GSOC post-credits scene (#30)

* [DOCS]: ReadMe update * [Windows]: Fixing [Windows build failer](#25) * [DOCS]: README.md bugfix * [WINDOWS]: fixing 'long long' Warning!!! "Acceleration is not possible" errors (gone from 50% unit test sucsess to 79%) The following tests FAILED: 4 - testFullRing (Failed) 6 - testInducedVoltage (Failed) 7 - testInducedVoltageFreq (Failed) 9 - testLHCFlatSpectrum (Failed) 23 - testTC5_Wake_impedance (Failed) * [Project]: Added cmake options for setting paths of data files for test and demo. Required for CLion IDE compilation from randomly named folders. Default "../demos/input_files" and "../unit-tests/references" * [Configuration]: debug options printer added * [MERGE]: tests fix * [Merge]: Code cleanup * [Merge]: update TEST_FILES use. * [Configuration]: added support for embedding demo and test reference data path's * [Merge]: minor bug fix * [Windows]: MinGW, OpenCL, boost.compute support Started documentation * [Documentation]: created benchmarks browser (html/js, 2d and 3d), described build and configuration process on Windows * [Windows]: Random number generator made similar to linux default * [Merge]: added changes from main brunch added pre optimization benchmarks showcasing OpenCL use * [CI]: OpenCL install * [CI]: Linux users now can provide sdk paths alike -DOPENCL_SDK_PATH=/usr/lib/x86_64-linux-gnu/ * [CI]: Minor bug fix * [CI]: minor fix * [CI]: minor fix * [Speed]: omega_RF indexes Added hybrilit pre-optemization release benchmarks * [Speed]: voltageVec and RfP->voltage transposition merge * [Speed]: dphiVec and RfP->phi_RF transposition merger * [Speed]: Updated benchmark data * [Benchmarks]: sinus result holder moved into iteration, specified arguments of TC1 benchmark * [Docs]: created stubs for planned content * [Speed]: Atomic histogram * [Speed] speed for TC1 on cpu final. x2.2 on i7. * [CI]: travis bug fix speed up HDD reads * [CI] minor CI boost compilation fix * [CI]: Travis OpenCL fixes * [Speed]: final CPU optimisation for TC1 * [Docs]: updated benchmark visualization * [Docs]: Benchmark visualization code and samples * [Docs]: added FAQ * [CI]: Fixing travis * [CI]: Fixing Travis * [CI]: Fixing TravisCI * [CI]: fixing AppVeyor * [Architecture]: Revert copy in kick * [CI]: fixing last unit-test * [CI]: fixing benchmarks build * [Benchmarks]: CPU and GPU examples added * [CI]: fixing appveyor * [CI]: appveyor.yml fix * [CI]: fixing appveyor OpenCl * [OpenCL]: made benchmark the only thing dependant on it * [CI]: fixed ifdefs
blond-org · Aug 29, 2016 · 86ed265 · 86ed265
1 parent 8984186
commit 86ed265
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Showing 56 changed files with 6,223 additions and 852 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,7 +1,7 @@
 *~
 *report
 *documentation
-build/*
+build*
 external/install/*
 external/build/*
 .idea*
diff --git a/.travis.yml b/.travis.yml
@@ -1,4 +1,6 @@
-sudo: false
+#note: OpenCL instructions taken from https://github.com/peastman/openmm/blob/a7ce5784bc1d728ef7088c10308fa61b9c87e1a9/.travis.yml
+sudo: required
+dist: trusty
 language: cpp
 
 os:
@@ -12,20 +14,23 @@ env:
     - BUILD_TYPE=Release
   global:
     - secure: 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
-
+    - OPENCL=true
+    - CUDA=false
+    - CMAKE_FLAGS="
+           -DOPENCL_INCLUDE_DIR=$HOME/AMDAPPSDK/include
+           -DOPENCL_LIBRARY=$HOME/AMDAPPSDK/lib/x86_64/libOpenCL.so"
 addons:
   apt:
     sources:
       - ubuntu-toolchain-r-test
-      - george-edison55-precise-backports
       - libreoffice/libreoffice-4-2
     packages:
       - cmake
       - cmake-data
       - gcc-4.8
       - g++-4.8
+      - opencl-headers
       - valgrind
-      - gcov-4.8
       - lcov
       - doxygen
       - graphviz
@@ -40,11 +45,23 @@ cache:
 before_install:
   - export CC=/usr/bin/gcc-4.8
   - export CXX=/usr/bin/g++-4.8
+  - if [[ "$OPENCL" == "true" ]]; then
+      wget https://jenkins.choderalab.org/userContent/AMD-APP-SDKInstaller-v3.0.130.135-GA-linux64.tar.bz2;
+      tar -xjf AMD-APP-SDK*.tar.bz2;
+      AMDAPPSDK=${HOME}/AMDAPPSDK;
+      export OPENCL_VENDOR_PATH=${AMDAPPSDK}/etc/OpenCL/vendors;
+      mkdir -p ${OPENCL_VENDOR_PATH};
+      sh AMD-APP-SDK*.sh --tar -xf -C ${AMDAPPSDK};
+      echo libamdocl64.so > ${OPENCL_VENDOR_PATH}/amdocl64.icd;
+      export LD_LIBRARY_PATH=${AMDAPPSDK}/lib/x86_64:${LD_LIBRARY_PATH};
+      chmod +x ${AMDAPPSDK}/bin/x86_64/clinfo;
+      ${AMDAPPSDK}/bin/x86_64/clinfo;
+    fi
 
