Restructuring, templating, and cleaning

.gitignore

@@ -0,0 +1,2 @@
+build/
+.vscode/

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "submodules/alignment_boilerplate"]
+	path = submodules/alignment_boilerplate
+	url = https://github.com/r-barnes/alignment_boilerplate.git

CMakeLists.txt

@@ -1,31 +1,72 @@
 cmake_minimum_required(VERSION 3.14 FATAL_ERROR)
 
-project(sw_GPU LANGUAGES C CXX CUDA)
+project(sw_GPU LANGUAGES CXX CUDA)
 
 set(CMAKE_CXX_STANDARD 14 CACHE STRING "")
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "")
 set(CMAKE_CUDA_STANDARD 14 CACHE STRING "")
 set(CMAKE_CUDA_EXTENSIONS OFF CACHE BOOL "")
 
 #find_package(timemory REQUIRED COMPONENTS headers cuda cupti compile-options arch)
-#find_package(cuda REQUIRED)
 find_package(OpenMP REQUIRED)
 
+add_subdirectory(submodules/alignment_boilerplate EXCLUDE_FROM_ALL)
 
-file(GLOB sources ${PROJECT_SOURCE_DIR}/ utils.cpp alignments.cpp kernel.cpp driver.cpp main.cpp)
-file(GLOB headers ${PROJECT_SOURCE_DIR}/utils.hpp alignments.hpp kernel.hpp driver.hpp)
+set(sources
+  src/driver.cpp
+)
 
-set_source_files_properties(${sources} PROPERTIES
-    LANGUAGE CUDA
-    LINKER_LANGUAGE CUDA)
+set(test_sources
+  unittest/test_blockShuffleReduce_with_index.cu
+  unittest/test_main.cpp
+  unittest/test_sequence_process.cu
+  unittest/test_warpReduceMax_with_index.cu
+)
 
-add_executable(program_gpu ${sources} ${headers})
-target_compile_options(program_gpu PUBLIC $<$<COMPILE_LANGUAGE:CUDA>:-gencode arch=compute_70,code=sm_70>)
+
+set_source_files_properties(${sources} ${test_sources} evaluation/main.cpp
+PROPERTIES
+  LANGUAGE CUDA
+  LINKER_LANGUAGE CUDA
+)
+
+add_library(gpu_bsw ${sources})
+target_include_directories(gpu_bsw PUBLIC include)
+target_link_libraries(gpu_bsw PUBLIC albp OpenMP::OpenMP_CXX)
 #target_link_libraries(program_gpu PUBLIC timemory OpenMP::OpenMP_CXX)
-target_link_libraries(program_gpu PUBLIC OpenMP::OpenMP_CXX)
-target_include_directories(program_gpu PUBLIC ${PROJECT_SOURCE_DIR})
+target_compile_options(gpu_bsw PUBLIC
+    $<$<COMPILE_LANGUAGE:CUDA>:-gencode=arch=compute_50,code=sm_50>
+    $<$<COMPILE_LANGUAGE:CUDA>:-gencode=arch=compute_52,code=sm_52>
+    $<$<COMPILE_LANGUAGE:CUDA>:-gencode=arch=compute_60,code=sm_60>
+    $<$<COMPILE_LANGUAGE:CUDA>:-gencode=arch=compute_61,code=sm_61>
+    $<$<COMPILE_LANGUAGE:CUDA>:-gencode=arch=compute_70,code=sm_70>
+    $<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler=-Wall,-Wextra>
+    # $<$<COMPILE_LANGUAGE:CUDA>:-G>
+)
 
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
 if(CMAKE_CUDA_COMPILER AND "CUDA" IN_LIST LANGUAGES)
-    target_compile_options(program_gpu PUBLIC $<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler -fopenmp>)
+    target_compile_options(gpu_bsw PUBLIC $<$<COMPILE_LANGUAGE:CUDA>:-Xcompiler -fopenmp>)
 endif()
+
+add_executable(program_gpu evaluation/main.cpp)
+target_link_libraries(program_gpu PRIVATE gpu_bsw)
+
+add_executable(unittest ${test_sources})
+target_link_libraries(unittest PRIVATE gpu_bsw)
+
+# add_executable(test unittest/test.cu)
+# target_link_libraries(test PRIVATE gpu_bsw)
+
+
+add_custom_target(
+    regression_tests ALL
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_BINARY_DIR}/regression_test
+    COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_CURRENT_SOURCE_DIR}/regression_test/* ${CMAKE_BINARY_DIR}/regression_test
+)
+
+add_custom_target(
+    test-data ALL
+    COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_BINARY_DIR}/test-data
+    COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_CURRENT_SOURCE_DIR}/test-data/* ${CMAKE_BINARY_DIR}/test-data
+)

README.md

@@ -20,25 +20,23 @@ so.**
 
 
 
-To Build:<br />
-mkdir build <br />
-cd build <br />
-cmake CMAKE_BUILD_TYPE=Release .. <br />
-make <br />
+To Build:
 
-<br />
-To Execute DNA test run: <br />
+    mkdir build 
+    cd build 
+    cmake CMAKE_BUILD_TYPE=Release .. 
+    make 
 
-./program_gpu dna ../test-data/dna-reference.fasta ../test-data/dna-query.fasta <br />
+To Execute DNA test run:
 
-To Execute Protein test run: <br />
+    ./program_gpu dna ../test-data/dna-reference.fasta ../test-data/dna-query.fasta output
 
-./program_gpu aa ../test-data/protein-reference.fasta ../test-data/protein-query.fasta <br />
+To Execute Protein test run:
+
+    ./program_gpu aa ../test-data/protein-reference.fasta ../test-data/protein-query.fasta output
 
-<br />
 Contact: mgawan@lbl.gov
 
-<br />
 If you use GPU-BSW in your project, please cite this repo as:  
 
 *Muaaz G. Awan, GPU accelerated Smith-Waterman for performing batch alignments (GPU-BSW), 2019, Github Repository: https://github.com/m-gul/GPU-BSW/*