Update sse2neon.h to latest for better support for Linux ARM64 #206

martin-g · 2023-10-10T13:58:32Z

Use sse2neon.h from https://github.com/DLTcollab/sse2neon/blob/de2817727c72fc2f4ce9f54e2db6e40ce0548414/sse2neon.h This is current master from 10.10.2023
_mm_shuffle_pd is provided by newer sse2neon.h

https://github.com/DLTcollab/sse2neon/blob/de2817727c72fc2f4ce9f54e2db6e40ce0548414/sse2neon.h#L5118

aarch64 does not support cpuid

martin-g · 2023-10-10T13:59:18Z

The Github Actions based CI will be enabled once this PR is merged to master branch.
Until then you could see results at my fork https://github.com/martin-g/beagle-lib/actions/runs/6470457082

* Use sse2neon.h from https://github.com/DLTcollab/sse2neon/blob/de2817727c72fc2f4ce9f54e2db6e40ce0548414/sse2neon.h This is current master from 10.10.2023 * _mm_shuffle_pd is provided by newer sse2neon.h https://github.com/DLTcollab/sse2neon/blob/de2817727c72fc2f4ce9f54e2db6e40ce0548414/sse2neon.h#L5118 * aarch64 does not support cpuid Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

msuchard · 2023-10-10T14:51:24Z

please test to make sure these changes work on an Apple M1/2 ... i am unsure about your changes to libhmsbeagle/CPU/BeagleCPUSSEPlugin.cpp ... then i am happy to merge.

martin-g · 2023-10-10T15:12:16Z

I don't have access to Apple M1/M2 but I will ask a colleague of mine to test it!

Yikun · 2023-10-11T03:17:04Z

I checked in my M1 pro env, it works! Please let me know if I can help more.

git checkout support-linux-aarch64
mkdir build
cd build
cmake ..
make -j

Detail log:

➜ code uname -a
Darwin jiangyikundeMacBook-Pro.local 22.2.0 Darwin Kernel Version 22.2.0: Fri Nov 11 02:03:51 PST 2022; root:xnu-8792.61.2~4/RELEASE_ARM64_T6000 arm64

➜  code java -version
openjdk version "1.8.0_322"
OpenJDK Runtime Environment (Zulu 8.60.0.21-CA-macos-aarch64) (build 1.8.0_322-b06)
OpenJDK 64-Bit Server VM (Zulu 8.60.0.21-CA-macos-aarch64) (build 25.322-b06, mixed mode)
➜  code gcc --version
Apple clang version 14.0.0 (clang-1400.0.29.202)
Target: arm64-apple-darwin22.2.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
➜  code cmake --version
cmake version 3.26.4

