Cmake cgns reader

.github/pull_request_template.md

@@ -0,0 +1,15 @@
+## Title of Pull Request
+
+Pull requests should target the `develop` branch.
+
+In your PR description please include:
+
+- a brief description
+- references to existing issues this PR fixes (if applicable)
+- for new functionality, please describe the test cases added to exercise it
+
+More information on PUMI development is here: 
+
+https://github.com/SCOREC/core/wiki/Developer-Guide
+
+Thank you for your contribution.

.github/workflows/cmake.yml

@@ -0,0 +1,46 @@
+name: CMake test matrix
+on:
+  push:
+    branches: [ develop ]
+  pull_request:
+    branches: [ develop ]
+jobs:
+  build:
+    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        compiler:
+          - { compiler: GNU, CC: gcc-10, CXX: g++-10 }
+          - { compiler: LLVM, CC: clang, CXX: clang++ }
+        build_type: [Debug, Release]
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: recursive
+
+    - name: install mpich and gcc
+      run: |
+           sudo apt update
+           sudo apt install gcc-10 g++-10 mpich
+
+    - name: Configure CMake
+      env:
+        MPICH_CXX: ${{matrix.compiler.CXX}}
+        MPICH_CC: ${{matrix.compiler.CC}}
+      run: cmake -S ${{github.workspace}} -B ${{github.workspace}}/build -DCMAKE_CXX_COMPILER=mpicxx -DCMAKE_C_COMPILER=mpicc -DCMAKE_VERBOSE_MAKEFILE=ON -DMESHES=${{github.workspace}}/pumi-meshes -DIS_TESTING=ON -DSCOREC_CXX_WARNINGS=ON -DCMAKE_BUILD_TYPE=${{matrix.build_type}}
+
+    - name: Build
+      env:
+        MPICH_CXX: ${{matrix.compiler.CXX}}
+        MPICH_CC: ${{matrix.compiler.CC}}
+      run: cmake --build ${{github.workspace}}/build --config ${{matrix.build_type}} -j
+
+    - name: Test
+      env:
+        MPICH_CXX: ${{matrix.compiler.CXX}}
+        MPICH_CC: ${{matrix.compiler.CC}}
+      working-directory: ${{github.workspace}}/build
+      run: ctest --output-on-failure -C ${{matrix.build_type}}

.gitmodules

@@ -1,3 +1,3 @@
 [submodule "pumi-meshes"]
 	path = pumi-meshes
-	url = https://github.com/SCOREC/pumi-meshes.git
+	url = ../../SCOREC/pumi-meshes.git

CITATION.cff

@@ -0,0 +1,45 @@
+cff-version: 1.1.0
+title: "PUMI"
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: "Ibanez"
+    given-names: "Daniel A."
+  - family-names: "Smith"
+    given-names: "Cameron W."
+    orcid: "https://orcid.org/0000-0001-9258-5226"  
+  - family-names: "Granzow"
+    given-names: "Brian"
+  - family-names: "Zaide"
+    given-names: "Daniel"
+  - family-names: "Hakimi"
+    given-names: "Morteza"
+  - family-names: "Seol"
+    given-names: "E. Seegyoung"
+date-released: 2021-06-25
+version: 2.2.6
+keywords:
+  - "unstructured meshes"
+  - "parallel"
+  - "mesh adaptation"
+  - "load balancing"
+  - "C++"
+  - "finite elements"
+references:
+  - type: article
+    authors:
+      - family-names: "Ibanez"
+        given-names: "Daniel A."
+      - family-names: "Seol"
+        given-names: "E. Seegyoung"
+      - family-names: "Smith"
+        given-names: "Cameron W."
+        orcid: "https://orcid.org/0000-0001-9258-5226"  
+      - family-names: "Shephard"
+        given-names: "Mark S."
+    title: "PUMI: Parallel Unstructured Mesh Infrastructure"
+    doi: "10.1145/2814935"
+    month: 6
+    year: 2016
+    volume: 42
+    issue: "3"
+    journal: "ACM Trans. Math. Softw"

CMakeLists.txt

@@ -6,15 +6,20 @@ endif()
 # This is the top level CMake file for the SCOREC build
 cmake_minimum_required(VERSION 3.0)
 
