Trilinos Master Merge PR Generator: Auto PR created to promote from master_merge_20250110_175815 branch to master

.github/workflows/codeql.yml

@@ -69,7 +69,7 @@ jobs:
       name: Get dependencies
       working-directory: ./packages/framework
       run: |
-          ./get_dependencies.sh --container
+          ./get_dependencies.sh
 
     - if: matrix.build-mode == 'manual'
       name: Generate CMake fragments

packages/PyTrilinos2/CMakeLists.txt

@@ -1,6 +1,3 @@
-# -*- cmake -*-
-
-
 # Set the package name
 TRIBITS_PACKAGE(PyTrilinos2 DISABLE_STRONG_WARNINGS)
 
@@ -27,11 +24,11 @@ PYTRILINOS2_CMAKE_ERROR
   ON )
 
 TRIBITS_ADD_OPTION_AND_DEFINE(PyTrilinos2_BINDER_VERBOSE
-  PYTRILINOS2_B_VERBOSE
+  PYTRILINOS2_VERBOSE
   "Increase the verbosity of binder."
   OFF )
 
-SET(PyTrilinos2_BINDER_NUM_FILES "100" CACHE STRING "Maxinum number of generated files by binder.")
+SET(PyTrilinos2_BINDER_NUM_FILES "150" CACHE STRING "Maxinum number of generated files by binder.")
 
 MESSAGE("-- Python3_EXECUTABLE:")
 IF(NOT DEFINED ${Python3_EXECUTABLE})
@@ -212,6 +209,10 @@ add_custom_command(
 add_custom_target(generate_include_name DEPENDS ${binder_include_name})
 add_dependencies(generate_include_name generate_ETI_name)
 
+ASSERT_DEFINED(
+  ${PACKAGE_NAME}_ENABLE_MueLu
+)
+
 set(BINDER_OPTIONS "")
 list(APPEND BINDER_OPTIONS --root-module PyTrilinos2)
 list(APPEND BINDER_OPTIONS --prefix ${CMAKE_CURRENT_BINARY_DIR}/binder)
@@ -223,8 +224,13 @@ ELSE()
 ENDIF()
 list(APPEND BINDER_OPTIONS --bind Teuchos)
 list(APPEND BINDER_OPTIONS --bind Tpetra)
-list(APPEND BINDER_OPTIONS --bind MueLu)
-IF(PYTRILINOS2_B_VERBOSE)
+list(APPEND BINDER_OPTIONS --bind Thyra)
+list(APPEND BINDER_OPTIONS --bind ThyraTpetraAdapters)
+list(APPEND BINDER_OPTIONS --bind Stratimikos)
+IF(${PACKAGE_NAME}_ENABLE_MueLu)
+  list(APPEND BINDER_OPTIONS --bind MueLu)
+ENDIF()
+IF(PYTRILINOS2_VERBOSE)
   list(APPEND BINDER_OPTIONS -v)
 ENDIF()
 IF(PYTRILINOS2_SUPPRESS_ERRORS)
@@ -346,7 +352,9 @@ ADD_SUBDIRECTORY( src )
 file(COPY ${PyTrilinos2PyFiles} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/PyTrilinos2/.)
 #file(COPY ${PyTrilinos2PyFilesSo} DESTINATION ${CMAKE_CURRENT_BINARY_DIR}/PyTrilinos2/.)
 
-SET(PyTrilinos2_PYTHONPATH "${CMAKE_CURRENT_BINARY_DIR}:$ENV{PYTHONPATH}")
+SET(PyTrilinos2_PYTHONPATH "${CMAKE_CURRENT_BINARY_DIR}")
+
+TRIBITS_ADD_EXAMPLE_DIRECTORIES(examples)
 
 TRIBITS_ADD_TEST_DIRECTORIES(test)
 

packages/PyTrilinos2/cmake/Dependencies.cmake

@@ -10,9 +10,11 @@
 SET(LIB_REQUIRED_DEP_PACKAGES
   Teuchos
   Tpetra
-  MueLu
-  )
-SET(LIB_OPTIONAL_DEP_PACKAGES)
+  Thyra
+  ThyraTpetraAdapters
+  Stratimikos
+)
+SET(LIB_OPTIONAL_DEP_PACKAGES MueLu)
 SET(TEST_REQUIRED_DEP_PACKAGES)
 SET(TEST_OPTIONAL_DEP_PACKAGES)
 SET(LIB_REQUIRED_DEP_TPLS)

packages/PyTrilinos2/cmake/PyTrilinos2MakeTest.cmake

@@ -1,17 +1,19 @@
 
 MACRO(PyTrilinos2_MAKE_MPI_TEST TEST_NAME)
 
