PROM DG advection

.gitmodules

@@ -4,5 +4,4 @@
 	branch = stable
 [submodule "extern/libROM"]
 	path = extern/libROM
-	url = https://github.com/LLNL/libROM.git
-	branch = mfem_fix
+	url = https://github.com/LLNL/libROM.git

CMakeLists.txt

@@ -163,7 +163,6 @@ pybind11_add_module(_pylibROM
 	bindings/pylibROM/mfem/pySampleMesh.cpp
 
 	bindings/pylibROM/python_utils/cpp_utils.hpp
-	bindings/pylibROM/python_utils/cpp_utils.cpp
 )
 message("building pylibROM...")
 

README.md

@@ -38,11 +38,11 @@ For parallel version, a manual installation is required:
 ```
 git clone https://github.com/mfem/PyMFEM.git
 cd PyMFEM
-python3 setup.py install --with-parallel
+python3 setup.py install --with-parallel --with-gslib
 ```
 On LC quartz, use `--user` flag:
 ```
-python3 setup.py install --with-parallel --user
+python3 setup.py install --with-parallel --with-gslib --user
 ```
 Make sure [`swig`](https://pypi.org/project/swig) is installed first. Also, the binary file must be located in `PATH` environment variable.
 

bindings/pylibROM/linalg/pyBasisReader.cpp

@@ -16,21 +16,51 @@ void init_BasisReader(pybind11::module_ &m) {
             py::arg("base_file_name"),
             py::arg("file_format") = Database::formats::HDF5
         )
-        .def("isNewBasis",(bool (BasisReader::*)(double)) &BasisReader::isNewBasis)
-        .def("getSpatialBasis",(Matrix* (BasisReader::*)(double)) &BasisReader::getSpatialBasis)
-        .def("getSpatialBasis",(Matrix* (BasisReader::*)(double,int)) &BasisReader::getSpatialBasis)
-        .def("getSpatialBasis",(Matrix* (BasisReader::*)(double,int,int)) &BasisReader::getSpatialBasis)
-        .def("getSpatialBasis",(Matrix* (BasisReader::*)(double,double)) &BasisReader::getSpatialBasis)
-        .def("getTemporalBasis",(Matrix* (BasisReader::*)(double)) &BasisReader::getTemporalBasis)
-        .def("getTemporalBasis",(Matrix* (BasisReader::*)(double,int)) &BasisReader::getTemporalBasis)
-        .def("getTemporalBasis",(Matrix* (BasisReader::*)(double,int,int)) &BasisReader::getTemporalBasis)
-        .def("getTemporalBasis",(Matrix* (BasisReader::*)(double,double)) &BasisReader::getTemporalBasis)
-        .def("getSingularValues",(Vector* (BasisReader::*)(double)) &BasisReader::getSingularValues)
-        .def("getSingularValues",(Vector* (BasisReader::*)(double,double)) &BasisReader::getSingularValues)
-        .def("getDim", (int (BasisReader::*)(const std::string,double)) &BasisReader::getDim)
-        .def("getNumSamples", (int (BasisReader::*)(const std::string,double)) &BasisReader::getNumSamples) 
-        .def("getSnapshotMatrix",(Matrix* (BasisReader::*)(double)) &BasisReader::getSnapshotMatrix)
-        .def("getSnapshotMatrix",(Matrix* (BasisReader::*)(double,int)) &BasisReader::getSnapshotMatrix)
-        .def("getSnapshotMatrix",(Matrix* (BasisReader::*)(double,int,int)) &BasisReader::getSnapshotMatrix)
+        .def("isNewBasis",(bool (BasisReader::*)(double)) &BasisReader::isNewBasis,
+            py::arg("time"))
+        .def("getSpatialBasis",(Matrix* (BasisReader::*)(double)) &BasisReader::getSpatialBasis,
+            py::arg("time"))
+        .def("getSpatialBasis",(Matrix* (BasisReader::*)(double,int)) &BasisReader::getSpatialBasis,
+            py::arg("time"),
+            py::arg("n"))
