Without isa-l (#78)

- Removes isa-l library to avoid build issues on cluster. --------- Co-authored-by: Will Dumm <wrhdumm@gmail.com> Co-authored-by: marybarker <marybarker103@gmail.com>
matsengrp · Apr 15, 2024 · a2f3486 · a2f3486
1 parent 8c165f2
commit a2f3486
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Showing 12 changed files with 281 additions and 228 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -8,12 +8,11 @@ if(CMAKE_VERSION VERSION_GREATER_EQUAL "3.24.0")
 endif()
 
 set(CMAKE_INTERPROCEDURAL_OPTIMIZATION yes)
-
 set(CMAKE_EXPORT_COMPILE_COMMANDS yes)
 
 include(FetchContent)
 
-if (USE_USHER)
+if(USE_USHER)
   FetchContent_Declare(oneTBB-src
     GIT_REPOSITORY https://github.com/oneapi-src/oneTBB
     GIT_TAG 2019_U9
@@ -89,21 +88,6 @@ endif()
 
 find_package(ZLIB)
 
-#ExternalProject_Add(isa-l
-#  GIT_REPOSITORY https://github.com/intel/isa-l.git
-#  GIT_TAG v2.30.0
-#  GIT_SHALLOW true
-#  GIT_PROGRESS true
-#  UPDATE_DISCONNECTED true
-#  PREFIX isa-l
-#  SOURCE_DIR isa-l/source
-#  BINARY_DIR isa-l/source
-#  INSTALL_DIR isa-l/install
-#  CONFIGURE_COMMAND ${CMAKE_COMMAND} -E env SED=/bin/sed GREP=/bin/grep ./autogen.sh && ${CMAKE_COMMAND} -E env AS=yasm ./configure --prefix=${CMAKE_BINARY_DIR}/isa-l/install --libdir=${CMAKE_BINARY_DIR}/isa-l/install
-#  BUILD_COMMAND make && make other
-#  INSTALL_COMMAND make install
-#)
-#set(isal_lib ${CMAKE_BINARY_DIR}/isa-l/install/libisal.a)
 set(STRICT_WARNINGS -Werror -fno-common -Wno-unknown-warning-option -Wno-pragmas -Wall -Wextra -pedantic -Wold-style-cast -Wshadow -Wconversion -Wcast-align -Wcast-qual -Wlogical-op -Wlogical-not-parentheses -Wredundant-decls -Wunreachable-code -Wparentheses -Wno-dangling-reference -Wno-ignored-optimization-argument)
 
 if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.0)
@@ -112,7 +96,8 @@ endif()
 
 function(larch_compile_opts PRODUCT)
   target_compile_options(${PRODUCT} PUBLIC -march=native -std=c++17 -pipe)
-  if (CMAKE_BUILD_TYPE EQUAL "DEBUG")
+
+  if(CMAKE_BUILD_TYPE EQUAL "DEBUG")
     target_compile_options(${PRODUCT} PUBLIC -fno-omit-frame-pointer -fno-stack-protector)
   endif()
 
@@ -142,26 +127,26 @@ endfunction()
 FIND_PACKAGE(Boost COMPONENTS program_options iostreams filesystem date_time REQUIRED)
 