-  FILE(COPY ${CMAKE_CURRENT_SOURCE_DIR}/${TEST_NAME}.py DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
-
   TRIBITS_ADD_TEST(
     ${Python3_EXECUTABLE}
     NOEXEPREFIX
     NOEXESUFFIX
     NAME ${TEST_NAME}
     ARGS "${TEST_NAME}.py"
     PASS_REGULAR_EXPRESSION "OK"
-    ENVIRONMENT "PYTHONPATH=${PyTrilinos2_PYTHONPATH}"
+    ENVIRONMENT "PYTHONPATH=${PyTrilinos2_PYTHONPATH}:$ENV{PYTHONPATH}"
     ${ARGN}
     )
 
+  TRIBITS_COPY_FILES_TO_BINARY_DIR(${TEST_NAME}_cp
+    SOURCE_FILES ${TEST_NAME}.py
+    CATEGORIES BASIC)
+
 ENDMACRO(PyTrilinos2_MAKE_MPI_TEST TEST_NAME)

packages/PyTrilinos2/cmake/PyTrilinos2_config.hpp.in

@@ -0,0 +1,6 @@
+#ifndef PYTILINOS2_CONFIG_HPP
+#define PYTILINOS2_CONFIG_HPP
+
+#cmakedefine HAVE_PYTRILINOS2_MUELU
+
+#endif

packages/PyTrilinos2/examples/CMakeLists.txt

@@ -0,0 +1,3 @@
+INCLUDE(PyTrilinos2MakeTest)
+
+PyTrilinos2_MAKE_MPI_TEST(exampleCG)

packages/PyTrilinos2/examples/CG.py → packages/PyTrilinos2/examples/exampleCG.py

@@ -149,6 +149,14 @@ def main():
         plt.plot(x0_view)
         plt.savefig('x0_view.png', dpi=800, bbox_inches='tight',pad_inches = 0)
 
+    success = True
+    if comm.getRank() == 0:
+        if success:
+            print("OK")
+        else:
+            print("FAIL")
+
+
 if __name__ == "__main__":
     comm = MPI.COMM_WORLD
     rank = comm.Get_rank()

packages/PyTrilinos2/python/__init__.py

@@ -10,3 +10,5 @@
 __version__ = '0.1.0'
 def version():
     return 'PyTrilinos2 version: ' + __version__
+
+from . PyTrilinos2 import *

