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Upgrade toolkits (#1878)

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Upgrade the version of related toolkits:
- upgrade llvm to 15.0
- upgrade wasi-sdk to 19.0
- upgrade emsdk to 3.1.28
- upgrade wabt to 1.0.31
- upgrade binaryen to 111

And upgrade the CI scripts, sample workload build scripts, Dockerfiles, and documents.
This commit is contained in:
Wenyong Huang
2023-02-02 09:42:25 +08:00
committed by GitHub
parent 1614ce12fa
commit 27e7e160af
43 changed files with 817 additions and 594 deletions
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15
samples/workload/bwa/CMakeLists.bwa_wasm.txt
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@ -1,11 +1,14 @@
# Copyright (C) 2019 Intel Corporation. All rights reserved.
# SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
cmake_minimum_required (VERSION 3.0)
cmake_minimum_required (VERSION 3.14)
project(bwa_wasm C)
include(${CMAKE_CURRENT_SOURCE_DIR}/../../cmake/preparation.cmake)
list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/../../cmake)
################ dependencies ################
find_package(Binaryen 111 REQUIRED)
################ LIBZ ################
set(LIBZ_SRC_DIR ${CMAKE_CURRENT_SOURCE_DIR}/../libz)
@ -86,12 +89,6 @@ add_executable(${PROJECT_NAME} ${BWA_SOURCE})
set_target_properties(${PROJECT_NAME} PROPERTIES OUTPUT_NAME bwa.wasm)
target_include_directories(${PROJECT_NAME}
PRIVATE
${WASI_SDK_HOME}/share/wasi-sysroot/include/libc/musl
${WASI_SDK_HOME}/share/wasi-sysroot/include/sse
)
target_compile_definitions(${PROJECT_NAME}
PRIVATE
USE_MALLOC_WRAPPERS
@ -117,7 +114,7 @@ target_link_libraries(${PROJECT_NAME} z_wasm wasi-emulated-process-clocks)
add_custom_target(bwa_wasm_opt ALL
COMMAND
${WASM_OPT} -Oz --enable-simd -o bwa.opt.wasm bwa.wasm
${Binaryen_WASM_OPT} -Oz --enable-simd -o bwa.opt.wasm bwa.wasm
BYPRODUCTS
${CMAKE_CURRENT_BINARY_DIR}/bwa.opt.wasm
WORKING_DIRECTORY

43
samples/workload/bwa/CMakeLists.txt
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@ -1,11 +1,19 @@
# Copyright (C) 2019 Intel Corporation. All rights reserved.
# SPDX-License-Identifier: Apache-2.0 WITH LLVM-exception
cmake_minimum_required (VERSION 2.8...3.16)
cmake_minimum_required (VERSION 3.14)
project(bwa_wasm)
include(${CMAKE_CURRENT_SOURCE_DIR}/../cmake/preparation.cmake)
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)
@ -13,7 +21,7 @@ include(ExternalProject)
################ libz ################
ExternalProject_Add(libz_src
GIT_REPOSITORY https://github.com/madler/zlib.git
GIT_TAG master
GIT_TAG 04f42ceca40f73e2978b50e93806c2a18c1281fc
GIT_PROGRESS ON
GIT_SHALLOW ON
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/libz
@ -27,7 +35,7 @@ ExternalProject_Add(libz_src
################ bwa ################
ExternalProject_Add(bwa
GIT_REPOSITORY https://github.com/lh3/bwa.git
GIT_TAG master
GIT_TAG 139f68fc4c3747813783a488aef2adc86626b01b
GIT_PROGRESS ON
GIT_SHALLOW ON
SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/bwa
@ -37,10 +45,29 @@ ExternalProject_Add(bwa
&& ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/CMakeLists.bwa_wasm.txt CMakeLists.txt
&& git apply ../bwa.patch
CONFIGURE_COMMAND ${CMAKE_COMMAND}
-DWASI_SDK_PREFIX=${WASI_SDK_HOME}
-DCMAKE_TOOLCHAIN_FILE=${WASI_SDK_HOME}/share/cmake/wasi-sdk.cmake
-DCMAKE_SYSROOT=${WASI_SDK_HOME}/share/wasi-sysroot
-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
INSTALL_COMMAND ${CMAKE_COMMAND} -E copy ./bwa.opt.wasm ${CMAKE_BINARY_DIR}/bwa.wasm
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
)

4
samples/workload/bwa/README.md
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@ -33,7 +33,7 @@ Firstly please build iwasm with simd support:
``` shell
$ cd <wamr dir>/product-mini/platforms/linux/
$ mkdir build && cd build
$ cmake .. -DWAMR_BUILD_SIMD=1
$ cmake ..
$ make
```
@ -41,6 +41,6 @@ Then compile wasm file to aot file and run:
``` shell
$ cd <wamr dir>/samples/workload/bwa/build
$ <wamr dir>/wamr-compiler/build/wamrc --enable-simd -o bwa.aot bwa.wasm
$ <wamr dir>/wamr-compiler/build/wamrc -o bwa.aot bwa.wasm
$ <wamr dir>/product-mini/platforms/linux/iwasm --dir=. bwa.aot index hs38DH.fa
```

1
samples/workload/bwa/build_workload.sh
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@ -1 +0,0 @@
../docker/build_workload.sh