 before_script:
   - mkdir build
   - cd build
-  - cmake -DWITH_FFTW=True -DWITH_GOOGLETEST=True -DWITH_BENCHMARK=True -DCMAKE_BUILD_TYPE=$BUILD_TYPE ..
+  - cmake -DWITH_FFTW=True -DWITH_GOOGLETEST=True -DWITH_BENCHMARK=True  -DBUILD_EXTERNALS=True -DOPENCL_SDK_PATH=$HOME/AMDAPPSDK -DCMAKE_BUILD_TYPE=$BUILD_TYPE -DARCHITECTURE="x64" ..
 
 script:
   - cmake --build . -- -j2 VERBOSE=1

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -11,6 +11,7 @@ include(ExternalProject)
 include(ProcessorCount)
 include(CTest)
 
+
 # Code editors usabilety feature
 set_property(GLOBAL PROPERTY USE_FOLDERS On)
 set(CMAKE_CONFIGURATION_TYPES "Debug;Release" CACHE STRING "We have optemized configuration for Debug and Release configurations")
@@ -21,14 +22,27 @@ set(SHARED_LIBRARY_ENABLED "True")
 set(EXTERNAL_INSTALL_DIR ${PROJECT_SOURCE_DIR}/external/install)
 set(TEST_ENABLED "True" CACHE STRING "Cerate unit-test projects")
 set(BENCHMARK_ENABLED "True" CACHE STRING "Cerate benchmark projects")
-set(ARCHITECTURE "x64" CACHE STRING "Set architecture 'x86' or 'x32'") # todo: find usages and  fix comment
-if(NOT ABSOLUTE_DATA_PATHS)
-   set(DATAFILES_DIR_DEMOS "../demos/input_files" CACHE STRING "Set demos input files path")
-   set(DATAFILES_DIR_TESTS "../unit-tests/references" CACHE STRING "Set unit-tests input files path")
+
+if (NOT DEFINED ARCHITECTURE)
+    set(ARCHITECTURE "Default" CACHE STRING "Set architecture 'x86' or 'x64'") # todo: find usages and  fix comment
+    # Project architecture
+    if ((${CMAKE_GENERATOR} MATCHES ".*(64).*") OR (${CMAKE_SIZEOF_VOID_P} MATCHES ".*(64).*"))
+        set(ARCHITECTURE "x64")
+        message(STATUS "architecture: ${ARCHITECTURE} detected from (${CMAKE_GENERATOR} and ${CMAKE_SIZEOF_VOID_P}) ")
+    endif ()
+endif ()
+
+
+set(WITH_COMPUTE "False" CACHE STRING "Should Build Boost.Compute library from source")
+set(BOOST_ROOT ${PROJECT_SOURCE_DIR}/external/build/boost CACHE STRING "Boost Library root")
+
+if (NOT ABSOLUTE_DATA_PATHS)
+    set(DATAFILES_DIR_DEMOS "../demos/input_files" CACHE STRING "Set demos input files path")
+    set(DATAFILES_DIR_TESTS "../unit-tests/references" CACHE STRING "Set unit-tests input files path")
 else ()
-   set(DATAFILES_DIR_DEMOS "${CMAKE_CURRENT_LIST_DIR}/demos/input_files" CACHE STRING "Set demos input files path")
-   set(DATAFILES_DIR_TESTS "${CMAKE_CURRENT_LIST_DIR}/unit-tests/references" CACHE STRING "Set unit-tests input files path")
-endif()
+    set(DATAFILES_DIR_DEMOS "${CMAKE_CURRENT_LIST_DIR}/demos/input_files" CACHE STRING "Set demos input files path")
+    set(DATAFILES_DIR_TESTS "${CMAKE_CURRENT_LIST_DIR}/unit-tests/references" CACHE STRING "Set unit-tests input files path")
+endif ()
 