packages/PyTrilinos2/scripts/PyTrilinos2_config.cfg

@@ -9,23 +9,77 @@
 
 +include <pybind11/stl.h>
 +include <pybind11/stl_bind.h>
+
+# Standard library
+-class std::basic_ios
+-class std::vector
+-class std::map
+-class std::integral_constant
+-class std::iterator
+-class std::reverse_iterator
+-class std::set
+
+# OpenMPI
+-class ompi_status_public_t
+-class ompi_request_t
+-class ompi_errhandler_t
+-class ompi_communicator_t
+
+###############################################################################
+# Teuchos
 +include <Teuchos_RCP.hpp>
-+custom_shared Teuchos::RCP
+
 +include_for_namespace Teuchos <PyTrilinos2_Teuchos_Custom.hpp>
 +add_on_binder_for_namespace Teuchos def_Teuchos_functions
-+add_on_binder_for_namespace Tpetra def_initialize_Kokkos
+
++custom_shared Teuchos::RCP
+
+-namespace Teuchos::Details
+
+-function Teuchos::Ptr::operator->
+-function Teuchos::Ptr::get
+-function Teuchos::Ptr::getRawPtr
+-function Teuchos::Array::data
+-function Teuchos::Array::getRawPtr
+-function Teuchos::ArrayRCP::getRawPtr
+-function Teuchos::ArrayView::access_private_ptr
+-function Teuchos::ArrayView::begin
+-function Teuchos::ArrayView::end
+-function Teuchos::ArrayView::data
+-function Teuchos::ArrayView::getRawPtr
+-class Teuchos::ArrayRCP<void>
+-class Teuchos::ArrayRCP<const void>
+-class Teuchos::Array<bool>
+-class Teuchos::Ptr<int>
+-class Teuchos::Ptr<long>
+-class Teuchos::Ptr<long int>
+-class Teuchos::Ptr<long long>
+-class Teuchos::Ptr<unsigned long>
+-class Teuchos::Ptr<long long int>
+-class Teuchos::Ptr<long unsigned int>
+-class Teuchos::Ptr<bool>
+-class Teuchos::Ptr<double>
+
++add_on_binder Teuchos::ParameterList def_ParameterList_member_functions
 -function Teuchos::ParameterList::sublist
 -function Teuchos::ParameterList::set
 -function Teuchos::ParameterList::get
-+add_on_binder Teuchos::ParameterList def_ParameterList_member_functions
-+include_for_namespace Tpetra <PyTrilinos2_Tpetra_Custom.hpp>
-+add_on_binder Tpetra::CrsGraph define_CrsGraph_member_functions
-+include <PyTrilinos2_Tpetra_Types.hpp>
-+add_on_binder Tpetra::CrsMatrix define_CrsMatrix_member_functions
-+add_on_binder Tpetra::Vector define_Vector_member_functions
-+add_on_binder Tpetra::MultiVector define_MultiVector_member_functions
--class Kokkos::View
--class Kokkos::DualView
+-class Teuchos::ParameterListAcceptorDefaultBase
+
+-class Teuchos::PromotionTraits
+-function Teuchos::Serializer::createObj
+-function Teuchos::TimeMonitor::computeGlobalTimerStatistics
+-class Teuchos::CommandLineProcessor::enum_opt_data_t
+-class Teuchos::CommandLineProcessor::TimeMonitorSurrogate
+-class Teuchos::RawWorkspace
+-function Teuchos::getRawMpiComm
+-function Teuchos::rcp_dynamic_cast
+-function Teuchos::ptr_dynamic_cast
+-class Teuchos::BLAS
+-class Teuchos::Describable
+
+###############################################################################
+# Kokkos
 -namespace Kokkos::Impl
 -namespace KokkosBlas
 -include <Cuda/Kokkos_Cuda_Instance.hpp>
@@ -91,88 +145,71 @@
 -include <OpenMP/Kokkos_OpenMP_Instance.hpp>
 -include <impl/Kokkos_HostThreadTeam.hpp>
 -include <impl/Kokkos_InitializationSettings.hpp>
--class Teuchos::ArrayView<ompi_status_public_t>
--class Teuchos::ArrayView<const ompi_status_public_t>
--class Teuchos::Serializer
--class Teuchos::PromotionTraits
--class Teuchos::CommandLineProcessor
--class Teuchos::Ptr<Teuchos::RCP<Teuchos::CommRequest<int> >>
--class Teuchos::ArrayView<Teuchos::RCP<Teuchos::CommRequest<int> >>
--class Teuchos::TimeMonitor
+-include <View/Kokkos_ViewLegacy.hpp>
+-include <View/Kokkos_ViewTraits.hpp>
+-include <View/Kokkos_ViewMapping.hpp>
+-class Kokkos::Device
+-class Kokkos::DualView
+-class Kokkos::DynRankView
+-class Kokkos::View
+
+###############################################################################
+# Tpetra
++add_on_binder_for_namespace Tpetra def_initialize_Kokkos
++include_for_namespace Tpetra <PyTrilinos2_Tpetra_Custom.hpp>
++include <PyTrilinos2_Tpetra_Types.hpp>
++add_on_binder Tpetra::CrsGraph define_CrsGraph_member_functions
++add_on_binder Tpetra::Vector define_Vector_member_functions
