created and tested bindings for hyperreduction

.github/workflows/ci.yml

@@ -63,6 +63,18 @@ jobs:
             pytest test_pyBasisReader.py --verbose
             echo run pyBasisWriter unit test
             pytest test_pyBasisWriter.py --verbose
+            echo run pyDEIM unit test
+            pytest test_pyDEIM.py --verbose
+            echo run pyGNAT unit test
+            pytest test_pyGNAT.py --verbose
+            echo run pyQDEIM unit test
+            pytest test_pyQDEIM.py --verbose
+            echo run pyS_OPT unit test
+            pytest test_pyS_OPT.py --verbose
+            echo run pySTSampling unit test
+            pytest test_pySTSampling.py --verbose
+            echo run pyUtilities unit test
+            pytest test_pyUtilities.py --verbose
   cmake-with-librom:
     runs-on: ubuntu-latest
     needs: [docker-librom-image]
@@ -115,6 +127,18 @@ jobs:
             pytest test_pyBasisReader.py --verbose
             echo run pyBasisWriter unit test
             pytest test_pyBasisWriter.py --verbose
+            echo run pyDEIM unit test
+            pytest test_pyDEIM.py --verbose
+            echo run pyGNAT unit test
+            pytest test_pyGNAT.py --verbose
+            echo run pyQDEIM unit test
+            pytest test_pyQDEIM.py --verbose
+            echo run pyS_OPT unit test
+            pytest test_pyS_OPT.py --verbose
+            echo run pySTSampling unit test
+            pytest test_pySTSampling.py --verbose
+            echo run pyUtilities unit test
+            pytest test_pyUtilities.py --verbose
   baseline:
     runs-on: ubuntu-latest
     needs: [docker-base-image]
@@ -164,4 +188,16 @@ jobs:
             pytest test_pyBasisReader.py --verbose
             echo run pyBasisWriter unit test
             pytest test_pyBasisWriter.py --verbose
+            echo run pyDEIM unit test
+            pytest test_pyDEIM.py --verbose
+            echo run pyGNAT unit test
+            pytest test_pyGNAT.py --verbose
+            echo run pyQDEIM unit test
+            pytest test_pyQDEIM.py --verbose
+            echo run pyS_OPT unit test
+            pytest test_pyS_OPT.py --verbose
+            echo run pySTSampling unit test
+            pytest test_pySTSampling.py --verbose
+            echo run pyUtilities unit test
+            pytest test_pyUtilities.py --verbose
 

CMakeLists.txt

@@ -143,7 +143,14 @@ pybind11_add_module(_pylibROM
 
     bindings/pylibROM/algo/pyDMD.cpp
 	bindings/pylibROM/algo/pyParametricDMD.cpp
-
+
+	bindings/pylibROM/hyperreduction/pyDEIM.cpp
+	bindings/pylibROM/hyperreduction/pyGNAT.cpp
+	bindings/pylibROM/hyperreduction/pyQDEIM.cpp
+	bindings/pylibROM/hyperreduction/pyS_OPT.cpp
+	bindings/pylibROM/hyperreduction/pySTSampling.cpp
+	bindings/pylibROM/hyperreduction/pyUtilities.cpp
+
 	bindings/pylibROM/utils/mpi_utils.cpp
 	bindings/pylibROM/utils/pyDatabase.hpp
 	bindings/pylibROM/utils/pyDatabase.cpp

bindings/pylibROM/__init__.py

@@ -1,3 +1,7 @@
+# from . import linalg
+# from . import algo
+# from . import utils
+# from . import hyperreduction
 # To add pure python routines to this module,
 # either define/import the python routine in this file.
 # This will combine both c++ bindings/pure python routines into this module.

bindings/pylibROM/hyperreduction/__init__.py

@@ -0,0 +1 @@
+from _pylibROM.hyperreduction import *

bindings/pylibROM/hyperreduction/pyDEIM.cpp

@@ -0,0 +1,22 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+#include <pybind11/operators.h>
+#include <pybind11/stl.h>
+#include "hyperreduction/DEIM.h"
+#include <vector>
+#include "linalg/Matrix.h"
+
+namespace py = pybind11;
+using namespace CAROM;
+
+
+void init_DEIM(pybind11::module_ &m) {
+   m.def("DEIM", [](const Matrix* f_basis,int num_f_basis_vectors_used,
+                  Matrix& f_basis_sampled_inv,int myid,int num_procs) {
+      int num_basis_vectors = std::min(num_f_basis_vectors_used, f_basis->numColumns());
+      std::vector<int> f_sampled_row(num_basis_vectors);
+      std::vector<int> f_sampled_rows_per_proc(num_procs);
+      DEIM(f_basis, num_f_basis_vectors_used,f_sampled_row, f_sampled_rows_per_proc,f_basis_sampled_inv, myid, num_procs);
+      return std::make_tuple(std::move(f_sampled_row), std::move(f_sampled_rows_per_proc));
+   });
+}

