Merge branch 'develop' into feature/remove-boost-from-core

Author: andrew-hardin

.clang-format

@@ -0,0 +1,50 @@
+---
+BasedOnStyle: Mozilla
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortBlocksOnASingleLine: true
+AllowShortCaseLabelsOnASingleLine: true
+AllowShortFunctionsOnASingleLine: All
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakAfterReturnType: None
+AlwaysBreakAfterDefinitionReturnType: None
+AlwaysBreakTemplateDeclarations: true
+BinPackArguments: false
+BinPackParameters: false
+BreakBeforeBraces: Custom
+BraceWrapping:
+  AfterClass: true
+  AfterControlStatement: true
+  AfterEnum: true
+  AfterFunction: true
+  AfterNamespace: false
+  AfterObjCDeclaration: false
+  AfterStruct: true
+  AfterUnion: true
+  AfterExternBlock: true
+  BeforeCatch: true
+  BeforeElse: true
+  IndentBraces: false
+  SplitEmptyFunction: false
+  SplitEmptyRecord: false
+  SplitEmptyNamespace: false
+BreakBeforeInheritanceComma: false
+ColumnLimit: 120
+CompactNamespaces: false
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+Cpp11BracedListStyle: true
+DerivePointerAlignment: false
+IndentCaseLabels: true
+IndentWidth: 4
+KeepEmptyLinesAtTheStartOfBlocks: false
+Language: Cpp
+PointerAlignment: Left
+ReflowComments: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: Never
+SpaceInEmptyParentheses: false
+SpacesInContainerLiterals: false
+SpacesInParentheses: false
+SpacesInSquareBrackets: false
+Standard: Cpp11

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,36 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: "[bug]"
+labels: bug
+assignees: ''
+
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Log**
+If applicable, copy paste the relevant log output (please embed the text in a markdown code tag "\`\`\`" )
+
+**Desktop (please complete the following and other pertinent information):**
+ - OS: [e.g. win 10, osx, ]
+ - PopSift version: please specify if you are using a release version or your own build
+   - Binary version (if applicable) [e.g. 2019.1]
+   - Commit reference (if applicable) [e.g. 08ddbe2]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: "[request]"
+labels: feature request
+assignees: ''
+
+---
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/ISSUE_TEMPLATE/question_help.md

@@ -0,0 +1,29 @@
+---
+name: Question or help needed
+about: Ask question or for help for issues not related to program failures (e.g. "where I can find this feature", "my image is not recognized", "which parameter setting shall I use" etc...)
+title: "[question]"
+labels: type:question
+assignees: ''
+
+---
+
+**Describe the problem**
+A clear and concise description of what the problem is.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Dataset**
+If applicable, add a link or *few* images to help better understand where the problem may come from.
+
+**Log**
+If applicable, copy paste the relevant log output (please embed the text in a markdown code tag "\`\`\`" )
+
+**Desktop (please complete the following and other pertinent information):**
+ - OS: [e.g. win 10, osx, ]
+ - PopSift version: please specify if you are using a release version or your own build
+   - Binary version (if applicable) [e.g. 2019.1]
+   - Commit reference (if applicable) [e.g. 08ddbe2]
+
+**Additional context**
+Add any other context about the problem here.

.github/pull_request_template.md

@@ -0,0 +1,29 @@
+<!-- Checklist before submission:
+
+ - I have read the [contribution guidelines](../CONTRIBUTING.md).
+ - I have updated the documentation, if applicable.
+ - I have ensured that the change is tested somewhere.
+ - I have followed the prevailing code style (for history readability and limit conflicts for maintainance).
+
+-->
+## Description
+
+
+
+## Features list
+
+<!--
+- [ ] Feature one. Fix #XXX
+- [ ] Improve something else
+- [ ] Connect to #3 (to declare link to issues without closing it when the PR is merged).
+- [X] Add "X" when it is done.
+-->
+
+
+## Implementation remarks
+
+
+<!--
+Explain main implementation choices.
+It is also the right place to ask for feedback and help when you hesitate on the implementation.
+-->

.github/stale.yml

@@ -0,0 +1,28 @@
+# Number of days of inactivity before an issue becomes stale
+daysUntilStale: 120
+# Number of days of inactivity before a stale issue is closed
+daysUntilClose: 7
+# Issues or Pull Requests with these labels will never be considered stale. Set to `[]` to disable
+exemptLabels:
+  - "do not close"
+
+# Set to true to ignore issues in a project (defaults to false)
+exemptProjects: true
+
+# Set to true to ignore issues in a milestone (defaults to false)
+exemptMilestones: true
+
+# Set to true to ignore issues with an assignee (defaults to false)
+exemptAssignees: true
+
+# Label to use when marking an issue as stale
+staleLabel: stale
+# Comment to post when marking an issue as stale. Set to `false` to disable
+markComment: >
+  This issue has been automatically marked as stale because it has not had
+  recent activity. It will be closed if no further activity occurs. Thank you
+  for your contributions.
+# Comment to post when closing a stale issue. Set to `false` to disable
+closeComment: >
+  This issue is closed due to inactivity. Feel free to re-open if new information
+  is available.

