Merge pull request #4 from CEED/fms-v0.2-dev

Final changes for FMS v0.2

.github/workflows/build-and-test.yaml

@@ -0,0 +1,69 @@
+# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
+# the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
+# reserved. See files LICENSE and NOTICE for details.
+#
+# This file is part of CEED, a collection of benchmarks, miniapps, software
+# libraries and APIs for efficient high-order finite element and spectral
+# element discretizations for exascale applications. For more information and
+# source code availability see http://github.com/ceed.
+#
+# The CEED research is supported by the Exascale Computing Project (17-SC-20-SC)
+# a collaborative effort of two U.S. Department of Energy organizations (Office
+# of Science and the National Nuclear Security Administration) responsible for
+# the planning and preparation of a capable exascale ecosystem, including
+# software, applications, hardware, advanced system engineering and early
+# testbed platforms, in support of the nation's exascale computing imperative.
+
+name: Build and test
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+env:
+  BUILD_C_FLAGS: -Wall -Wextra -pedantic -Werror
+  BUILD_CXX_FLAGS: -Wall -Wextra -pedantic -Werror
+
+jobs:
+  build-and-test:
+    runs-on: ${{matrix.os}}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        build-type: [Debug, Release]
+    name: ${{matrix.os}}-${{matrix.build-type}}
+
+    steps:
+    - uses: actions/checkout@v2
+      with:
+        submodules: recursive
+
+    - name: Configure
+      run: |
+        cmake \
+          -B ${{github.workspace}}/build \
+          -DCMAKE_BUILD_TYPE=${{matrix.build-type}} \
+          -DFMS_ENABLE_TESTS=ON \
+          -DCMAKE_C_FLAGS="$BUILD_C_FLAGS" \
+          -DCMAKE_CXX_FLAGS="$BUILD_CXX_FLAGS" \
+          -DCMAKE_INSTALL_PREFIX=${{github.workspace}}/install \
+          -DCMAKE_VERBOSE_MAKEFILE=ON
+
+    - name: Build
+      run: |
+        cmake \
+          --build ${{github.workspace}}/build \
+          --config ${{matrix.build-type}}
+
+    - name: Install
+      run: |
+        cmake \
+          --build ${{github.workspace}}/build \
+          --config ${{matrix.build-type}} \
+          --target install
+
+    - name: Test
+      working-directory: ${{github.workspace}}/build
+      run: ctest -C ${{matrix.build-type}} --output-on-failure

.github/workflows/check-style.yaml

@@ -0,0 +1,37 @@
+# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
+# the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
+# reserved. See files LICENSE and NOTICE for details.
+#
+# This file is part of CEED, a collection of benchmarks, miniapps, software
+# libraries and APIs for efficient high-order finite element and spectral
+# element discretizations for exascale applications. For more information and
+# source code availability see http://github.com/ceed.
+#
+# The CEED research is supported by the Exascale Computing Project (17-SC-20-SC)
+# a collaborative effort of two U.S. Department of Energy organizations (Office
+# of Science and the National Nuclear Security Administration) responsible for
+# the planning and preparation of a capable exascale ecosystem, including
+# software, applications, hardware, advanced system engineering and early
+# testbed platforms, in support of the nation's exascale computing imperative.
+
+name: Check style
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  check-style:
+    runs-on: ubuntu-20.04
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v2
+
+    - name: Get astyle
+      run: sudo apt-get install astyle
+
+    - name: Check style
+      run: ./apply-style.sh

.gitignore

@@ -6,4 +6,4 @@ data/
 *.out
 
 # IDE directories
-.vscode/
+.vscode/

CHANGELOG

@@ -0,0 +1,24 @@
+                            ███████ ███    ███ ███████
+                            ██      ████  ████ ██
+                            █████   ██ ████ ██ ███████
+                            ██      ██  ██  ██      ██
+                            ██      ██      ██ ███████
+
+                 CEED's high-order Field and Mesh Specification
+
+
+Version 0.2, released on Sep 10, 2021
+=====================================
+
+- Added support for writing and reading FmsDataCollections both in ASCII and
+  binary format via Conduit.
+
+- Visualization for FMS files is available in VisIt v3.2, visit.llnl.gov.
+
+- Added regression and code styling.
+
+
+Version 0.1, released on Jul 8, 2018
+====================================
+
+- Initial release.

CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (c) 2017, Lawrence Livermore National Security, LLC. Produced at
+# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
 # the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
 # reserved. See files LICENSE and NOTICE for details.
 #
@@ -17,8 +17,9 @@
 # We use the C_STANDARD target property introduced in CMake 3.1
 cmake_minimum_required (VERSION 3.1)
 
-# Project name
-project(FMS VERSION 0.1 LANGUAGES C)
+# Project name and version.
+# The version is also defined in the files: fms.h and Doxyfile.
+project(FMS VERSION 0.2 LANGUAGES C)
 
 # Optional demo - see examples/README.md for more information
 option(FMS_ENABLE_DEMO "Enable the PUMI + MFEM demo" OFF)
@@ -37,7 +38,8 @@ endif()
 # Setup thirdparty dependencies
 # Optional conduit implementation for IO functions
 if(CONDUIT_DIR)
-  find_package(Conduit 0.5.1 REQUIRED
+  enable_language(CXX)
+  find_package(Conduit 0.7.1 REQUIRED
     HINTS ${CONDUIT_DIR}
     NO_DEFAULT_PATH)
   set(FMS_HAVE_CONDUIT TRUE)
@@ -67,9 +69,9 @@ if(FMS_ENABLE_DEMO)
   endif()
 
   if(PUMI_DIR)
-    find_package(SCOREC 2.1.0 REQUIRED 
-      CONFIG 
-      HINTS ${PUMI_DIR} 
+    find_package(SCOREC 2.1.0 REQUIRED
+      CONFIG
+      HINTS ${PUMI_DIR}
       NO_DEFAULT_PATH)
     set(FMS_HAVE_PUMI TRUE)
     message(STATUS "Demo using PUMI: ${SCOREC_DIR}")

Doxyfile

@@ -38,7 +38,7 @@ PROJECT_NAME           = "FMS"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER         = v0.1
+PROJECT_NUMBER         = v0.2
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -2034,7 +2034,7 @@ PERLMOD_MAKEVAR_PREFIX =
 # C-preprocessor directives found in the sources and include files.
 # The default value is: YES.
 
-ENABLE_PREPROCESSING   = NO
+ENABLE_PREPROCESSING   = YES
 
 # If the MACRO_EXPANSION tag is set to YES, doxygen will expand all macro names
 # in the source code. If set to NO, only conditional compilation will be

LICENSE

@@ -1,6 +1,6 @@
 BSD 2-Clause License
 
-Copyright (c) 2017 Lawrence Livermore National Security, LLC.
+Copyright (c) 2021 Lawrence Livermore National Security, LLC.
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -1,7 +1,17 @@
-# FMS: CEED's high-order Field and Mesh Specification
+                            ███████ ███    ███ ███████
+                            ██      ████  ████ ██
+                            █████   ██ ████ ██ ███████
+                            ██      ██  ██  ██      ██
+                            ██      ██      ██ ███████
+
+                 CEED's high-order Field and Mesh Specification
+
 
 [![License](https://img.shields.io/badge/License-BSD%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
 [![Documentation](https://codedocs.xyz/CEED/FMS.svg)](https://codedocs.xyz/CEED/FMS/)
+[![Build and Test (GH Actions)](https://github.com/CEED/FMS/actions/workflows/build-and-test.yaml/badge.svg?branch=master)](https://github.com/CEED/FMS/actions?query=workflow%3Abuild-and-test)
+[![Build and Test (GH Actions)](https://github.com/CEED/FMS/actions/workflows/check-style.yaml/badge.svg?branch=master)](https://github.com/CEED/FMS/actions?query=workflow%3Acheck-style)
+
 
 ## High-Order Data Description
 
@@ -16,6 +26,9 @@ solutions and meshes, as those depicted below, as well as non-standard finite
 elements, such as Nedelec and Raviart-Thomas elements. See the [FMS
 documentation](doc/fms.md) for more details.
 
+Initial support for the FMS file formats is available in
+[VisIt](https://visit.llnl.gov/) version 3.2.
+
 ![High-order mesh and solution](doc/triple-pt-2x2.png)
 
 The following diagram illustrates the current and planned components of FMS.
@@ -42,7 +55,8 @@ exchange and high-order visualization and data analysis.
 
