Update master branch for first prototyp release (#2)

* Ir (#1)

* update script, needs refactoring

* update

* fix benchmark

* run at least for 10 ts

* rename GKOBase to GKOlduBase

* create ldu and Ldu matrices

* add ldu GKOCG and GKOBiCGStab

* add Ldu matrix

* add asymetric solver

* clean up

* start implementing of stopping criteria

* add common file

* update common

* inject c++14

* update

* use modified boxTurb16 case

* update benchmark

* keep CF constant

* start reuse sorting idx

* add IR solver, make sorting optional

* add line buffering, further cli args

* Add basic implementation of storing sorting idxs

* add IR implementation

* make sorting default

* store gkomatrix

* add common.C

* make executor an IOPtr

* prepare for forHLR test

* fix block clean for different block start syntax

* transfer to desktop

* hardcoded stored omp executor

* load different executor

* fix min/maxIter bug

* debug reference executor issue

* add clang format to keep formating constant

* fix cuda executor

* clean up

* clean up

* remove unneeded bash benchmark script

* format + prepare preconditioner

* run omp benchmarks for different number of threads

* make pressure solver settings compatible with OF8

* changed size of cases

* fix benchmarking folders

* set dns case boundaries to walls

* Fix several compiler warnings, reordering issues,

* create additional executor to force eager copy

* log succes state of run, keep retrying on failure at least for now

* move OpenFoam stopping criterion to separate file

* Use Foam switches to read dictionary entries

* Make export system a free function, clean logger and imports

* Move IterationLogger to common.H

* Fix execution if sysMatrix is not stored

if sysMatrix is not stored and thus the gkomatrix_ptr==NULL the system
matrix is recreated

* fix loop ctr

* Fix IR solver

- initialize IR with CG
- remove BJ for now

* Add Solver classes to distinguish between OF and GKO solvers, set time out for runs, fix log files