.travis.yml

@@ -34,7 +34,7 @@ env:
     - POPSIFT_APP_INSTALL=${POPSIFT_APP_BUILD}/install
     # CMAKE
     # - CMAKE_URL="https://cmake.org/files/v3.6/cmake-3.6.1-Linux-x86_64.tar.gz"
-    - CMAKE_URL="https://cmake.org/files/v3.4/cmake-3.4.1-Linux-x86_64.tar.gz"
+    - CMAKE_URL="https://cmake.org/files/v3.13/cmake-3.13.5-Linux-x86_64.tar.gz"
     - CMAKE_ROOT=${TRAVIS_BUILD_DIR}/cmake
     - CMAKE_SOURCE=${CMAKE_ROOT}/source
     - CMAKE_INSTALL=${CMAKE_ROOT}/install

CHANGES.md

@@ -0,0 +1,22 @@
+# PopSift Changelog
+
+All notable changes to this project are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [Unreleased]
+
+### Added
+
+### Changed
+
+### Fixed
+
+### Removed
+
+## [1.0.0] - YYYY-MM-DD
+
+- Support for cuda 9 and 10
+- Support for RTX architecture
+- Optional grid filtering

CMakeLists.txt

@@ -1,16 +1,22 @@
 # CMake below 3.4 does not work with CUDA separable compilation at all
-cmake_minimum_required(VERSION 3.4)
+cmake_minimum_required(VERSION 3.12)
 
-project(PopSift VERSION 1.0.0)
+project(PopSift VERSION 1.0.0 LANGUAGES CXX)
+
+# Set build path as a folder named as the platform (linux, windows, darwin...) plus the processor type
+set(EXECUTABLE_OUTPUT_PATH "${PROJECT_BINARY_DIR}/${CMAKE_SYSTEM_NAME}-${CMAKE_SYSTEM_PROCESSOR}")
+set(LIBRARY_OUTPUT_PATH "${PROJECT_BINARY_DIR}/${CMAKE_SYSTEM_NAME}-${CMAKE_SYSTEM_PROCESSOR}")
+
+option(PopSift_BUILD_EXAMPLES "Build PopSift applications."  ON)
+option(PopSift_USE_NVTX_PROFILING     "Use CUDA NVTX for profiling." OFF)
+option(PopSift_ERRCHK_AFTER_KERNEL     "Synchronize and check CUDA error after every kernel." OFF)
+option(PopSift_USE_POSITION_INDEPENDENT_CODE "Generate position independent code." ON)
+option(PopSift_USE_GRID_FILTER "Switch off grid filtering to massively reduce compile time while debugging other things." ON)
+option(PopSift_USE_NORMF "The __normf function computes Euclidian distance on large arrays. Fast but stability is uncertain." OFF)
+option(PopSift_USE_TEST_CMD "Add testing step for functional verification" OFF)
+option(PopSift_NVCC_WARNINGS "Switch on several additional warning for CUDA nvcc" OFF)
+option(BUILD_SHARED_LIBS "Build shared libraries" ON)
 
-OPTION(PopSift_BUILD_EXAMPLES "Build PopSift applications."  ON)
-OPTION(PopSift_USE_NVTX_PROFILING     "Use CUDA NVTX for profiling." OFF)
-OPTION(PopSift_ERRCHK_AFTER_KERNEL     "Synchronize and check CUDA error after every kernel." OFF)
-OPTION(PopSift_USE_POSITION_INDEPENDENT_CODE "Generate position independent code." ON)
-OPTION(PopSift_USE_GRID_FILTER "Switch off grid filtering to massively reduce compile time while debugging other things." ON)
-OPTION(PopSift_USE_NORMF "The __normf function computes Euclidian distance on large arrays. Fast but stability is uncertain." OFF)
-OPTION(PopSift_USE_TEST_CMD "Add testing step for functional verification" OFF)
-OPTION(PopSift_NVCC_WARNINGS "Switch on several additional warning for CUDA nvcc" OFF)
 
 if(PopSift_USE_POSITION_INDEPENDENT_CODE)
   set(CMAKE_POSITION_INDEPENDENT_CODE ON)
@@ -26,14 +32,20 @@ else()
   message(STATUS "Building in ${CMAKE_BUILD_TYPE} configuration")
 endif()
 