bindings/pylibROM/hyperreduction/pyGNAT.cpp

@@ -0,0 +1,34 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+#include <pybind11/operators.h>
+#include <pybind11/stl.h>
+#include "hyperreduction/GNAT.h"
+#include "linalg/Matrix.h"
+
+namespace py = pybind11;
+using namespace CAROM;
+
+void init_GNAT(pybind11::module_ &m) {
+   m.def("GNAT", [](const Matrix* f_basis,
+                    const int num_f_basis_vectors_used,
+                    Matrix& f_basis_sampled_inv,
+                    const int myid,
+                    const int num_procs,
+                    const int num_samples_req,
+                    std::vector<int>& init_samples){  
+
+        const int num_basis_vectors = std::min(num_f_basis_vectors_used, f_basis->numColumns());
+        const int num_samples = num_samples_req > 0 ? num_samples_req : num_basis_vectors;
+        std::vector<int> f_sampled_row(num_samples);
+        std::vector<int> f_sampled_rows_per_proc(num_procs);
+        GNAT(f_basis, num_f_basis_vectors_used, f_sampled_row, f_sampled_rows_per_proc,
+             f_basis_sampled_inv, myid, num_procs, num_samples_req,&init_samples);
+     return std::make_tuple(std::move(f_sampled_row), std::move(f_sampled_rows_per_proc));
+    },py::arg("f_basis"),
+    py::arg("num_f_basis_vectors_used"),
+    py::arg("f_basis_sampled_inv"),
+    py::arg("myid"),
+    py::arg("num_procs"),
+    py::arg("num_samples_req") = -1,
+    py::arg("init_samples") =  std::vector<int>(0));
+}

bindings/pylibROM/hyperreduction/pyQDEIM.cpp

@@ -0,0 +1,21 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+#include <pybind11/operators.h>
+#include <pybind11/stl.h>
+#include "hyperreduction/QDEIM.h"
+#include <vector>
+#include "linalg/Matrix.h"
+
+namespace py = pybind11;
+using namespace CAROM;
+
+void init_QDEIM(pybind11::module_ &m) {
+   m.def("QDEIM", [](const Matrix* f_basis,int num_f_basis_vectors_used,
+                  Matrix& f_basis_sampled_inv,const int myid,const int num_procs,const int num_samples_req) {
+      std::vector<int> f_sampled_row(num_samples_req);
+      std::vector<int> f_sampled_rows_per_proc(num_procs);
+      QDEIM(f_basis, num_f_basis_vectors_used,f_sampled_row, f_sampled_rows_per_proc,f_basis_sampled_inv, myid, num_procs,num_samples_req);
+      return std::make_tuple(std::move(f_sampled_row), std::move(f_sampled_rows_per_proc));
+   });
+}
+

bindings/pylibROM/hyperreduction/pySTSampling.cpp

@@ -0,0 +1,39 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+#include <pybind11/operators.h>
+#include <pybind11/stl.h>
+#include "librom.h"
+#include "python_utils/cpp_utils.hpp"
+
+namespace py = pybind11;
+using namespace CAROM;
+
+
+void init_STSampling(pybind11::module_ &m) {
+    m.def("SpaceTimeSampling", [](const Matrix* s_basis,
+                  const Matrix* t_basis,
+                  const int num_f_basis_vectors_used,
+                  py::array_t<int>&  f_sampled_row,
+                  py::array_t<int>& f_sampled_rows_per_proc,
+                  Matrix& s_basis_sampled,
+                  const int myid,
+                  const int num_procs,
+                  const int num_t_samples_req = -1,  
+                  const int num_s_samples_req = -1,
+                  const bool excludeFinalTime = false) {
+      std::vector<int> t_samples(num_t_samples_req);
+      SpaceTimeSampling(s_basis, t_basis,num_f_basis_vectors_used,t_samples,getVectorPointer(f_sampled_row), getVectorPointer(f_sampled_rows_per_proc), s_basis_sampled, myid, num_procs, num_t_samples_req,num_s_samples_req,excludeFinalTime);
+      return std::move(t_samples);
+    }, py::arg("s_basis"), py::arg("t_basis"), py::arg("num_f_basis_vectors_used"),
+       py::arg("f_sampled_row"), py::arg("f_sampled_rows_per_proc"),
+       py::arg("s_basis_sampled"), py::arg("myid"), py::arg("num_procs"),
+       py::arg("num_t_samples_req") = -1, py::arg("num_s_samples_req") = -1,
+       py::arg("excludeFinalTime") = false);
+
+    m.def("GetSampledSpaceTimeBasis", [](std::vector<int> const& t_samples,
+                              const Matrix* t_basis,
+                              Matrix const& s_basis_sampled,
+                              Matrix& f_basis_sampled_inv) {
+      GetSampledSpaceTimeBasis(t_samples,t_basis,s_basis_sampled,f_basis_sampled_inv);
+    });
+}

