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[22.03-LTS-SP3]-O3 -flto -flto-partition=one -fipa-prefetch选项编译hmmer报Segmentation fault:during GIMPLE pass: vrp
已完成
#I96ID7
缺陷
erin_dan
创建于
2024-03-07 09:35
**【标题描述】-O3 -flto -flto-partition=one -fipa-prefetch选项编译hmmer报Segmentation fault:during GIMPLE pass: vrp** **一、缺陷信息** **【环境信息】** 软件信息 - OS版本及分支信息:openEuler22.03-LTS-SP3 - 内核信息:5.10.0-182.0.0.95.oe2203sp3.aarch64 - 发现问题的组件版本信息:gcc-10.3.1-51.oe2203sp3.aarch64 ``` 使用内建 specs。 COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/10.3.1/lto-wrapper 目标:aarch64-linux-gnu 配置为:../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,fortran,objc,obj-c++,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl --without-cloog --enable-gnu-indirect-function --build=aarch64-linux-gnu --with-stage1-ldflags=' -Wl,-z,relro,-z,now' --with-boot-ldflags=' -Wl,-z,relro,-z,now' --disable-bootstrap --with-multilib-list=lp64 --enable-bolt 线程模型:posix Supported LTO compression alg ``` **【问题复现步骤】** 1.配置环境变量: ``` export PATH=/usr/bin:$PATH export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH export CC="gcc -O3 -flto -flto-partition=one -fipa-prefetch" export CXX="g++ -O3 -flto -flto-partition=one -fipa-prefetch" export FC="gfortran -O3 -flto -flto-partition=one -fipa-prefetch" ``` 2.将编译器工具链中的./libexec/gcc/aarch64-linux-gnu/10.3.1/liblto_plugin.so.0.0.0拷贝至系统/usr/lib64/bfd-plugins目录,并进行软连接 ``` ln -s liblto_plugin.so.0.0.0 liblto_plugin.so.0 ln -s liblto_plugin.so.0.0.0 liblto_plugin.so ``` 3.安装openmpi ``` 安装依赖包:yum install numactl-devel-* systemd-devel-* wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.4.tar.gz tar -xf openmpi-4.0.4.tar.gz cd openmpi-4.0.4 ./configure --prefix=/path/openmpi-4.0.4 --enable-pretty-print-stacktrace --enable-orterun-prefix-by-default --enable-mpi-cxx --enable-mpi-fortran --with-cma --enable-mpi1-compatibility make -j96 make install export PATH=/path/openmpi-4.0.4/bin:$PATH export LD_LIBRARY_PATH=/path/openmpi-4.0.4/lib:$LD_LIBRARY_PATH export INCLUDE=/path/openmpi-4.0.4/include:$INCLUDE ``` 4.安装hmmer ``` 安装依赖包:yum install -y autoconf 源码下载: https://github.com/EddyRivasLab/hmmer/archive/refs/heads/h3-arm.zip https://github.com/EddyRivasLab/easel/archive/refs/heads/master.zip unzip h3-arm.zip unzip master.zip -d hmmer-h3-arm/ mv hmmer-h3-arm/ hmmer-3.3.2 cd hmmer-3.3.2/ mv easel-master easel autoconf ./configure --prefix=/path/hmmer-3.3.2/hmmer-install --enable-mpi --enable-neon CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77 make -j96 make check 可参考:https://www.hikunpeng.com/document/detail/zh/kunpenghpcs/prtg-osc/kylin_kunpeng_hmmer_332_02_0008.html ``` **【实际结果】** 
**【标题描述】-O3 -flto -flto-partition=one -fipa-prefetch选项编译hmmer报Segmentation fault:during GIMPLE pass: vrp** **一、缺陷信息** **【环境信息】** 软件信息 - OS版本及分支信息:openEuler22.03-LTS-SP3 - 内核信息:5.10.0-182.0.0.95.oe2203sp3.aarch64 - 发现问题的组件版本信息:gcc-10.3.1-51.oe2203sp3.aarch64 ``` 使用内建 specs。 COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/libexec/gcc/aarch64-linux-gnu/10.3.1/lto-wrapper 目标:aarch64-linux-gnu 配置为:../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,fortran,objc,obj-c++,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl --without-cloog --enable-gnu-indirect-function --build=aarch64-linux-gnu --with-stage1-ldflags=' -Wl,-z,relro,-z,now' --with-boot-ldflags=' -Wl,-z,relro,-z,now' --disable-bootstrap --with-multilib-list=lp64 --enable-bolt 线程模型:posix Supported LTO compression alg ``` **【问题复现步骤】** 1.配置环境变量: ``` export PATH=/usr/bin:$PATH export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH export CC="gcc -O3 -flto -flto-partition=one -fipa-prefetch" export CXX="g++ -O3 -flto -flto-partition=one -fipa-prefetch" export FC="gfortran -O3 -flto -flto-partition=one -fipa-prefetch" ``` 2.将编译器工具链中的./libexec/gcc/aarch64-linux-gnu/10.3.1/liblto_plugin.so.0.0.0拷贝至系统/usr/lib64/bfd-plugins目录,并进行软连接 ``` ln -s liblto_plugin.so.0.0.0 liblto_plugin.so.0 ln -s liblto_plugin.so.0.0.0 liblto_plugin.so ``` 3.安装openmpi ``` 安装依赖包:yum install numactl-devel-* systemd-devel-* wget https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.4.tar.gz tar -xf openmpi-4.0.4.tar.gz cd openmpi-4.0.4 ./configure --prefix=/path/openmpi-4.0.4 --enable-pretty-print-stacktrace --enable-orterun-prefix-by-default --enable-mpi-cxx --enable-mpi-fortran --with-cma --enable-mpi1-compatibility make -j96 make install export PATH=/path/openmpi-4.0.4/bin:$PATH export LD_LIBRARY_PATH=/path/openmpi-4.0.4/lib:$LD_LIBRARY_PATH export INCLUDE=/path/openmpi-4.0.4/include:$INCLUDE ``` 4.安装hmmer ``` 安装依赖包:yum install -y autoconf 源码下载: https://github.com/EddyRivasLab/hmmer/archive/refs/heads/h3-arm.zip https://github.com/EddyRivasLab/easel/archive/refs/heads/master.zip unzip h3-arm.zip unzip master.zip -d hmmer-h3-arm/ mv hmmer-h3-arm/ hmmer-3.3.2 cd hmmer-3.3.2/ mv easel-master easel autoconf ./configure --prefix=/path/hmmer-3.3.2/hmmer-install --enable-mpi --enable-neon CC=mpicc CXX=mpicxx FC=mpif90 F77=mpif77 make -j96 make check 可参考:https://www.hikunpeng.com/document/detail/zh/kunpenghpcs/prtg-osc/kylin_kunpeng_hmmer_332_02_0008.html ``` **【实际结果】** 
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