 if(${USE_USHER})
-include_directories(deps/usher/)
-file(GLOB MATOPTIMIZE_SRC
-  "deps/usher/src/matOptimize/apply_move/*.cpp"
-  "deps/usher/src/matOptimize/Profitable_Moves_Enumerators/*.cpp"
-  "deps/usher/src/matOptimize/Fitch_Sankoff.cpp"
-  "deps/usher/src/matOptimize/mutation_annotated_tree.cpp"
-  "deps/usher/src/matOptimize/mutation_annotated_tree_nuc_util.cpp"
-  "deps/usher/src/matOptimize/mutation_annotated_tree_node.cpp"
-  "deps/usher/src/matOptimize/mutation_annotated_tree_load_store.cpp"
-  "deps/usher/src/matOptimize/mutation_annotated_tree_nuc_utils.cpp"
-  "deps/usher/src/matOptimize/optimize_inner_loop.cpp"
-  "deps/usher/src/matOptimize/Mutation_Collection.cpp"
-  "deps/usher/src/matOptimize/condense.cpp"
-  "deps/usher/src/matOptimize/reassign_states.cpp"
-  "deps/usher/src/matOptimize/detailed_mutations_load.cpp"
-  "deps/usher/src/matOptimize/detailed_mutations_store.cpp"
-  "deps/usher/src/matOptimize/optimize_tree.cpp"
-  "deps/usher/src/matOptimize/priority_conflict_resolver.cpp"
-  "deps/usher/src/matOptimize/check_samples.cpp"
-)
+  include_directories(deps/usher/)
+  file(GLOB MATOPTIMIZE_SRC
+    "deps/usher/src/matOptimize/apply_move/*.cpp"
+    "deps/usher/src/matOptimize/Profitable_Moves_Enumerators/*.cpp"
+    "deps/usher/src/matOptimize/Fitch_Sankoff.cpp"
+    "deps/usher/src/matOptimize/mutation_annotated_tree.cpp"
+    "deps/usher/src/matOptimize/mutation_annotated_tree_nuc_util.cpp"
+    "deps/usher/src/matOptimize/mutation_annotated_tree_node.cpp"
+    "deps/usher/src/matOptimize/mutation_annotated_tree_load_store.cpp"
+    "deps/usher/src/matOptimize/mutation_annotated_tree_nuc_utils.cpp"
+    "deps/usher/src/matOptimize/optimize_inner_loop.cpp"
+    "deps/usher/src/matOptimize/Mutation_Collection.cpp"
+    "deps/usher/src/matOptimize/condense.cpp"
+    "deps/usher/src/matOptimize/reassign_states.cpp"
+    "deps/usher/src/matOptimize/detailed_mutations_load.cpp"
+    "deps/usher/src/matOptimize/detailed_mutations_store.cpp"
+    "deps/usher/src/matOptimize/optimize_tree.cpp"
+    "deps/usher/src/matOptimize/priority_conflict_resolver.cpp"
+    "deps/usher/src/matOptimize/check_samples.cpp"
+  )
 endif()
 
 function(larch_link_opts PRODUCT)
@@ -177,6 +162,7 @@ function(larch_link_opts PRODUCT)
   target_link_libraries(${PRODUCT} PUBLIC nlohmann_json::nlohmann_json)
   target_link_libraries(${PRODUCT} PUBLIC ${Protobuf_LIBRARIES})
   target_link_libraries(${PRODUCT} PUBLIC ${Boost_LIBRARIES})
+
   if(${USE_USHER})
     target_link_libraries(${PRODUCT} PUBLIC ${TBB_IMPORTED_TARGETS} -lstdc++fs)
   else()
@@ -211,49 +197,46 @@ endif()
 larch_link_opts(larch)
 
 if(${USE_USHER})
-add_library(usher
-  ${MATOPTIMIZE_SRC}
-  src/usher_globals.cpp)
-target_compile_options(usher PRIVATE -march=native -std=c++17 -w -fno-omit-frame-pointer  -DUSE_USHER)
+  add_library(usher
+    ${MATOPTIMIZE_SRC}
+    src/usher_globals.cpp)
+  target_compile_options(usher PRIVATE -march=native -std=c++17 -w -fno-omit-frame-pointer -DUSE_USHER)
 
-if(${USE_ASAN})
-  target_compile_options(usher PUBLIC -O0 -g3 -fsanitize=address,undefined -fno-sanitize-recover)
-elseif(${USE_TSAN})
-  target_compile_options(usher PUBLIC -O0 -g3 -fsanitize=thread)
-endif()
+  if(${USE_ASAN})
+    target_compile_options(usher PUBLIC -O0 -g3 -fsanitize=address,undefined -fno-sanitize-recover)
+  elseif(${USE_TSAN})
+    target_compile_options(usher PUBLIC -O0 -g3 -fsanitize=thread)
+  endif()
 