CMake suite maintained and supported by Kitware (kitware.com/cmake).
➜  code echo $JAVA_HOME
/Users/yikun/Library/Java/JavaVirtualMachines/azul-1.8.0_322/Contents/Home
➜  code cd beagle-lib
➜  beagle-lib git:(master) git checkout support-linux-aarch64
branch 'support-linux-aarch64' set up to track 'origin/support-linux-aarch64'.
Switched to a new branch 'support-linux-aarch64'
➜  beagle-lib git:(support-linux-aarch64) mkdir build
➜  beagle-lib git:(support-linux-aarch64) cd build
➜  build git:(support-linux-aarch64) cmake ..
-- The C compiler identification is AppleClang 14.0.0.14000029
-- The CXX compiler identification is AppleClang 14.0.0.14000029
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /Library/Developer/CommandLineTools/usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /Library/Developer/CommandLineTools/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- BEAGLE_VERSION = 4.0.0
-- BEAGLE_PLUGIN_VERSION = 40
-- Found JNI: /Users/yikun/Library/Java/JavaVirtualMachines/azul-1.8.0_322/Contents/Home/include  found components: AWT JVM
-- JAVA_HOME=/Users/yikun/Library/Java/JavaVirtualMachines/azul-1.8.0_322/Contents/Home
-- JNI_INCLUDE_DIRS=/Users/yikun/Library/Java/JavaVirtualMachines/azul-1.8.0_322/Contents/Home/include;/Users/yikun/Library/Java/JavaVirtualMachines/azul-1.8.0_322/Contents/Home/include/darwin;/Users/yikun/Library/Java/JavaVirtualMachines/azul-1.8.0_322/Contents/Home/include
-- JNI_LIBRARIES=/Users/yikun/Library/Java/JavaVirtualMachines/azul-1.8.0_322/Contents/Home/jre/lib/libjawt.dylib;/Users/yikun/Library/Java/JavaVirtualMachines/azul-1.8.0_322/Contents/Home/jre/lib/server/libjvm.dylib
-- macOS universal (x86_64 / arm64) build
-- Performing Test COMPILER_OPT_ARCH_NATIVE_SUPPORTED
-- Performing Test COMPILER_OPT_ARCH_NATIVE_SUPPORTED - Failed
-- Performing Test COMPILER_OPT_ARCH_AVX_SUPPORTED
-- Performing Test COMPILER_OPT_ARCH_AVX_SUPPORTED - Failed
-- Not using libtools for plugins
-- Looking for CL_VERSION_3_0
-- Looking for CL_VERSION_3_0 - not found
-- Looking for CL_VERSION_2_2
-- Looking for CL_VERSION_2_2 - not found
-- Looking for CL_VERSION_2_1
-- Looking for CL_VERSION_2_1 - not found
-- Looking for CL_VERSION_2_0
-- Looking for CL_VERSION_2_0 - not found
-- Looking for CL_VERSION_1_2
-- Looking for CL_VERSION_1_2 - found
-- Found OpenCL: /Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/System/Library/Frameworks/OpenCL.framework (found version "1.2")
-- OpenCL Includes: /Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/System/Library/Frameworks/OpenCL.framework
-- OpenCL Libraries: /Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/System/Library/Frameworks/OpenCL.framework
CUDA_TOOLKIT_ROOT_DIR not found or specified
-- Could NOT find CUDA (missing: CUDA_TOOLKIT_ROOT_DIR CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
-- Configuring done (1.7s)
-- Generating done (0.0s)
-- Build files have been written to: /Users/yikun/code/beagle-lib/build
➜  build git:(support-linux-aarch64) make -j
[  8%] Building OpenCL kernels
[ 12%] Building CXX object libhmsbeagle/CPU/CMakeFiles/hmsbeagle-cpu.dir/BeagleCPUPlugin.cpp.o
[ 12%] Building CXX object libhmsbeagle/CMakeFiles/hmsbeagle.dir/benchmark/BeagleBenchmark.cpp.o
[ 20%] Building CXX object libhmsbeagle/CMakeFiles/hmsbeagle.dir/benchmark/linalg.cpp.o
[ 20%] Building CXX object libhmsbeagle/CPU/CMakeFiles/hmsbeagle-cpu-sse.dir/BeagleCPUSSEPlugin.cpp.o
[ 25%] Building CXX object libhmsbeagle/CMakeFiles/hmsbeagle.dir/beagle.cpp.o
[ 29%] Building CXX object libhmsbeagle/CMakeFiles/hmsbeagle.dir/plugin/Plugin.cpp.o
[ 33%] Building CXX object libhmsbeagle/CMakeFiles/hmsbeagle.dir/plugin/UnixSharedLibrary.cpp.o