 ## Building
 
-You can get started with the default build configuration using the command line listed below. Checkout the [build documentation](doc/build.md) for more info.
+You can get started with the default build configuration using the command line
+listed below. Checkout the [build documentation](doc/build.md) for more info.
 
 ```console
 mkdir build
@@ -61,7 +75,7 @@ or by leaving a comment in the [issue tracker](https://github.com/CEED/FMS/issue
 The following copyright applies to each file in the CEED software suite, unless
 otherwise stated in the file:
 
-> Copyright (c) 2017, Lawrence Livermore National Security, LLC. Produced at the
+> Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at the
 > Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights reserved.
 
 See files LICENSE and NOTICE for details.

apply-style.sh

@@ -0,0 +1,72 @@
+#!/bin/bash
+
+# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
+# the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
+# reserved. See files LICENSE and NOTICE for details.
+#
+# This file is part of CEED, a collection of benchmarks, miniapps, software
+# libraries and APIs for efficient high-order finite element and spectral
+# element discretizations for exascale applications. For more information and
+# source code availability see http://github.com/ceed.
+#
+# The CEED research is supported by the Exascale Computing Project (17-SC-20-SC)
+# a collaborative effort of two U.S. Department of Energy organizations (Office
+# of Science and the National Nuclear Security Administration) responsible for
+# the planning and preparation of a capable exascale ecosystem, including
+# software, applications, hardware, advanced system engineering and early
+# testbed platforms, in support of the nation's exascale computing imperative.
+
+function main()
+{
+  cd $(dirname "$0")
+  fms_astyle_file="fms.astylerc"
+  if [[ ! -r "${fms_astyle_file}" ]]; then
+    echo "FMS's astyle format file not found: '${fms_astyle_file}'. Stop."
+    exit 21
+  fi
+
+  find_astyle
+
+  local old_IFS="${IFS}"
+  IFS=$'\n'
+  format_files=($(git ls-files "*.[ch]" "*.[ch]pp"))
+  if [[ "$?" -ne 0 ]]; then
+    echo "Error getting list of C/C++ source files from Git. Stop."
+    exit 22
+  fi
+  IFS="${old_IFS}"
+
+  if ${astyle_bin} --options="${fms_astyle_file}" "${format_files[@]}" | \
+     grep "Formatted"; then
+    printf "\nPlease make sure the changes are committed.\n\n"
+    return 1
+  else
+    printf "All source files are properly formatted.\n"
+  fi
+  return 0
+} # end of function 'main'
+
+function find_astyle()
+{
+  astyle_req_version="Artistic Style Version 3.1"
+  astyle_bin_list=("${ASTYLE_BIN:-astyle}" astyle-3.1)
+  for astyle_bin in "${astyle_bin_list[@]}"; do
+    if ! command -v "${astyle_bin}" > /dev/null 2>&1; then
+      continue
+    fi
+    astyle_version="$("${astyle_bin}" --version)"
+    if [[ "${astyle_version}" != "${astyle_req_version}" ]]; then
+      continue
+    fi
+    return 0
+  done
+  echo "Required astyle version not found: '${astyle_req_version}'."
+  printf "Astyle commands tried:"
+  printf " '%s'" "${astyle_bin_list[@]}"
+  printf ".\n"
+  exit 23
+} # end of function 'find_astyle'
+
+
+# Invoke the 'main' function
+main "$@"

doc/build.md

@@ -60,4 +60,4 @@ cd build
 cmake -DFMS_DIR=*fms/install/prefix* ..
 make
 ./main
-```
+```

examples/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (c) 2020, Lawrence Livermore National Security, LLC. Produced at
+# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
 # the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
 # reserved. See files LICENSE and NOTICE for details.
 #

examples/demo_pumi_mfem/CMakeLists.txt

@@ -1,4 +1,4 @@
-# Copyright (c) 2020, Lawrence Livermore National Security, LLC. Produced at
+# Copyright (c) 2021, Lawrence Livermore National Security, LLC. Produced at
 # the Lawrence Livermore National Laboratory. LLNL-CODE-734707. All Rights
 # reserved. See files LICENSE and NOTICE for details.
 #

examples/demo_pumi_mfem/demo_pumi_mfem.cpp

@@ -123,7 +123,7 @@ int main(int argc, char *argv[]) {
   }
 
   // Edges
-  FmsInt nvtxs = 2;
+  const FmsInt nvtxs = 2;
   FmsInt num_edges = 0;
   int edge[nvtxs];
   itr = pumi_mesh->begin(1);
@@ -157,7 +157,7 @@ int main(int argc, char *argv[]) {
   pumi_mesh->end(itr);
 
   // Define Face based on edge Id's
-  FmsInt nedges = 3;
+  const FmsInt nedges = 3;
   int face[nedges];
   int num_triangles = 0;
   itr = pumi_mesh->begin(2);
@@ -191,7 +191,7 @@ int main(int argc, char *argv[]) {
   pumi_mesh->end(itr);
 
   // Define Elem based on face Id's
-  FmsInt nfaces = 4;
+  const FmsInt nfaces = 4;
   FmsEntityReordering EntReord;
   int tetOrd[4] = {0,1,3,2}; // PUMI order for tet element faces
   EntReord[FMS_TETRAHEDRON] = &tetOrd[0];

examples/include-fms/main.cpp

@@ -6,4 +6,4 @@ int main(int, char**) {
   auto a = FmsMeshConstruct(&m);
   printf("Hello %d\n", a);
   return a;
-}
+}