-target_include_directories(usher PUBLIC include)
-target_include_directories(usher PUBLIC ${Protobuf_INCLUDE_DIR})
-target_include_directories(usher PUBLIC ${CMAKE_CURRENT_BINARY_DIR}/range-v3/install/include)
+  target_include_directories(usher PUBLIC include)
+  target_include_directories(usher PUBLIC ${Protobuf_INCLUDE_DIR})
+  target_include_directories(usher PUBLIC ${CMAKE_CURRENT_BINARY_DIR}/range-v3/install/include)
 
-#target_include_directories(usher PUBLIC ${CMAKE_CURRENT_BINARY_DIR}/isa-l/install/include)
-add_dependencies(usher range-v3)
+  add_dependencies(usher range-v3)
 
-#add_dependencies(usher isa-l)
-target_include_directories(usher PUBLIC ${PROTO_OUT_DIR}/deps/usher)
-larch_link_opts(usher)
-target_link_libraries(usher PRIVATE ${Boost_LIBRARIES} ZLIB::ZLIB ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS})
+  target_include_directories(usher PUBLIC ${PROTO_OUT_DIR}/deps/usher)
+  larch_link_opts(usher)
+  target_link_libraries(usher PRIVATE ${Boost_LIBRARIES} ZLIB::ZLIB ${MPI_CXX_LIBRARIES} ${MPI_CXX_LINK_FLAGS})
 
-#target_link_libraries(usher PUBLIC ${CMAKE_BINARY_DIR}/isa-l/install/libisal.a)
-set_target_properties(usher
-  PROPERTIES CXX_CLANG_TIDY ""
-)
+  set_target_properties(usher
+    PROPERTIES CXX_CLANG_TIDY ""
+  )
 
-add_library(larch-usher-glue
-  src/usher_glue.cpp)
-larch_compile_opts(larch-usher-glue)
-target_compile_options(larch-usher-glue PRIVATE ${STRICT_WARNINGS})
-larch_link_opts(larch-usher-glue)
-target_link_libraries(larch-usher-glue PUBLIC usher)
-add_dependencies(larch-usher-glue larch usher)
-set_target_properties(larch-usher-glue
-  PROPERTIES CXX_CLANG_TIDY ""
-)
+  add_library(larch-usher-glue
+    src/usher_glue.cpp)
+  larch_compile_opts(larch-usher-glue)
+  target_compile_options(larch-usher-glue PRIVATE ${STRICT_WARNINGS})
+  larch_link_opts(larch-usher-glue)
+  target_link_libraries(larch-usher-glue PUBLIC usher)
+  add_dependencies(larch-usher-glue larch usher)
+  set_target_properties(larch-usher-glue
+    PROPERTIES CXX_CLANG_TIDY ""
+  )
 endif()
 
 larch_executable(larch-test
   test/main.cpp
-  #test/test_ambiguous_vcf.cpp
+  test/test_ambiguous_vcf.cpp
   test/test_ambiguities.cpp
   test/test_compact_genome.cpp
   test/test_count_trees.cpp
@@ -278,12 +261,13 @@ larch_executable(larch-test
   test/test_write_parsimony.cpp
 )
 target_compile_options(larch-test PRIVATE ${STRICT_WARNINGS})
+
 if(${USE_USHER})
-target_link_libraries(larch-test PUBLIC larch-usher-glue usher)
-add_dependencies(larch-test larch-usher-glue)
-set_target_properties(larch-test
-  PROPERTIES CXX_CLANG_TIDY ""
-)
+  target_link_libraries(larch-test PUBLIC larch-usher-glue usher)
+  add_dependencies(larch-test larch-usher-glue)
+  set_target_properties(larch-test
+    PROPERTIES CXX_CLANG_TIDY ""
+  )
 endif()
 
 larch_executable(merge
@@ -293,10 +277,10 @@ larch_executable(dag2dot
   tools/dag2dot.cpp)
 
