使用Intel C/C++ Compiler搭配Intel MKL编译R

Posted 2021-06-18 CompBioLab

1. 安装环境

名称	值
OS	Ubuntu 18.04
Disk space	> 30 GiB
Memory	≥ 1G

2. 安装Intel oneAPI (含C/C++编译器、MKL库)

  
    
    
  
 
   
 
    
 
     
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wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
 
    
 
    
 
     
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sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
 
    
 
    
 
     
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echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
 
    
 
    
 
     
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sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
 
    
 
    
 
     
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sudo apt-get install intel-basekit intel-hpckit -y
 
    
 
   
 
  

3. 安装R编译依赖

  
    
    
  
 
   
 
    
 
     
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sudo apt-get install subversion ccache texlive texlive-fonts-extra texlive-latex-extra libx11-dev libpcre2-dev libjpeg-dev libpng-dev libtiff-dev libxmu-dev libxt-dev libreadline-dev default-jre libbz2-dev libcurl4-gnutls-dev texinfo default-jdk -y
 
    
 
   
 
  

4. 设置编译前环境

环境变量/传递给编译器的参数			
   
     
     
   
 
    
 
     
 
      
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export PATH=/opt/intel/oneapi/compiler/latest/linux/bin/intel64:$PATH
 
     
 
     
 
      
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source /opt/intel/oneapi/mkl/latest/env/vars.sh intel64
 
     
 
     
 
      
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export _intel_arch=intel64
 
     
 
     
 
      
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export _intel_lib=mkl_intel_lp64
 
     
 
     
 
      
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export MKL="-L${MKLROOT}/lib/intel64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lmkl_rt -lpthread -lm -ldl"
 
     
 
     
 
      
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export _intel_cc_opt="-O3 -fPIC -m64 -march=native -fp-model precise -fp-model source -I${MKLROOT}/include"
 
     
 
    
 
   
FLAGS for compiler 


    
      
      
    
 
     
 
      
 
       
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export LDFLAGS="-qopenmp"
 
      
 
      
 
       
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export CFLAGS="${_intel_cc_opt}"
 
      
 
      
 
       
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export CXXFLAGS="${_intel_cc_opt}"
 
      
 
      
 
       
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export FFLAGS="${_intel_cc_opt}"
 
      
 
      
 
       
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export FCFLAGS="${_intel_cc_opt}"
 
      
 
     
 
    Redirect compiler prerequisite to Intel C/C++/Fortran Compiler

  
    
    
  
 
   
 
    
 
     
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export CC="icc"
 
    
 
    
 
     
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export CXX="icpc"
 
    
 
    
 
     
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export F77="ifort"
 
    
 
    
 
     
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export FC="ifort"
 
    
 
    
 
     
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export AR="xiar"
 
    
 
    
 
     
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export LD="xild"
 
    
 
    
 
     
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export LD_LIBRARY_PATH=/opt/intel/oneapi/compiler/latest/linux/compiler/lib/intel64
 
    
 
    
 
     
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source /opt/intel/oneapi/mkl/latest/env/vars.sh ${_intel_arch}
 
    
 
   
 
  		

According to this bug report^[6], the javah binary has been removed from OpenJDK 10 and the java header generator should be called "javac -h". If we search for "JAVAH" in R source tree, we could find this in /configure.ac:

   
     
     
   
 
    
 
     
 
      
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custom_JAVA_LIBS="${JAVA_LIBS}"
 
     
 
     
 
      
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custom_JAVA_CPPFLAGS="${JAVA_CPPFLAGS}"
 
     
 
     
 
      
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custom_JAVA_LD_LIBRARY_PATH="${JAVA_LD_LIBRARY_PATH}"
 
     
 
     
 
      
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custom_JAVA="${JAVA}"
 
     
 
     
 
      
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custom_JAVAC="${JAVAC}"
 
     
 
     
 
      
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custom_JAVAH="${JAVAH}"
 
     
 
     
 
      
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custom_JAR="${JAR}"
 
     
 
    
 
   
which means we could manually do this 

    
      
      
    
 
     
 
      
 
       
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export JAVAH="/usr/bin/javac -h"
 
      
 
     
 
    
PS: It works

5. 开始编译R

PS: 因为本次同时编译了4.0.5和development branch的R，因此图混着用了，除了dev branch性能稍好一些以外大概的东西应该都展示清楚了(

  
    
    
  
 
   
 
    
 
     
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cd /tmp/
 
    
 
    
 
     
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wget "https://cran.r-project.org/src/base-prerelease/R-latest.tar.gz" -q
 
    
 
    
 
     
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tar zxf R-latest.tar.gz && rm R-latest.tar.gz
 
    
 
    
 
     
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cd R-latest/
 
    
 
    
 
     
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sed -i '/^#undef HAVE_MATHERR/d' src/include/config.h.in
 
    
 
    
 
     
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./configure --prefix=/usr --libdir=/usr/lib/R/ --sysconfdir=/etc/R --datarootdir=/usr/share rsharedir=/usr/share/R/ rincludedir=/usr/include/R/ rdocdir=/usr/share/doc/R/ --with-x --enable-R-shlib --with-blas="$MKL" --with-lapack --with-tcltk LIBnn=lib
 
    
 
    
 
     
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make
 
    
 
   
 
  

6. 使用

		
  
    
    
  
 
   
 
    
 
     
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pwd ##先把R-devel文件夹放入用户目录，再将当前目录加入环境变量PATH里
 
    
 
    
 
     
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export PATH=/home/username/R-devel/bin:$PATH
 
    
 
   
 
  

7. 测试

跑分试试，左侧为4.0.5，右侧为dev branch r80254 (2021-05-01)

  
    
    
  
 
   
 
    
 
     
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Rscript ./dgemm.R
 
    
 
   
 
  

References

[1]  https://community.intel.com/t5/Intel-oneAPI-Math-Kernel-Library/Build-R-with-Intel-MKL-shared-library/td-p/1034642?profile.language=en
[2] https://community.intel.com/t5/Intel-C-Compiler/Error-when-compiling-R-from-source-code-ubuntu-18-04/td-p/1176401
[3]  https://aur.archlinux.org/packages/r-mkl/
[4]  https://cran.r-project.org/doc/manuals/r-release/R-admin.html
[5]  https://community.intel.com/t5/Intel-oneAPI-Math-Kernel-Library/Build-R-with-Intel-MKL-shared-library/td-p/1034642?profile.language=en

[6] bug report: https://bugs.launchpad.net/ubuntu/+source/ceph/+bug/1766995