+        .def("getSpatialBasis",(Matrix* (BasisReader::*)(double,int,int)) &BasisReader::getSpatialBasis,
+            py::arg("time"),
+            py::arg("start_col"),
+            py::arg("end_col"))
+        .def("getSpatialBasis",(Matrix* (BasisReader::*)(double,double)) &BasisReader::getSpatialBasis,
+            py::arg("time"),
+            py::arg("ef").noconvert())
+        .def("getTemporalBasis",(Matrix* (BasisReader::*)(double)) &BasisReader::getTemporalBasis,
+            py::arg("time"))
+        .def("getTemporalBasis",(Matrix* (BasisReader::*)(double,int)) &BasisReader::getTemporalBasis,
+            py::arg("time"),
+            py::arg("n"))
+        .def("getTemporalBasis",(Matrix* (BasisReader::*)(double,int,int)) &BasisReader::getTemporalBasis,
+            py::arg("time"),
+            py::arg("start_col"),
+            py::arg("end_col"))
+        .def("getTemporalBasis",(Matrix* (BasisReader::*)(double,double)) &BasisReader::getTemporalBasis,
+            py::arg("time"),
+            py::arg("ef").noconvert())
+        .def("getSingularValues",(Vector* (BasisReader::*)(double)) &BasisReader::getSingularValues,
+            py::arg("time"))
+        .def("getSingularValues",(Vector* (BasisReader::*)(double,double)) &BasisReader::getSingularValues,
+            py::arg("time"),
+            py::arg("ef"))
+        .def("getDim", (int (BasisReader::*)(const std::string,double)) &BasisReader::getDim,
+            py::arg("kind"),
+            py::arg("time"))
+        .def("getNumSamples", (int (BasisReader::*)(const std::string,double)) &BasisReader::getNumSamples,
+            py::arg("kind"),
+            py::arg("time"))
+        .def("getSnapshotMatrix",(Matrix* (BasisReader::*)(double)) &BasisReader::getSnapshotMatrix,
+            py::arg("time"))
+        .def("getSnapshotMatrix",(Matrix* (BasisReader::*)(double,int)) &BasisReader::getSnapshotMatrix,
+            py::arg("time"),
+            py::arg("n"))
+        .def("getSnapshotMatrix",(Matrix* (BasisReader::*)(double,int,int)) &BasisReader::getSnapshotMatrix,
+            py::arg("time"),
+            py::arg("start_col"),
+            py::arg("end_col"))
         .def("__del__", [](BasisReader& self) { self.~BasisReader(); }); // Destructor
 }

bindings/pylibROM/mfem/pySampleMesh.cpp

@@ -47,21 +47,24 @@ void init_mfem_SampleMesh(pybind11::module_ &m) {
             ParFiniteElementSpace *spfes_target = self.GetSampleFESpace(space);
 
             // deep copy of the spfes_target.
-            void *spfes_address = extractSwigPtrAddress(spfespace);
+            void *spfes_address = extractSwigPtr<void>(spfespace);
             ParFiniteElementSpace *spfes = new (spfes_address) ParFiniteElementSpace(*spfes_target);
         })
 
         .def("GetSampleMesh", [](CAROM::SampleMeshManager& self, py::object &sppmesh){
             ParMesh *sppmesh_target = self.GetSampleMesh();
 
             // deep copy of the spfes_target.
-            void *sppmesh_address = extractSwigPtrAddress(sppmesh);
+            void *sppmesh_address = extractSwigPtr<void>(sppmesh);
             ParMesh *sample_pmesh = new (sppmesh_address) ParMesh(*sppmesh_target);
         })
 
         .def("GetNumVarSamples", &CAROM::SampleMeshManager::GetNumVarSamples)
 