 if(${USE_USHER})
-larch_executable(larch-usher
-  tools/larch-usher.cpp
-)
-target_compile_options(larch-usher PRIVATE ${STRICT_WARNINGS})
-target_link_libraries(larch-usher PRIVATE larch-usher-glue)
-add_dependencies(larch-usher larch-usher-glue)
+  larch_executable(larch-usher
+    tools/larch-usher.cpp
+  )
+  target_compile_options(larch-usher PRIVATE ${STRICT_WARNINGS})
+  target_link_libraries(larch-usher PRIVATE larch-usher-glue)
+  add_dependencies(larch-usher larch-usher-glue)
 endif()
diff --git a/README.md b/README.md
@@ -14,40 +14,61 @@ To get a recent cmake, download from `https://cmake.org/download/`, for example:
 
 `wget https://github.com/Kitware/CMake/releases/download/v3.23.1/cmake-3.23.1-linux-x86_64.tar.gz`
 
-To setup a conda environment capable of building Larch, use the environment
+Build Environments
+------------------
+
+* singularity 3.5.3
+* conda 22.9.0
+
+Larch can be built utilizing a Singularity container or a Conda environment.
+
+To build Singularity image, use the definition provided:
+
+`singularity build larch-singularity.sif larch-singularity.def`
+`singularity shell larch-singularity.sif --net`
+
+To setup a conda environment capable of building Larch, use:
+
+`conda create -n larch`
+`conda activate larch`
+`conda install --channel "conda-forge" --update-deps --override-channels cmake make cxx-compiler openmpi openmpi-mpicc openmpi-mpicxx boost-cpp automake autoconf libtool yasm ucx zlib`
+
+To setup a conda environment capable of building Larch including development tools, create `larch-dev` using the environment
 file provided:
 
 `conda env create -f environment.yml`
 
-
 Building
 --------
 
+`git submodule update --init --recursive`
 `mkdir build`
-
 `cd build`
-
 `cmake -DCMAKE_BUILD_TYPE=Debug ..`
-
 `make -j16`
 
-Optionally add -DCMAKE_CXX_CLANG_TIDY="clang-tidy" to enable clang-tidy.
-
-Optionally add -DUSE_ASAN=yes to enable asan and ubsan.
+Cmake build options:
+  - add `-DCMAKE_CXX_CLANG_TIDY="clang-tidy"` to enable clang-tidy.
+  - add `-DUSE_ASAN=yes` to enable asan and ubsan.
 
 Running
 -------
 
 From the build directory:
 
 `ln -s ../data`
-
 `./larch-test`
 
 Passing *nocatch* to the tests executable will allow exceptions to escape, which is useful for debugging. A gdb session can be started with `gdb --args build/larch-test nocatch`.
 
-*--list* produces a list of all available tests, along with an ID number.
-*--range* runs tests by ID in [begin, end] range arguments.
+larch-test options:
+
+- `nocatch` allows test exceptions to escape, which is useful for debugging. A gdb session can be started with `gdb --args build/larch-test nocatch`.
+- `--list` produces a list of all available tests, along with an ID number.
+- `--range` runs tests by ID with a string of comma-separated range or single ID arguments [e.g. 1-5,7,9,12-13].
+- `-tag` excludes tests with a given tag.
+- `+tag` includes tests with a given tag.
+- For example, the `-tag "slow"` removes tests which require an long runtime to complete.
 
 Third-party
 -----------

diff --git a/build.sh b/build.sh
diff --git a/environment.yml b/environment.yml
@@ -4,22 +4,27 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - git
-  - isa-l
+  - cmake=3.19.6
+  - make
   - cxx-compiler
-  - mafft
-  - boost-cpp
   - openmpi
+  - openmpi-mpicc
+  - openmpi-mpicxx
+  - boost-cpp
+  - automake
+  - autoconf
+  - libtool
+  - yasm
+  - ucx
+  - zlib
+
+  - git
+  - mafft
   - python
   - rsync
   - wget
-  - cmake=3.19.6
-  - autoconf
-  - protobuf=3.12.3
-  - make
   - openssh
   - gdb
   - bzip2
   - backports.lzma
-  - libtool
-  - automake
+  - protobuf=3.12.3