diff options
Diffstat (limited to 'fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa')
5 files changed, 260 insertions, 0 deletions
diff --git a/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/.gitignore b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/.gitignore new file mode 100644 index 000000000..cd7209590 --- /dev/null +++ b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/.gitignore @@ -0,0 +1,4 @@ +build +libz +bwa +include diff --git a/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/CMakeLists.bwa_wasm.txt b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/CMakeLists.bwa_wasm.txt new file mode 100644 index 000000000..a8d1d8821 --- /dev/null +++ b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/CMakeLists.bwa_wasm.txt @@ -0,0 +1,124 @@ +# Copyright (C) 2019 Intel Corporation. All rights reserved. +# SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception + +cmake_minimum_required (VERSION 3.14) + +project(bwa_wasm C) + +list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake) + +################ dependencies ################ +find_package(Binaryen 111 REQUIRED) + +################ LIBZ ################ +set(LIBZ_SRC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../libz) +add_library(z_wasm STATIC + ${LIBZ_SRC_DIR}/adler32.c + ${LIBZ_SRC_DIR}/compress.c + ${LIBZ_SRC_DIR}/crc32.c + ${LIBZ_SRC_DIR}/deflate.c + ${LIBZ_SRC_DIR}/gzclose.c + ${LIBZ_SRC_DIR}/gzlib.c + ${LIBZ_SRC_DIR}/gzread.c + ${LIBZ_SRC_DIR}/gzwrite.c + ${LIBZ_SRC_DIR}/infback.c + ${LIBZ_SRC_DIR}/inffast.c + ${LIBZ_SRC_DIR}/inflate.c + ${LIBZ_SRC_DIR}/inftrees.c + ${LIBZ_SRC_DIR}/trees.c + ${LIBZ_SRC_DIR}/uncompr.c + ${LIBZ_SRC_DIR}/zutil.c +) + +set_target_properties(z_wasm PROPERTIES LINKER_LANGUAGE C) + +target_compile_definitions(z_wasm PRIVATE Z_HAVE_UNISTD_H _LARGEFILE64_SOURCE=1) + +target_compile_options(z_wasm + PRIVATE + -Wno-unused-function + -Wno-unused-variable +) + +target_include_directories(z_wasm + PUBLIC + ${LIBZ_SRC_DIR} +) + +################ BWA_WASM ################ +set(BWA_SRC_DIR ${CMAKE_CURRENT_SOURCE_DIR}) +set(BWA_SOURCE + ${BWA_SRC_DIR}/utils.c + ${BWA_SRC_DIR}/kthread.c + ${BWA_SRC_DIR}/kstring.c + ${BWA_SRC_DIR}/ksw.c + ${BWA_SRC_DIR}/bwt.c + ${BWA_SRC_DIR}/bntseq.c + ${BWA_SRC_DIR}/bwa.c + ${BWA_SRC_DIR}/bwamem.c + ${BWA_SRC_DIR}/bwamem_pair.c + ${BWA_SRC_DIR}/bwamem_extra.c + ${BWA_SRC_DIR}/malloc_wrap.c + ${BWA_SRC_DIR}/QSufSort.c + ${BWA_SRC_DIR}/bwt_gen.c + ${BWA_SRC_DIR}/rope.c + ${BWA_SRC_DIR}/rle.c + ${BWA_SRC_DIR}/is.c + ${BWA_SRC_DIR}/bwtindex.c + ${BWA_SRC_DIR}/bwashm.c + ${BWA_SRC_DIR}/bwase.c + ${BWA_SRC_DIR}/bwaseqio.c + ${BWA_SRC_DIR}/bwtgap.c + ${BWA_SRC_DIR}/bwtaln.c + ${BWA_SRC_DIR}/bamlite.c + ${BWA_SRC_DIR}/bwape.c + ${BWA_SRC_DIR}/kopen.c + ${BWA_SRC_DIR}/pemerge.c + ${BWA_SRC_DIR}/maxk.c + ${BWA_SRC_DIR}/bwtsw2_core.c + ${BWA_SRC_DIR}/bwtsw2_main.c + ${BWA_SRC_DIR}/bwtsw2_aux.c + ${BWA_SRC_DIR}/bwt_lite.c + ${BWA_SRC_DIR}/bwtsw2_chain.c + ${BWA_SRC_DIR}/fastmap.c + ${BWA_SRC_DIR}/bwtsw2_pair.c + ${BWA_SRC_DIR}/main.c +) + +add_executable(${PROJECT_NAME} ${BWA_SOURCE}) + +set_target_properties(${PROJECT_NAME} PROPERTIES OUTPUT_NAME bwa.wasm) + +target_compile_definitions(${PROJECT_NAME} + PRIVATE + USE_MALLOC_WRAPPERS + __SSE__ __SSE2__ __SSE4_1__ + _WASI_EMULATED_MMAN _WASI_EMULATED_SIGNAL _WASI_EMULATED_PROCESS_CLOCKS +) + +target_compile_options(${PROJECT_NAME} + PRIVATE + -Wno-unused-function + -Wno-unused-variable + -msimd128 +) + +target_link_options(${PROJECT_NAME} + PRIVATE + -Wno-unused-command-line-argument + LINKER:--allow-undefined,--export=__heap_base,--export=__data_end + LINKER:-z,stack-size=1048576 +) + +target_link_libraries(${PROJECT_NAME} z_wasm wasi-emulated-process-clocks) + +add_custom_target(bwa_wasm_opt ALL + COMMAND + ${Binaryen_WASM_OPT} -Oz --enable-simd -o bwa.opt.wasm bwa.wasm + BYPRODUCTS + ${CMAKE_CURRENT_BINARY_DIR}/bwa.opt.wasm + WORKING_DIRECTORY + ${CMAKE_CURRENT_BINARY_DIR} +) + +add_dependencies(bwa_wasm_opt ${PROJECT_NAME}) diff --git a/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/CMakeLists.txt b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/CMakeLists.txt new file mode 100644 index 000000000..5db52a38b --- /dev/null +++ b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/CMakeLists.txt @@ -0,0 +1,73 @@ +# Copyright (C) 2019 Intel Corporation. All rights reserved. +# SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception + +cmake_minimum_required (VERSION 3.14) + +project(bwa_wasm) + +list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../cmake) + +################ dependencies ################ +find_package(Python3 REQUIRED) +find_package(WASISDK 16.0 REQUIRED) +execute_process( + COMMAND ${Python3_EXECUTABLE} ${CMAKE_CURRENT_LIST_DIR}/../../../test-tools/pick-up-emscripten-headers/collect_files.py --install ../include --loglevel=ERROR + WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR} +) + +####################################### +include(ExternalProject) + +################ libz ################ +ExternalProject_Add(libz_src + GIT_REPOSITORY https://github.com/madler/zlib.git + GIT_TAG 04f42ceca40f73e2978b50e93806c2a18c1281fc + GIT_PROGRESS ON + GIT_SHALLOW ON + SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/libz + UPDATE_COMMAND "" + PATCH_COMMAND "" + CONFIGURE_COMMAND "" + BUILD_COMMAND "" + INSTALL_COMMAND "" +) + +################ bwa ################ +ExternalProject_Add(bwa + GIT_REPOSITORY https://github.com/lh3/bwa.git + GIT_TAG 139f68fc4c3747813783a488aef2adc86626b01b + GIT_PROGRESS ON + GIT_SHALLOW ON + SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/bwa + DEPENDS libz_src + UPDATE_COMMAND git clean -ffdx && git checkout -- * + && ${CMAKE_COMMAND} -E echo "Copying pre-installed CMakeLists.txt" + && ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.bwa_wasm.txt CMakeLists.txt + && git apply ../bwa.patch + CONFIGURE_COMMAND ${CMAKE_COMMAND} + -DWASI_SDK_PREFIX=${WASISDK_HOME} + -DCMAKE_TOOLCHAIN_FILE=${WASISDK_TOOLCHAIN} + -DCMAKE_SYSROOT=${WASISDK_SYSROOT} + -DCMAKE_C_FLAGS=-isystem\ ${CMAKE_CURRENT_SOURCE_DIR}/../include/sse\ -isystem\ ${CMAKE_CURRENT_SOURCE_DIR}/../include/libc/musl + ${CMAKE_CURRENT_SOURCE_DIR}/bwa + BUILD_COMMAND make bwa_wasm_opt -j 4 + INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_if_different ./bwa.opt.wasm ${CMAKE_CURRENT_BINARY_DIR}/bwa.wasm +) + +################ bwa data ################ +ExternalProject_Add(bwa-kit + PREFIX bwa-kit + URL https://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.15_x64-linux.tar.bz2/download + URL_HASH SHA256=0a7b11971bc7916b68e9df35a364afe77cb3000df02ffb3a6fbd1aff9be5878c + DOWNLOAD_NAME bwakit-0.7.15_x64-linux.tar.bz2 + DOWNLOAD_EXTRACT_TIMESTAMP ON + DOWNLOAD_NO_EXTRACT OFF + DOWNLOAD_NO_PROGRESS ON + UPDATE_COMMAND "" + PATCH_COMMAND "" + CONFIGURE_COMMAND "" + BUILD_COMMAND "" + INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_if_different + ${CMAKE_CURRENT_BINARY_DIR}/bwa-kit/src/bwa-kit/resource-GRCh38/hs38DH-extra.fa + ${CMAKE_CURRENT_BINARY_DIR}/hs38DH-extra.fa +) diff --git a/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/README.md b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/README.md new file mode 100644 index 000000000..a8fbe3e69 --- /dev/null +++ b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/README.md @@ -0,0 +1,46 @@ +"bwa" sample introduction +============== + +This sample demonstrates how to build [bwa](https://github.com/lh3/bwa) into +WebAssembly with simd support and run it with iwasm. + +## Preparation + +please refer to [installation instructions](../README.md). + +## Build + +``` shell +$ mkdir build && cd build +$ cmake .. +$ make +# to verify +$ ls bwa.wasm +``` + +## Download sample data + +Download the bwa-0.7.15 binary package from +[such an address](https://sourceforge.net/projects/bio-bwa/files/bwakit/bwakit-0.7.15_x64-linux.tar.bz2/download), +a sample data file named **hs38DH.fa** will be used later. + +If want more data, please refer to http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/ + +## Run workload + +Firstly please build iwasm with simd support: + +``` shell +$ cd <wamr dir>/product-mini/platforms/linux/ +$ mkdir build && cd build +$ cmake .. +$ make +``` + +Then compile wasm file to aot file and run: + +``` shell +$ cd <wamr dir>/samples/workload/bwa/build +$ <wamr dir>/wamr-compiler/build/wamrc -o bwa.aot bwa.wasm +$ <wamr dir>/product-mini/platforms/linux/iwasm --dir=. bwa.aot index hs38DH.fa +``` diff --git a/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/bwa.patch b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/bwa.patch new file mode 100644 index 000000000..5599ca319 --- /dev/null +++ b/fluent-bit/lib/wasm-micro-runtime-WAMR-1.2.2/samples/workload/bwa/bwa.patch @@ -0,0 +1,13 @@ +diff --git a/utils.c b/utils.c +index 9ceb1be..323299f 100644 +--- a/utils.c ++++ b/utils.c +@@ -301,6 +301,7 @@ long peakrss(void) + #ifdef __linux__ + return r.ru_maxrss * 1024; + #else +- return r.ru_maxrss; ++ /*return r.ru_maxrss;*/ ++ return 0; + #endif + } |