 # Packages
 set(EXTERNAL_INSTALL_DIR ${PROJECT_SOURCE_DIR}/external/install CACHE STRING "External libraries installation folder (with subfolders lib and include)")
@@ -50,7 +64,6 @@ if (NOT DEFINED WITH_GOOGLETEST)
     endif ()
 endif ()
 
-set(GOOGLETEST_ROOT ${PROJECT_SOURCE_DIR}/external/googletest/ CACHE STRING "Google Test source root")
 
 if (NOT DEFINED WITH_BENCHMARK)
     if (MSVC)
@@ -60,7 +73,9 @@ if (NOT DEFINED WITH_BENCHMARK)
     endif ()
 endif ()
 
-set(BENCHMARK_ROOT ${PROJECT_SOURCE_DIR}/external/benchmark CACHE STRING "Google Benchmark Library root")
+set(GOOGLETEST_ROOT ${PROJECT_SOURCE_DIR}/external/build/googletest/ CACHE STRING "Google Test source root")
+set(BENCHMARK_ROOT ${PROJECT_SOURCE_DIR}/external/build/benchmark CACHE STRING "Google Benchmark Library root")
+
 
 set(WITH_FORMAT "False" CACHE STRING "Clang-Format all project files on build (requires clang-format)")
 
@@ -74,18 +89,12 @@ if (NOT N EQUAL 0)
     set(ctest_test_args ${ctest_test_args} PARALLEL_LEVEL ${N})
 endif ()
 
-# Project architecture
-set(ARCHITECTURE "Default" CACHE STRING "Two architectures avaliable 'Dafault' and 'x64', it is impartant for external libraries")
-if ((${CMAKE_GENERATOR} MATCHES ".*(64).*") OR (${CMAKE_SIZEOF_VOID_P} MATCHES ".*(64).*"))
-    set(ARCHITECTURE "x64")
-    message(STATUS "architecture: ${ARCHITECTURE} detected from (${CMAKE_GENERATOR} and ${CMAKE_SIZEOF_VOID_P}) ")
-endif ()
-
 #Compiler, Linker options
 #Compiler settings
 #MSVC vs Other
+
+add_definitions(-D_USE_MATH_DEFINES) #needed for VDT
 if (MSVC)
-    add_definitions(-D_USE_MATH_DEFINES) #needed for VDT
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /bigobj -Zm500  /MP${N} /openmp /fp:precise ")
     set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE}  /GR-")
 else ()
@@ -96,18 +105,19 @@ else ()
     endif ()
 
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -std=c++11 -fopenmp -Wall -pedantic -fno-rtti -Wunused -ffast-math")
-    set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -g3") #-fsanitize=address -fno-omit-frame-pointer ")
+    set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -g3 -O0 -fno-omit-frame-pointer -fprofile-arcs -ftest-coverage") # -fsanitize=address
     set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -march=native")
 
     if (TEST_ENABLED STREQUAL "True")
+        LIST(APPEND LIBRARIES gcov)
         set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")
         set(CMAKE_EXE_LINKER_FLAGS_DEBUG "${CMAKE_EXE_LINKER_FLAGS_DEBUG} --coverage")
     else ()
         message(STATUS "code test coveredge is enabeled only in Debug mode")
     endif ()
 
     if (USE_FFTW_OMP)
-        set(LIBRARIES ${LIBRARIES} fftw3_omp)
+        LIST(APPEND LIBRARIES fftw3_omp)
         set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DUSE_FFTW_OMP")
     endif ()
 endif ()
@@ -160,54 +170,60 @@ if ((NOT WITH_BENCHMARK) AND BENCHMARK_ENABLED)
     find_library(BENCHMARK_LIB NAME benchmark REQUIRED)
 endif ()
 