* fix formating

* Fix typos in smoothSolver class

* Fix int to unsingned long conversion

* Add initial CMakeLists file

* Add basic cmake files

* Fix return type warning

* move setting device_exec to separate function

* add third_party folder

* Update README.md

* Update README.md

* Use FOAM_ enviromental variables

* install libginkgo.so files along with libOGL.so if no external ginkgo is used

* Create a initial cmake.yml file

* clone and source OpenFOAM

* Fix non ascii symbol

* display OpenFOAM folder content

* show content of OpenFOAM-8 folder

* Update cmake.yml

* set OpenFOAM env variables manually

* add build badge

* Update Readme file

* remove Test folder since it is no longer needed

* re-enable exporting the system matrix, rhs and initial guess

* Read maxBlockSize from dictionary

* Rename controlDict_ member variable to dictionary_

* Make BiCGStabFactory consistent with CGFactory

* Clean unneeded comment

* Fix sorting bounds of sorting_idxs

* Update cmake.yml

* add basic travis file

* remove github actions file

* update .travis.yml

* fix OpenFOAM path

* update travis file

* compile full OpenFOAM for now

* install openmpi-dev

* install flexc++

* add OpenFOAM-dev to build matrix

* add fl dev

* install openfoam from the repository

* for now just test if OGL builds

* add build badge

* fix sourcing depending on of version

* switch to ubuntu 20.04

* make OGL_USE_EXTERNAL_GINKGO an option

* use --no-check-certificate since importing the key fails regularily

* pass --no-check-certificate to wget

* fix type of tmp_col_idxs and tmp_row_idxs

* sort the system matrix to avoid  cuda convergence issue

* add preconditioner to path

* remove benchmark script to separate repository

* fix find_package

* Fix find_package execution after external ginkgo was included #5

Co-authored-by: tcojean <[email protected]>

* Add OpenFOAM version shields

Co-authored-by: tcojean <[email protected]>

.clang-format

@@ -0,0 +1,108 @@
+---
+Language:        Cpp
+# BasedOnStyle:  Google
+AccessModifierOffset: -4
+AlignAfterOpenBracket: Align
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlines: Left
+AlignOperands:   true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakAfterReturnType: None
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: true
+BinPackParameters: true
+BraceWrapping:
+  AfterClass:      false
+  AfterControlStatement: false
+  AfterEnum:       false
+  AfterFunction:   true
+  AfterNamespace:  false
+  AfterObjCDeclaration: false
+  AfterStruct:     false
+  AfterUnion:      false
+  BeforeCatch:     false
+  BeforeElse:      false
+  IndentBraces:    false
+  SplitEmptyFunction: false
+  SplitEmptyRecord: false
+  SplitEmptyNamespace: false
+BreakBeforeBinaryOperators: None
+BreakBeforeBraces: Custom
+BreakBeforeInheritanceComma: false
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: false
+BreakConstructorInitializers: BeforeColon
+BreakAfterJavaFieldAnnotations: false
+BreakStringLiterals: true
+ColumnLimit:     80
+CommentPragmas:  '^ IWYU pragma:'
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: true
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+DisableFormat:   false
+ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros:
+  - foreach
+  - Q_FOREACH
+  - BOOST_FOREACH
+IncludeCategories:
+  - Regex:           '^<.*\.h>'
+    Priority:        1
+  - Regex:           '^<.*'
+    Priority:        2
+  - Regex:           '.*'
+    Priority:        3
+IncludeIsMainRegex: '([-_](test|unittest))?$'
+IndentCaseLabels: false
+IndentWidth:     4
+IndentWrappedFunctionNames: false
+JavaScriptQuotes: Leave
+JavaScriptWrapImports: true
+KeepEmptyLinesAtTheStartOfBlocks: false
+MacroBlockBegin: ''
+MacroBlockEnd:   ''
+MaxEmptyLinesToKeep: 2
+NamespaceIndentation: None
+ObjCBlockIndentWidth: 2
+ObjCSpaceAfterProperty: false
+ObjCSpaceBeforeProtocolList: false
+PenaltyBreakAssignment: 2
+PenaltyBreakBeforeFirstCallParameter: 1
+PenaltyBreakComment: 300
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Right
+ReflowComments:  true
+SortIncludes:    true
+SortUsingDeclarations: true
+SpaceAfterCStyleCast: false
+SpaceAfterTemplateKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 2
+SpacesInAngles:  false
+SpacesInContainerLiterals: true
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard:        Cpp11
+TabWidth:        8
+UseTab:          Never
+...
+

.travis.yml

@@ -0,0 +1,44 @@
+language: cpp
+sudo: true
+compiler:
+ - gcc
+
+dist: focal
+os:
+  - linux
+
+env:
+    - VERSION=8
+    - VERSION=7
+
+cache:
+  directories:
+  - $HOME/OpenFOAM
+
+
+addons:
+  apt:
+    update: true
+    packages:
+      - flexc++
+      - libfl-dev
+      - lcov
+      - libopenmpi-dev
+
+before_install:
+  - sudo sh -c "wget --no-check-certificate -O - https://dl.openfoam.org/gpg.key | apt-key add -"
+  - sudo add-apt-repository http://dl.openfoam.org/ubuntu
+  - sudo apt update
+
+install:
+  - sudo apt-get -y install openfoam$VERSION
+  - source /opt/openfoam$VERSION/etc/bashrc
+
+before_script:
+  - cmake --version
+  - mkdir build
+  - cd build
+  - cmake ..
+
+script:
+  - make -j4