-set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3")
-set(CMAKE_C_FLAGS_RELEASE   "${CMAKE_C_FLAGS_RELEASE}   -O3")
+# for some reason this line is necessary to propagate the standard to nvcc
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CUDA_STANDARD 11)
+set(CMAKE_CUDA_STANDARD_REQUIRED ON)
+
+# ==============================================================================
+# GNUInstallDirs CMake module
+# - Define GNU standard installation directories
+# - Provides install directory variables as defined by the GNU Coding Standards.
+# ==============================================================================
+include(GNUInstallDirs)
 
-# set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -G")
-# set(CMAKE_C_FLAGS_DEBUG   "${CMAKE_C_FLAGS_DEBUG}   -G")
 
 if(BUILD_SHARED_LIBS)
   message(STATUS "BUILD_SHARED_LIBS ON")
@@ -53,6 +65,9 @@ endif()
 # Require threads because of std::thread.
 find_package(Threads REQUIRED)
 
+###################
+#  CUDA
+###################
 find_package(CUDA 7.0 REQUIRED)
 
 if(NOT CUDA_FOUND)
@@ -136,9 +151,9 @@ if( ( CUDA_VERSION VERSION_EQUAL "7.5" ) OR ( CUDA_VERSION VERSION_GREATER "7.5"
 endif()
 
 if(PopSift_USE_NORMF AND CUDA_VERSION VERSION_GREATER "7.4")
-  set(HAVE_NORMF   1)
+  set(PopSift_HAVE_NORMF   1)
 else()
-  set(HAVE_NORMF   0)
+  set(PopSift_HAVE_NORMF   0)
 endif()
 
 if( ( CUDA_VERSION VERSION_EQUAL "9.0" ) OR ( CUDA_VERSION VERSION_GREATER "9.0") )
@@ -160,7 +175,9 @@ cuda_find_library_local_first(CUDA_CUDADEVRT_LIBRARY cudadevrt "\"cudadevrt\" li
 if(PopSift_USE_NVTX_PROFILING)
   # library required for NVTX profiling of the CPU
   cuda_find_library_local_first(CUDA_NVTX_LIBRARY nvToolsExt "NVTX library")
-  add_definitions(-DUSE_NVTX)
+  set(PopSift_USE_NVTX 1)
+else()
+  set(PopSift_USE_NVTX 0)
 endif()
 
 add_subdirectory(src)
@@ -175,5 +192,27 @@ CONFIGURE_FILE(
   "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
   IMMEDIATE @ONLY)
 ADD_CUSTOM_TARGET(uninstall
-  "${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake") 
-
+  "${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
+
+
+######################################
+# SUMMARY
+######################################
+message("\n")
+message("******************************************")
+message("Building configuration:\n")
+message(STATUS "PopSift version: " ${PROJECT_VERSION})
+message(STATUS "Build type: " ${CMAKE_BUILD_TYPE})
+message(STATUS "Build Shared libs: " ${BUILD_SHARED_LIBS})
+message(STATUS "Build examples: " ${PopSift_BUILD_EXAMPLES})
+message(STATUS "Generate position independent code: " ${PopSift_USE_POSITION_INDEPENDENT_CODE})
+message(STATUS "Use CUDA NVTX for profiling: " ${PopSift_USE_NVTX_PROFILING})
+message(STATUS "Synchronize and check CUDA error after every kernel: " ${PopSift_ERRCHK_AFTER_KERNEL})
+message(STATUS "Grid filtering: " ${PopSift_USE_GRID_FILTER})
+message(STATUS "Testing step: " ${PopSift_USE_TEST_CMD})
+message(STATUS "Link with static Boost libraries: " ${PopSift_BOOST_USE_STATIC_LIBS})
+message(STATUS "Additional warning for CUDA nvcc: " ${PopSift_NVCC_WARNINGS})
+message(STATUS "Compiling for CUDA CCs: ${PopSift_CUDA_CC_LIST}")
+message(STATUS "Install path: " ${CMAKE_INSTALL_PREFIX})
+message("\n******************************************")
+message("\n")