[ 37%] Linking CXX shared library libhmsbeagle.dylib
[ 37%] Built target hmsbeagle
[ 41%] Building CXX object libhmsbeagle/JNI/CMakeFiles/hmsbeagle-jni.dir/beagle_BeagleJNIWrapper.cpp.o
Making OpenCL SP state count = 16
Making OpenCL SP state count = 32
Making OpenCL SP state count = 48
Making OpenCL SP state count = 64
Making OpenCL SP state count = 80
Making OpenCL SP state count = 128
Making OpenCL SP state count = 192
[ 45%] Linking CXX shared library libhmsbeagle-jni.jnilib
Making OpenCL SP state count = 256
Making OpenCL DP state count = 16 DP
Making OpenCL DP state count = 32 DP
[ 45%] Built target hmsbeagle-jni
Making OpenCL DP state count = 48 DP
Making OpenCL DP state count = 64 DP
Making OpenCL DP state count = 80 DP
Making OpenCL DP state count = 128 DP
Making OpenCL DP state count = 192 DP
Making OpenCL DP state count = 256 DP
[ 45%] Built target OpenKernels
[ 54%] Building CXX object libhmsbeagle/GPU/CMake_OpenCL/CMakeFiles/hmsbeagle-opencl.dir/__/KernelResource.cpp.o
[ 54%] Building CXX object libhmsbeagle/GPU/CMake_OpenCL/CMakeFiles/hmsbeagle-opencl.dir/__/GPUInterfaceOpenCL.cpp.o
[ 58%] Building CXX object libhmsbeagle/GPU/CMake_OpenCL/CMakeFiles/hmsbeagle-opencl.dir/__/OpenCLPlugin.cpp.o
[ 62%] Building CXX object libhmsbeagle/GPU/CMake_OpenCL/CMakeFiles/hmsbeagle-opencl.dir/__/KernelLauncher.cpp.o
[ 66%] Building CXX object libhmsbeagle/GPU/CMake_OpenCL/CMakeFiles/hmsbeagle-opencl.dir/__/GPUImplHelper.cpp.o
/Users/yikun/code/beagle-lib/libhmsbeagle/GPU/GPUInterfaceOpenCL.cpp:1089:5: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    sprintf(deviceDescription,
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
/Users/yikun/code/beagle-lib/libhmsbeagle/GPU/GPUInterfaceOpenCL.cpp:1089:5: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations]
    sprintf(deviceDescription,
    ^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here
__deprecated_msg("This function is provided for compatibility reasons only.  Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.")
^
/Library/Developer/CommandLineTools/SDKs/MacOSX13.1.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg'
        #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg)))
                                                      ^
1 warning generated.
[ 70%] Linking CXX shared library libhmsbeagle-opencl.so
[ 70%] Built target hmsbeagle-opencl
[ 75%] Linking CXX shared library libhmsbeagle-cpu-sse.so
[ 75%] Built target hmsbeagle-cpu-sse
[ 79%] Linking CXX shared library libhmsbeagle-cpu.so
[ 79%] Built target hmsbeagle-cpu
[ 83%] Building CXX object examples/CMakeFiles/synthetictest.dir/synthetictest/linalg.cpp.o
[ 91%] Building CXX object examples/CMakeFiles/hmctest.dir/hmctest/hmctest.cpp.o
[ 91%] Building CXX object examples/CMakeFiles/synthetictest.dir/synthetictest/synthetictest.cpp.o
[ 95%] Linking CXX executable hmctest
[ 95%] Built target hmctest
[100%] Linking CXX executable synthetictest
[100%] Built target synthetictest
➜  build git:(support-linux-aarch64) ll libhmsbeagle/
total 512
drwxr-xr-x  6 yikun  staff   192B Oct 11 11:12 CMakeFiles
drwxr-xr-x  9 yikun  staff   288B Oct 11 11:12 CPU
drwxr-xr-x  6 yikun  staff   192B Oct 11 11:12 GPU
drwxr-xr-x  6 yikun  staff   192B Oct 11 11:12 JNI
-rw-r--r--  1 yikun  staff    14K Oct 11 11:12 Makefile
-rw-r--r--  1 yikun  staff   5.5K Oct 11 11:12 cmake_install.cmake
-rw-r--r--  1 yikun  staff   272B Oct 11 11:12 hmsbeagle-1.pc
-rw-r--r--  1 yikun  staff   1.8K Oct 11 11:12 hmsbeagle-1ConfigVersion.cmake
-rwxr-xr-x  1 yikun  staff   222K Oct 11 11:12 libhmsbeagle.1.dylib
lrwxr-xr-x  1 yikun  staff    20B Oct 11 11:12 libhmsbeagle.dylib -> libhmsbeagle.1.dylib