CMakeLists.txt

@@ -0,0 +1,137 @@
+cmake_minimum_required(VERSION 3.9)
+
+project(OGL LANGUAGES C CXX DESCRIPTION "A wrapper for Ginkgo solver to provide GPGPU capabilities to OpenFOAM")
+
+if(NOT DEFINED ENV{FOAM_SRC})
+    message(FATAL_ERROR "You must source OpenFOAM before building OGL")
+endif()
+
+# Configuration options
+
+include(cmake/build_type_helpers.cmake)
+list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake/Modules/")
+
+include(CheckIncludeFileCXX)
+option(OGL_USE_EXTERNAL_GINKGO "Use external ginkgo" FALSE)
+
+include(CheckIncludeFileCXX)
+check_include_file_cxx(cxxabi.h GKO_HAVE_CXXABI_H)
+
+include(cmake/package_helpers.cmake)
+include(cmake/build_helpers.cmake)
+include(cmake/install_helpers.cmake)
+ginkgo_find_package(Ginkgo "Ginkgo::ginkgo" FALSE 1.4.0)
+
+add_subdirectory(third_party)
+
+# If ginkgo wasn't found so far look for the third_party installation
+if (NOT Ginkgo_FOUND)
+  find_package(Ginkgo 1.4.0 REQUIRED PATHS ${CMAKE_CURRENT_BINARY_DIR}/third_party/ginkgo/build/install/lib/cmake)
+endif()
+
+# To interface with ginkgo at least C++ 14 is needed
+set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_POSITION_INDEPENDENT_CODE ON)
+
+
+set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -Wall -O0 -ggdb")
+set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} \
+  -Wall -Wpedantic -Wextra -march=native -fopenmp -fPIC"
+  )
+
+if ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
+  set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+    set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} \
+      -fno-omit-frame-pointer \
+      -fsanitize=address"
+    )
+
+  set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} \
+    -fno-omit-frame-pointer \
+    -Rpass=loop-vectorize \
+      -ffast-math \
+      "
+      #-Rpass-analysis=loop-vectorize \
+      #-Rpass-missed=loop-vectorize \
+      )
+
+elseif ("${CMAKE_CXX_COMPILER_ID}" MATCHES "GNU")
+
+    add_definitions(-DWITH_GNU)
+
+    set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} \
+      --coverage\
+      -fprofile-arcs \
+      -fsanitize=address \
+      -ggdb3 \
+      -ftest-coverage"
+)
+
+    set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} \
+        -ffast-math \
+        -march=native  \
+        -ftree-vectorize \
+        -rdynamic \
+        "
+        # -fopt-info-vec-missed"
+        )
+endif()
+
+option(BUILD_SHARED_LIBS "Build shared library" ON)
+add_library(OGL  ""  )
+
+add_compile_definitions(
+  WM_LABEL_SIZE=32
+  WM_ARCH_OPTION=64
+  NoRepository
+  linux64
+  WM_DP
+  )
+
+target_sources(OGL
+  PRIVATE
+lduMatrix/GKOlduBase/GKOlduBase.C
+lduMatrix/GKOCG/GKOCG.C
+lduMatrix/GKOIR/GKOIR.C
+lduMatrix/GKOBiCGStab/GKOBiCGStab.C
+LduMatrix/GKOLduBase/GKOLduBase.C
+LduMatrix/GKOACG/GKOACG.C
+  PUBLIC
+lduMatrix/GKOlduBase/GKOlduBase.H
+lduMatrix/GKOCG/GKOCG.H
+lduMatrix/GKOIR/GKOIR.H
+lduMatrix/GKOBiCGStab/GKOBiCGStab.H
+LduMatrix/GKOLduBase/GKOLduBase.H
+LduMatrix/GKOACG/GKOACG.H
+  )
+
+
+target_include_directories(OGL
+  PUBLIC
+  $ENV{FOAM_SRC}/OpenFOAM/lnInclude
+  $ENV{FOAM_SRC}/meshTools/lnInclude
+  $ENV{FOAM_SRC}/finiteVolume/lnInclude
+  $ENV{FOAM_SRC}/OSspecific/POSIX/lnInclude
+    common/
+    lduMatrix/GKOlduBase
+    LduMatrix/GKOLduBase
+  )
+
+
+target_link_libraries(OGL
+  PUBLIC
+    Ginkgo::ginkgo
+  )
+
+install(TARGETS OGL 
+    DESTINATION $ENV{FOAM_USER_LIBBIN}
+    )
+
+if(NOT ${OGL_USE_EXTERNAL_GINKGO})
+install(DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/third_party/ginkgo/build/install/lib/
+    DESTINATION $ENV{FOAM_USER_LIBBIN}
+    )
+endif()
+