-if (NOT (EXISTS ${PROJECT_SOURCE_DIR}/external/build))
-    execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory ${PROJECT_SOURCE_DIR}/external/build)
-else ()
-    execute_process(COMMAND ${CMAKE_COMMAND} -E remove_directory ${PROJECT_SOURCE_DIR}/external/build/)
-    execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory ${PROJECT_SOURCE_DIR}/external/build)
-endif ()
+if (BUILD_EXTERNALS)
+    if (NOT (EXISTS ${PROJECT_SOURCE_DIR}/external/build))
+        execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory ${PROJECT_SOURCE_DIR}/external/build)
+    else ()
+        execute_process(COMMAND ${CMAKE_COMMAND} -E remove_directory ${PROJECT_SOURCE_DIR}/external/build/)
+        execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory ${PROJECT_SOURCE_DIR}/external/build)
+    endif ()
+
+    message(STATUS "Building required started...")
+
+    execute_process(
+            COMMAND ${CMAKE_COMMAND}
+            #options
+            -DWITH_FFTW=${WITH_FFTW}
+            -DWITH_BENCHMARK=${WITH_BENCHMARK}
+            -DWITH_GOOGLETEST=${WITH_GOOGLETEST}
+            -DWITH_COMPUTE=${WITH_COMPUTE}
+            #destinations
+            -DINSTALL_DIR=${EXTERNAL_INSTALL_DIR}
+            -DCOMPILE_FLAGS=${COMPILE_FLAGS}
+            -DGOOGLETEST_ROOT=${GOOGLETEST_ROOT}
+            -DBENCHMARK_ROOT=${BENCHMARK_ROOT}
+            -DGOOGLETEST_ROOT=${GOOGLETEST_ROOT}
+            -DBOOST_ROOT=${BOOST_ROOT}
+            #forward all collected compilation arguments
+            -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} # relevant only for Make-like build files
+            -DCMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}
+            -DCMAKE_CXX_FLAGS_DEBUG=${CMAKE_CXX_FLAGS_DEBUG}
+            -DCMAKE_CXX_FLAGS_RELEASE=${CMAKE_CXX_FLAGS_RELEASE}
+            -DCMAKE_EXE_LINKER_FLAGS_RELEASE=${CMAKE_EXE_LINKER_FLAGS_RELEASE}
+            -DCMAKE_EXE_LINKER_FLAGS_DEBUG=${CMAKE_EXE_LINKER_FLAGS_DEBUG}
+            -v
+            -G "${CMAKE_GENERATOR}"
+            ${PROJECT_SOURCE_DIR}/external/
+            WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/external/build
+    )
 
-message(STATUS "Building required started...")
-
-execute_process(
-        COMMAND ${CMAKE_COMMAND}
-        #options
-        -DWITH_FFTW=${WITH_FFTW}
-        -DWITH_BENCHMARK=${WITH_BENCHMARK}
-        -DWITH_GOOGLETEST=${WITH_GOOGLETEST}
-        #destinations
-        -DINSTALL_DIR=${EXTERNAL_INSTALL_DIR}
-        -DCOMPILE_FLAGS=${COMPILE_FLAGS}
-        -DGOOGLETEST_ROOT=${GOOGLETEST_ROOT}
-        -DBENCHMARK_ROOT=${BENCHMARK_ROOT}
-        -DGOOGLETEST_ROOT=${GOOGLETEST_ROOT}
-        #forward all collected compilation arguments
-        -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} # relevant only for Make-like build files
-        -DCMAKE_CXX_FLAGS=${CMAKE_CXX_FLAGS}
-        -DCMAKE_CXX_FLAGS_DEBUG=${CMAKE_CXX_FLAGS_DEBUG}
-        -DCMAKE_CXX_FLAGS_RELEASE=${CMAKE_CXX_FLAGS_RELEASE}
-        -DCMAKE_EXE_LINKER_FLAGS_RELEASE=${CMAKE_EXE_LINKER_FLAGS_RELEASE}
-        -DCMAKE_EXE_LINKER_FLAGS_DEBUG=${CMAKE_EXE_LINKER_FLAGS_DEBUG}
-        -v
-        -G "${CMAKE_GENERATOR}"
-        ${PROJECT_SOURCE_DIR}/external/
-        WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/external/build
-)
-
-message(STATUS "building external projects begins")
-execute_process(
-        COMMAND cmake --build . --config Release
-        WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/external/build
-)
-if (WIN32 AND NOT MINGW)
+    message(STATUS "building external projects begins")
     execute_process(
-            COMMAND cmake --build . --config Debug
+            COMMAND cmake --build . --config Release
             WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/external/build
     )
+
+    if (WIN32 AND NOT MINGW)
+        execute_process(
+                COMMAND cmake --build . --config Debug
+                WORKING_DIRECTORY ${PROJECT_SOURCE_DIR}/external/build
+        )
+    endif ()
+    message(STATUS "building external projects ended")
+
 endif ()
-message(STATUS "building external projects ended")
 