++add_on_binder Tpetra::MultiVector define_MultiVector_member_functions
++add_on_binder Tpetra::CrsMatrix define_CrsMatrix_member_functions
 -namespace Tpetra::Details
 -namespace Tpetra::Import_Util
--namespace Teuchos::Details
 -namespace Tpetra::KokkosRefactor
--function Tpetra::Details::isInterComm
--function Tpetra::SrcDistObject::operator=
--function Teuchos::TimeMonitor::computeGlobalTimerStatistics
--function Teuchos::mpiErrorCodeToString
--class Teuchos::CommandLineProcessor::enum_opt_data_t
--class Teuchos::CommandLineProcessor::TimeMonitorSurrogate
--class Teuchos::RawWorkspace
--class std::ostream
--class std::basic_ios
--class std::vector
--class std::map
--class std::integral_constant
--class std::integral_constant
--class std::iterator
--class std::reverse_iterator
--class Teuchos::ArrayView
--class Teuchos::ArrayRCP
--class Teuchos::Array
--class Teuchos::Describable
--class Teuchos::BLAS
--function Teuchos::fancyOStream
--class Teuchos::ParameterListAcceptorDefaultBase
--class Teuchos::Dependency
--class Teuchos::DependencySheet
--class Teuchos::MpiCommRequestBase<int>
--function Teuchos::getRawMpiComm
--class Teuchos::OpaqueWrapper<ompi_communicator_t *>
--class Teuchos::OpaqueWrapper<ompi_errhandler_t *>
--function Teuchos::Details::setMpiReductionOp
--function Teuchos::Details::getMpiOpForEReductionType
--function Tpetra::Details::extractMpiCommFromTeuchos
--class Teuchos::OpaqueWrapper<ompi_errhandler_t *>
--function Teuchos::Details::setMpiReductionOp
--function Teuchos::Details::getMpiOpForEReductionType
--function Tpetra::Details::PackCrsGraphImpl::packRow
+-class Tpetra::BlockCrsMatrix
 -class Tpetra::Details::DistributorPlan
+-class Tpetra::Directory
+-class Tpetra::Distribution
+-class Tpetra::Distribution1D
+-class Tpetra::Distribution2D
+-class Tpetra::DistributionLowerTriangularBlock
+-class Tpetra::DistributionMM
 -class Tpetra::DistributionType
--namespace Xpetra
--class Thyra::VectorSpaceBase
--class Thyra::ProductVectorSpace
--class Tpetra::Details::DistributorPlan
 -class Tpetra::Distributor
--class Tpetra::DistributionType
+-class Tpetra::LowerTriangularBlockOperator
 -class Tpetra::distributorSendTypes
+-class Tpetra::ImportExportData
+-function Tpetra::Details::extractMpiCommFromTeuchos
+-function Tpetra::Details::isInterComm
+-function Tpetra::Details::PackCrsGraphImpl::packRow
+-function Tpetra::SrcDistObject::operator=
+
+###############################################################################
+# Xpetra
+-namespace Xpetra
+
+###############################################################################
+# MueLu
+-class MueLu::BaseClass
+-class MueLu::Describable
 -class MueLu::FactoryAcceptor
+-class MueLu::FactoryBase
 -class MueLu::FactoryFactory
--class MueLu::FactoryManagerBase
 -class MueLu::FactoryManager
--class MueLu::FactoryBase
+-class MueLu::FactoryManagerBase
 -class MueLu::Hierarchy
 -class MueLu::HierarchyManager
+-class MueLu::Level
 -class MueLu::TimeMonitor
--class MueLu::Describable
--class Kokkos::Device
--class Tpetra::DistributionType
--class Tpetra::Directory
--class Tpetra::Distribution
--class Tpetra::Distribution1D
--class Tpetra::Distribution2D
--class Tpetra::DistributionMM
--class Tpetra::DistributionLowerTriangularBlock
--class MueLu::BaseClass
--function Teuchos::rcp_dynamic_cast
--class Teuchos::VerboseObjectBase
--class MueLu::VerboseObject
--class Tpetra::BlockCrsMatrix
--class Kokkos::DynRankView
 -class MueLu::VariableContainer
--class Tpetra::LowerTriangularBlockOperator
--class MueLu::Level
--class MueLu::Hierarchy
--class std::set
--class Teuchos::Ptr
+-class MueLu::VerboseObject
++include <Stratimikos_MueLuHelpers.hpp>
+
+###############################################################################
+# Thyra
++include <Thyra_VectorSpaceFactoryBase.hpp>
+-class Thyra::ProductVectorSpace
+-class Thyra::RowStatLinearOpBase
+-class Thyra::ScaledLinearOpBase
+-class Thyra::LinearOpSourceBase
++include_for_namespace Thyra <PyTrilinos2_Thyra_Custom.hpp>
++add_on_binder Thyra::LinearOpWithSolveBase define_solve