bindings/pylibROM/hyperreduction/pyS_OPT.cpp

@@ -0,0 +1,47 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+#include <pybind11/operators.h>
+#include <pybind11/stl.h>
+#include <vector>
+#include "hyperreduction/S_OPT.h"
+#include "linalg/Matrix.h"
+
+namespace py = pybind11;
+using namespace CAROM;
+
+void init_S_OPT(pybind11::module_ &m) {
+   m.def("S_OPT", [](
+      const Matrix* f_basis,
+      int num_f_basis_vectors_used,
+      Matrix& f_basis_sampled_inv,
+      const int myid,
+      const int num_procs,
+      const int num_samples_req,
+      std::vector<int> &init_samples,
+      bool qr_factorize) {
+
+      // S_OPT checks if f_sample_row and f_sample_rows_per_proc have the right sizes.
+      // Initialize them with the right size.
+      const int num_basis_vectors =
+         std::min(num_f_basis_vectors_used, f_basis->numColumns());
+      const int num_samples = num_samples_req > 0 ? num_samples_req :
+                              num_basis_vectors;
+      std::vector<int> f_sampled_row(num_samples);
+      std::vector<int> f_sampled_rows_per_proc(num_procs);
+
+      S_OPT(f_basis, num_f_basis_vectors_used, f_sampled_row,
+            f_sampled_rows_per_proc, f_basis_sampled_inv, myid,
+            num_procs, num_samples_req, &init_samples, qr_factorize);
+
+      return std::make_tuple(std::move(f_sampled_row),
+                             std::move(f_sampled_rows_per_proc));
+   },
+   py::arg("f_basis"),
+   py::arg("num_f_basis_vectors_used"),
+   py::arg("f_basis_sampled_inv"),
+   py::arg("myid"),
+   py::arg("num_procs"),
+   py::arg("num_samples_req") = -1,
+   py::arg("init_samples") = std::vector<int>(0),
+   py::arg("qr_factorize") = false);
+}

bindings/pylibROM/hyperreduction/pyUtilities.cpp

@@ -0,0 +1,18 @@
+#include <pybind11/pybind11.h>
+#include <pybind11/numpy.h>
+#include <pybind11/operators.h>
+#include <pybind11/stl.h>
+#include "hyperreduction/Utilities.h"
+#include "mpi.h"
+
+
+namespace py = pybind11;
+using namespace CAROM;
+
+void init_Utilities(pybind11::module_ &m) {
+    py::class_<RowInfo>(m, "RowInfo")
+        .def(py::init<>())
+        .def_readwrite("row_val", &RowInfo::row_val)
+        .def_readwrite("row", &RowInfo::row)
+        .def_readwrite("proc", &RowInfo::proc);
+}

bindings/pylibROM/pylibROM.cpp

@@ -21,6 +21,14 @@ void init_IncrementalSVD(pybind11::module_ &m);
 void init_DMD(pybind11::module_ &);
 void init_ParametricDMD(pybind11::module_ &m);
 
+//hyperreduction
+void init_DEIM(pybind11::module_ &m);
+void init_GNAT(pybind11::module_ &m);
+void init_QDEIM(pybind11::module_ &m);
+void init_S_OPT(pybind11::module_ &m);
+void init_STSampling(pybind11::module_ &m);
+void init_Utilities(pybind11::module_ &m);
+
 //utils
 void init_mpi_utils(pybind11::module_ &m);
 void init_Database(pybind11::module_ &m);
@@ -57,6 +65,13 @@ PYBIND11_MODULE(_pylibROM, m) {
     init_DMD(algo);
     init_ParametricDMD(algo);
 
+    py::module hyperreduction = m.def_submodule("hyperreduction");
+    init_DEIM(hyperreduction);
+    init_GNAT(hyperreduction);
+    init_QDEIM(hyperreduction);
+    init_S_OPT(hyperreduction);
+    init_STSampling(hyperreduction);
+    init_Utilities(hyperreduction);
     // py::module mfem = m.def_submodule("mfem");
     // init_mfem_Utilities(mfem);
 

bindings/pylibROM/python_utils/cpp_utils.hpp

@@ -50,5 +50,4 @@ T* getVectorPointer(py::array_t<T> &u_in)
 
     return static_cast<T*>(buf_info.ptr);
 }
-
 #endif

tests/test_BasisGenerator.py

@@ -1,9 +1,19 @@
 import sys
-
-sys.path.append("../../build")
-import pylibROM.linalg as libROM
-from pylibROM.utils import Database
+import pytest
+try:
+    # import pip-installed package
+    import pylibROM
+    import pylibROM.linalg as libROM
+    from pylibROM.utils import Database
+except ModuleNotFoundError:
+    # If pip-installed package is not found, import cmake-built package
+    sys.path.append("../build")
+    import _pylibROM as pylibROM
+    import _pylibROM.linalg as libROM
+    from _pylibROM.utils import Database
 import numpy as np 
+import h5py
+
 
 # Create an instance of BasisGenerator
 options = libROM.Options(4, 20, 3, True, True)