameters mp;
mp.optsteps3d = 5;
OptimizeVolume (mp, self);
}),py::call_guard<py::gil_scoped_release>())
},py::call_guard<py::gil_scoped_release>())
.def ("OptimizeMesh2d", [](Mesh & self)
{
self.CalcLocalH(0.5);
MeshingParameters mp;
mp.optsteps2d = 5;
Optimize2d (self, mp);
},py::call_guard<py::gil_scoped_release>())
.def ("Refine", FunctionPointer
([](Mesh & self)
@ -975,12 +984,17 @@ DLL_HEADER void ExportNetgenMeshing(py::module &m)
},
py::arg("name"), py::arg("set")=true)
.def ("Scale", FunctionPointer([](Mesh & self, double factor)
{
for(auto i = 0; i<self.GetNP();i++)
self.Point(i).Scale(factor);
}))
.def ("Scale", [](Mesh & self, double factor)
{
for(auto i = 0; i<self.GetNP();i++)
self.Point(i).Scale(factor);
})
.def ("Copy", [](Mesh & self)
{
auto m2 = make_shared<Mesh> ();
*m2 = self;
return m2;
})
;
m.def("ImportMesh", [](const string& filename)

4
libsrc/visualization/vssolution.cpp
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@ -4005,8 +4005,8 @@ namespace netgen
Array<int> compress(n3);
NgProfiler::StartTimer (timer_vals);
Array<double,PointIndex::BASE> vertval(mesh->GetNV());
Array<bool,PointIndex::BASE> posval(mesh->GetNV());
Array<double,PointIndex::BASE> vertval(mesh->GetNP());
Array<bool,PointIndex::BASE> posval(mesh->GetNP());
for (PointIndex pi = vertval.Begin(); pi < vertval.End(); pi++)
{
Point<3> vert = (*mesh)[pi];

6
tests/build_mpi.sh Normal file
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@ -0,0 +1,6 @@
cd
mkdir -p build/netgen
cd build/netgen
cmake ../../src/netgen -DUSE_CCACHE=ON -DUSE_MPI=ON
make -j12
make install

5
tests/dockerfile_mpi Normal file
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@ -0,0 +1,5 @@
FROM ubuntu:18.04
ENV DEBIAN_FRONTEND=noninteractive
MAINTAINER Matthias Hochsteger <matthias.hochsteger@tuwien.ac.at>
RUN apt-get update && apt-get -y install python3 libpython3-dev libxmu-dev tk-dev tcl-dev cmake git g++ libglu1-mesa-dev ccache python3-pytest python3-numpy python3-tk clang-tidy python3-distutils clang libopenmpi-dev openmpi-bin gfortran
ADD . /root/src/netgen