martin-g · 2023-10-11T05:13:27Z

Thank you, @Yikun !

martin-g · 2023-10-11T05:19:24Z

I see that there are some more usages of __ARM64_ARCH_8__ in the plugin related code:

grep -rnHi '__ARM64_ARCH_8__' *
libhmsbeagle/CPU/BeagleCPUPlugin.cpp:20:#ifdef __ARM64_ARCH_8__
libhmsbeagle/CPU/BeagleCPUSSEPlugin.cpp:27:#ifdef __ARM64_ARCH_8__
libhmsbeagle/CPU/BeagleCPUSSEPlugin.cpp:164:#if defined(__ARM64_ARCH_8__)

IMO those should be replaced with __aarch64__ for better compatibility.

@Yikun Could you please do the following test on Mac ARM64:

$ cat > test.c
#if !defined(__aarch64__)
    #error __aarch64__ is not defined
#endif

#if !defined(__arm64__)
    #error __arm64__ is not defined
#endif

#if !defined(__ARM64_ARCH_8__)
    #error __ARM64_ARCH_8__ is not defined
#endif

#if !defined(__APPLE__)
    #error __APPLE__ is not defined
#endif

int main() {
	return 0;
}
Ctrl+D

$ gcc test.c

and paste the output

Yikun · 2023-10-11T07:47:52Z

➜  bioconda-recipes git:(aarch64) ✗ cat test.c
#if !defined(__aarch64__)
    #error __aarch64__ is not defined
#endif

#if !defined(__arm64__)
    #error __arm64__ is not defined
#endif

#if !defined(__ARM64_ARCH_8__)
    #error __ARM64_ARCH_8__ is not defined
#endif

#if !defined(__APPLE__)
    #error __APPLE__ is not defined
#endif

int main() {
        return 0;
}
➜  bioconda-recipes git:(aarch64) ✗ gcc test.c
➜  bioconda-recipes git:(aarch64) ✗ echo $?
0

martin-g · 2023-10-11T07:58:51Z

Thank you again, @Yikun !

Here is the result on Linux ARM64:

gcc test.c
test.c:6:6: error: #error __arm64__ is not defined
    6 |     #error __arm64__ is not defined
      |      ^~~~~
test.c:10:6: error: #error __ARM64_ARCH_8__ is not defined
   10 |     #error __ARM64_ARCH_8__ is not defined
      |      ^~~~~
test.c:14:6: error: #error __APPLE__ is not defined
   14 |     #error __APPLE__ is not defined
      |      ^~~~~

I am going to replace __ARM64_ARCH_8__ with __aarch64__ in the plugin code!

It is supported by both Mac M1/M2 and Linux ARM64 Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

martin-g · 2023-10-11T08:19:46Z

The CI checks passed on my fork: martin-g#2

msuchard · 2023-10-13T12:47:07Z

i can also confirm my M2 that (1) BEAGLE compiles both with and without NEON and that BEAST run-times (as expected) differ btw the generated (with and without NEON) libraries. thank you for your effort here!!!

martin-g · 2023-10-13T13:56:10Z

Awesome!
May I ask for a new release/tag please ? Thank you!

msuchard · 2023-10-13T14:16:21Z

done

martin-g force-pushed the support-linux-aarch64 branch from f730df2 to 5d28f8a Compare October 10, 2023 14:03

martin-g force-pushed the support-linux-aarch64 branch from 5d28f8a to 458fe43 Compare October 10, 2023 14:04

martin-g marked this pull request as draft October 10, 2023 14:05

martin-g marked this pull request as ready for review October 10, 2023 14:14

Replace __ARM64_ARCH_8__ with __aarch64__

4b77564

It is supported by both Mac M1/M2 and Linux ARM64 Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>

martin-g mentioned this pull request Oct 12, 2023

ask about compiling on arm. bio-arm/bio-arm.github.io#12

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msuchard merged commit 6d909c2 into beagle-dev:master Oct 13, 2023

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Update sse2neon.h to latest for better support for Linux ARM64 #206

Update sse2neon.h to latest for better support for Linux ARM64 #206

martin-g commented Oct 10, 2023

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msuchard commented Oct 13, 2023

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msuchard commented Oct 13, 2023

Update sse2neon.h to latest for better support for Linux ARM64 #206

Update sse2neon.h to latest for better support for Linux ARM64 #206

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