-project(SCOREC VERSION 2.2.2 LANGUAGES CXX C)
+project(SCOREC VERSION 2.2.7 LANGUAGES CXX C)
 
 include(cmake/bob.cmake)
 include(cmake/xsdk.cmake)
 
-option(SCOREC_ENABLE_CXX11 "enable compilation with c++11 support" NO)
-
 option(USE_XSDK_DEFAULTS "enable the XDSK v0.3.0 default configuration" NO)
 
+#requre c++11 without extensions
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSION OFF)
+if(NOT ENABLE_CGNS)
+  set(CMAKE_CXX_STANDARD 11)
+endif()
+
 xsdk_begin_package()
 bob_begin_package()
 
@@ -32,16 +37,11 @@ if(NOT USE_XSDK_DEFAULTS)
   bob_begin_cxx_flags()
   bob_end_cxx_flags()
   set(CMAKE_C_FLAGS "${CMAKE_CXX_FLAGS}")
-  if(SCOREC_ENABLE_CXX11)
-    if(ENABLE_CGNS)
-      bob_cxx14_flags()
-    else()
-      bob_cxx14_flags()
-    endif()
-  else()
-    if(ENABLE_CGNS)
-      bob_cxx14_flags()
-    endif()
+  if(ENABLE_CGNS) #takes precedence over SCOREC_ENABLE_CXX11
+    message(STATUS "enabling cxx14")
+    bob_cxx14_flags()
+  elseif(SCOREC_ENABLE_CXX11)
+    bob_cxx11_flags()
   endif()
 endif()
 message(STATUS "CMAKE_CXX_FLAGS = ${CMAKE_CXX_FLAGS}")
@@ -58,6 +58,9 @@ message(STATUS "CMAKE_C_FLAGS = ${CMAKE_C_FLAGS}")
 option(IS_TESTING "Build for CTest" OFF)
 message(STATUS "IS_TESTING: ${IS_TESTING}")
 
+set(MESHES "${CMAKE_SOURCE_DIR}/pumi-meshes" CACHE STRING "Directory of test meshes")
+message(STATUS "MESHES: ${MESHES}")
+
 option(BUILD_EXES "Build executables" ON)
 message(STATUS "BUILD_EXES: ${BUILD_EXES}")
 
@@ -78,7 +81,7 @@ set(VALGRIND_ARGS "" CACHE STRING
   "the command line arguments to VALGRIND")
 
 # smoke test target - a few tests are defined later with the 'SMOKE_TEST' label
-add_custom_target(test_install
+add_custom_target(check
   COMMAND ${CMAKE_CTEST_COMMAND} -L SMOKE_TEST
   COMMENT "running a smoke test on the installed binaries")
 
@@ -102,6 +105,7 @@ option(SKIP_SIMMETRIX_VERSION_CHECK "enable at your own risk; it may result in u
 option(ENABLE_SIMMETRIX "Build with Simmetrix support" OFF)
 message(STATUS "ENABLE_SIMMETRIX: ${ENABLE_SIMMETRIX}")
 option(ENABLE_OMEGA_H "Enable the Omega_h interface" OFF)
+option(PUMI_USE_OMEGA_H_VERSION "Specify the Omega_h version PUMI should use" 10.0.0)
 message(STATUS "ENABLE_OMEGA_H: ${ENABLE_OMEGA_H}")
 
 if(ENABLE_SIMMETRIX)
@@ -126,16 +130,17 @@ endif()
 if(ENABLE_OMEGA_H)
   # find the omega_h library
   set(SCOREC_USE_Omega_h_DEFAULT ${ENABLE_OMEGA_H})
-  set(Omega_h_REQUIRED_VERSION 9.0.0)
+  set(Omega_h_REQUIRED_VERSION ${PUMI_USE_OMEGA_H_VERSION})
   bob_public_dep(Omega_h)
 endif()
 
 if(ENABLE_CGNS)
-  find_package(CGNS)
+  set(SCOREC_USE_CGNS_DEFAULT ${ENABLE_CGNS})
+  bob_public_dep(CGNS)
+  #CGNS does not provide cmake targets :(
   include_directories(SYSTEM ${CGNS_INCLUDE_DIR})
-  #
-  find_package(HDF5) 
-  #
+  set(SCOREC_USE_HDF5_DEFAULT ${ENABLE_CGNS})
+  bob_public_dep(HDF5)
   add_definitions(-DHAVE_CGNS)
 endif()
 