-        .def("GetSampledValues", &CAROM::SampleMeshManager::GetSampledValues)
+        .def("GetSampledValues", [](CAROM::SampleMeshManager &self, const std::string variable, py::object &v, CAROM::Vector &s){
+            Vector *v_ptr = extractSwigPtr<Vector>(v);
+            self.GetSampledValues(variable, *v_ptr, s);
+        })
 
         .def("GetSampleElements", &CAROM::SampleMeshManager::GetSampleElements)
 

bindings/pylibROM/python_utils/cpp_utils.hpp

@@ -88,9 +88,6 @@ get1DArrayFromPtr(T *ptr, const int nelem, bool free_when_done=false)
                      get1DArrayBufferHandle(ptr, free_when_done));
 }
 
-void *
-extractSwigPtrAddress(const py::handle &swig_target);
-
 template<typename T>
 T*
 extractSwigPtr(const py::handle &swig_target)

docker/librom/Dockerfile

@@ -23,7 +23,7 @@ RUN sudo git clone https://github.com/LLNL/libROM.git
 WORKDIR ./libROM
 RUN sudo git pull
 # pylibROM is currently based on a specific commit of the libROM.
-RUN sudo git checkout mfem_fix
+RUN sudo git checkout 0809d7d09dc24f0963c38fc8c0a2649948142ba0
 WORKDIR ./build
 RUN sudo cmake .. -DCMAKE_TOOLCHAIN_FILE=${TOOLCHAIN_FILE} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DUSE_MFEM=${USE_MFEM} -DMFEM_USE_GSLIB=${MFEM_USE_GSLIB}
 # RUN sudo cmake .. -DCMAKE_TOOLCHAIN_FILE=${TOOLCHAIN_FILE} -DCMAKE_BUILD_TYPE=${BUILD_TYPE} -DUSE_MFEM=OFF

examples/data/beam-hex-nurbs.mesh

@@ -0,0 +1,143 @@
+MFEM NURBS mesh v1.0
+
+#
+# MFEM Geometry Types (see mesh/geom.hpp):
+#
+# SEGMENT     = 1
+# SQUARE      = 3
+# CUBE        = 5
+#
+
+dimension
+3
+
+elements
+2
+1 5 0 1 4 5 6 7 10 11
+2 5 1 2 3 4 7 8 9 10
+
+boundary
+10
+3 3 5 4 1 0
+3 3 0 1 7 6
+3 3 4 5 11 10
+1 3 5 0 6 11
+3 3 6 7 10 11
+3 3 4 3 2 1
+3 3 1 2 8 7
+2 3 2 3 9 8
+3 3 3 4 10 9
+3 3 7 8 9 10
+
+edges
+20
+0 0 1
+0 5 4
+0 6 7
+0 11 10
+1 1 2
+1 4 3
+1 7 8
+1 10 9
+2 0 5
+2 1 4
+2 2 3
+2 6 11
+2 7 10
+2 8 9
+3 0 6
+3 1 7
+3 2 8
+3 3 9
+3 4 10
+3 5 11
+
+vertices
+12
+
+knotvectors
+4
+1 5 0 0 1 2 3 4 4
+1 5 0 0 1 2 3 4 4
+1 2 0 0 1 1
+1 2 0 0 1 1
+
+weights
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+1
+
+FiniteElementSpace
+FiniteElementCollection: NURBS1
+VDim: 3
+Ordering: 1
+
+0 0 0
+4 0 0
+8 0 0
+8 1 0
+4 1 0
+0 1 0
+0 0 1
+4 0 1
+8 0 1
+8 1 1
+4 1 1
+0 1 1
+1 0 0
+2 0 0
+3 0 0
+3 1 0
+2 1 0
+1 1 0
+1 0 1
+2 0 1
+3 0 1
+3 1 1
+2 1 1
+1 1 1
+5 0 0
+6 0 0
+7 0 0
+7 1 0
+6 1 0
+5 1 0
+5 0 1
+6 0 1
+7 0 1
+7 1 1
+6 1 1
+5 1 1