-message(STATUS "Building required libraries complete")
+message(STATUS "Building required librasries complete")
 # path to external libraries and headers
 include_directories(${EXTERNAL_INSTALL_DIR}/include)
 link_directories(${EXTERNAL_INSTALL_DIR}/lib)
@@ -228,10 +244,6 @@ if (WITH_FFTW)
                 NO_DEFAULT_PATH
                 )
     endif ()
-
-    add_custom_command(TARGET ALL PRE_BUILD
-            COMMAND ${CMAKE_COMMAND} -E copy_directory
-            "${EXTERNAL_INSTALL_DIR}/bin/" $<TARGET_FILE_DIR>)
 endif ()
 
 
@@ -252,7 +264,7 @@ endfunction(assign_source_group)
 
 # main library
 include_directories(include)
-SET(LIBRARIES
+LIST(APPEND LIBRARIES
         ${FFTW_LIB}
         )
 
@@ -277,6 +289,18 @@ else ()
 endif ()
 target_link_libraries(blond ${LIBRARIES})
 
+if (WITH_FFTW)
+    if (MSVC)
+        add_custom_command(TARGET blond PRE_BUILD
+                COMMAND ${CMAKE_COMMAND} -E copy_directory
+                "${EXTERNAL_INSTALL_DIR}/bin/fftw/$(Configuration)" $<TARGET_FILE_DIR:blond>)
+    else ()
+        add_custom_command(TARGET blond PRE_BUILD
+                COMMAND ${CMAKE_COMMAND} -E copy_directory
+                "${EXTERNAL_INSTALL_DIR}/bin/" $<TARGET_FILE_DIR:blond>)
+    endif ()
+endif ()
+
 #SET_TARGET_PROPERTIES(blond PROPERTIES LINKER_LANGUAGE CXX)
 
 # demo executables
@@ -286,7 +310,6 @@ file(GLOB EXECUTABLE_SOURCES "demos/*.cpp")
 set(EXECUTABLE_FILES ${EXECUTABLE_SOURCES})
 
 
-
 # demo dependencies
 
 foreach (src ${EXECUTABLE_FILES})
@@ -362,7 +385,7 @@ endif ()
 if (BENCHMARK_ENABLED)
     if (WITH_BENCHMARK)
         if (WIN32 AND NOT MINGW)
-            link_directories(${EXTERNAL_INSTALL_DIR}/lib/fftw/$(Configuration)/)
+            link_directories(${EXTERNAL_INSTALL_DIR}/lib/benchmark/$(Configuration)/)
             find_library(BENCHMARK_LIB
                     NAMES benchmark libbenchmark
                     PATHS "${EXTERNAL_INSTALL_DIR}/lib/benchmark/Debug"
@@ -381,22 +404,26 @@ if (BENCHMARK_ENABLED)
     message(STATUS "generating benchmark executables")
     LIST(APPEND LIBRARIES ${BENCHMARK_LIB})
 
-    if (MSVC)
-        LIST(APPEND LIBRARIES Shlwapi)
+    if (MSVC OR MINGW)
+        LIST(APPEND LIBRARIES shlwapi)
     else ()
         LIST(APPEND LIBRARIES pthread)
     endif ()
 
     file(GLOB BENCHMARK_SOURCES "./benchmarks/*.cpp")
+    file(GLOB_RECURSE BENCHMARK_PROTOTYPES "./benchmarks/prototypes/*.h")
+    include_directories(benchmarks/prototypes/)
     set(BENCHMARK_FILES ${BENCHMARK_SOURCES})
 
+    file(GLOB BENCHMARK_CONFIGURATIONS "./benchmarks/*.cmake")
+    include(${BENCHMARK_CONFIGURATIONS})
+
     foreach (src ${BENCHMARK_FILES})
         file(RELATIVE_PATH testfile ${CMAKE_CURRENT_SOURCE_DIR} ${src})
         string(REPLACE ".cpp" "" testname ${testfile})
         string(REPLACE "benchmarks/" "" testname ${testname})
-        add_executable(${testname} ${src})
+        add_executable(${testname} ${src} ${BENCHMARK_PROTOTYPES})
         target_link_libraries(${testname} ${LIBRARIES})
-        add_test(${testname} ${testname})
     endforeach ()
 
     enable_testing()

diff --git a/Doxyfile b/Doxyfile
@@ -751,6 +751,10 @@ WARN_LOGFILE           =
 
 INPUT                  = ./src/ \
                          ./include/ \
+                         ./docs/ \
+                         ./unit-tests/ \
+                         ./demos/ \
+                         ./benchmarks/
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -786,7 +790,8 @@ FILE_PATTERNS          = *.c \
                          *.hxx \
                          *.hpp \
                          *.h++ \
-                         *.py
+                         *.py \
+                         *.md
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.