@@ -155,6 +160,7 @@ add_subdirectory(pumi)
 add_subdirectory(ma)
 add_subdirectory(crv)
 add_subdirectory(spr)
+add_subdirectory(ree)
 add_subdirectory(sam)
 add_subdirectory(phasta)
 add_subdirectory(stk)
@@ -165,10 +171,23 @@ add_subdirectory(omega_h)
 add_library(core INTERFACE)
 target_link_libraries(core INTERFACE ${SCOREC_EXPORTED_TARGETS})
 if(ENABLE_CGNS)
-  target_link_libraries(core INTERFACE ${CGNS_LIBRARIES} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES})
+  target_link_libraries(core INTERFACE ${CMAKE_DL_LIBS}) #HDF5 uses dlopen
+  target_compile_features(core INTERFACE cxx_std_14)
+else()
+  target_compile_features(core INTERFACE cxx_std_11)
 endif()
 scorec_export_library(core)
 
+#check for mallinfo2
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU" OR ${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")
+  include(CheckCXXSymbolExists)
+  check_cxx_symbol_exists(mallinfo2 "malloc.h" PUMI_HAS_MALLINFO2)
+  if(PUMI_HAS_MALLINFO2)
+    target_compile_definitions(core INTERFACE -DPUMI_HAS_MALLINFO2)
+    target_compile_definitions(pcu PRIVATE -DPUMI_HAS_MALLINFO2)
+  endif()
+endif()
+
 if(BUILD_EXES)
   add_subdirectory(test)
 endif()

README.md

@@ -1,7 +1,5 @@
 # SCOREC Core #
 
-[![Coverity Scan Build Status](https://scan.coverity.com/projects/6698/badge.svg)](https://scan.coverity.com/projects/scorec-core)
-
 The SCOREC Core is a set of C/C++ libraries for unstructured mesh
 simulations on supercomputers.
 
@@ -26,6 +24,7 @@ For more information, start at our
 * MTH: Math containers and routines
 * CRV: Support for curved meshes with Bezier Shapes
 * PYCORE: Python Wrappers (see python_wrappers/README.md for build instructions)
+* REE: Residual based implicit error estimator
 
 ### How do I get set up? ###
 
@@ -53,3 +52,11 @@ For more information, start at our
 
 * If you have a usage question or have found a bug please post an [issue](https://github.com/SCOREC/core/issues).
 * Otherwise, email [Cameron Smith](https://www.scorec.rpi.edu/~cwsmith) and pumi@scorec.rpi.edu.
+
+### Citing PUMI
+
+If you use these tools, please cite the following paper:
+
+Daniel A. Ibanez, E. Seegyoung Seol, Cameron W. Smith, and Mark S. Shephard. 2016. PUMI: Parallel Unstructured Mesh Infrastructure. ACM Trans. Math. Softw. 42, 3, Article 17 (May 2016), 28 pages. DOI: https://doi.org/10.1145/2814935
+
+We would be happy to provide feedback on journal submissions using PUMI prior to publication.

apf/CMakeLists.txt

@@ -25,14 +25,21 @@ set(SOURCES
   apfShape.cc
   apfIPShape.cc
   apfHierarchic.cc
+  apfPolyBasis1D.cc
+  apfNedelec.cc
+  apfL2Shapes.cc
+  apfH1Shapes.cc
   apfVector.cc
   apfVectorElement.cc
   apfVectorField.cc
+  apfMixedVectorElement.cc
+  apfMixedVectorField.cc
   apfPackedField.cc
   apfNumbering.cc
   apfMixedNumbering.cc
   apfAdjReorder.cc
   apfVtk.cc
+  apfVtkPieceWiseFields.cc
   apfFieldData.cc
   apfTagData.cc
   apfCoordData.cc
@@ -98,12 +105,6 @@ target_link_libraries(apf
      mth
    )
 
-
-if(ENABLE_CGNS)
-  message(STATUS ${CGNS_LIBRARIES})
-  target_link_libraries(apf PRIVATE ${CGNS_LIBRARIES} ${HDF5_LIBRARIES} ${HDF5_HL_LIBRARIES})
-endif(ENABLE_CGNS)
-
 scorec_export_library(apf)
 
 bob_end_subdir()