问题描述
我一直在抓我的头一个多星期，没有回答我的问题。
我想用英特尔MKL 作为共享库。这里是我用来测试我的配置的小脚本：
＃！ / bin / sh
export MKL = / opt / intel / compilers_and_libraries_2016.0.109 / linux / mkl
MKL =-L $ {_ mkllibpath} \
-Wl， - start-group \
-lmkl_gf_lp64 \
-lmkl_gnu_thread \
-lmkl_core \
-Wl， - end-group \
-lgomp -lpthread
./configure --prefix = / usr \
--libdir = / usr / lib \
--datarootdir = / usr / share \
rsharedir = / usr / share / R / \
rincludedir = / usr / include / R / \
rdocdir = / usr / share / doc / R / \
--with -blas =$ {MKL}\
--with-lapack \
--enable-R-shlib
make -j4
此小脚本执行以下操作：
- 使用gcc和gfortran在x86_64上构建R
- 使用gnu线程构建R
- 将路径导出到英特尔MKL库
- 将BLAS动态链接到intel MKL
现在我开始疯狂的部分。
在一个系统上， Archlinux ，构建将允许我在build目录下面输入ldd的内容。
$ ldd bin / exec / R
.....
libmkl_gf_lp64.so => /opt/intel/mkl/lib/intel64/libmkl_gf_lp64.so（0x00007f7707797000）
libmkl_core.so => /opt/intel/mkl/lib/intel64/libmkl_core.so（0x00007f7705c2a000）
libmkl_gnu_thread.so => /opt/intel/mkl/lib/intel64/libmkl_gnu_thread.so（0x00007f7704ed3000）
libimf.so => /opt/intel/lib/libimf.so（0x00007f7704814000）
libintlc.so.5 => /opt/intel/lib/libintlc.so.5（0x00007f770284b000）
.......
这正是我要找的。现在，相同的脚本与英特尔MKL安装在相同的路径，运行 Fedora22 。
$ ldd bin / exec / R
linux-vdso.so.1（0x00007ffe9a9c5000）
libR.so => /usr/lib64/R/lib/libR.so（0x00007f45d9b69000）
libgomp.so.1 => /lib64/libgomp.so.1（0x00007f45d9947000）
libpthread.so.0 => /lib64/libpthread.so.0（0x00007f45d972a000）
libc.so.6 => /lib64/libc.so.6（0x00007f45d936a000）
libblas.so.3 => /lib64/libblas.so.3（0x00007f45d9111000）
libgfortran.so.3 => /lib64/libgfortran.so.3（0x00007f45d8de5000）
......
正如所见，根本没有链接到英特尔MKL。
我玩过各种制作选项，LD_PATHS，链接器选项等;我已经检查环境变量;我检查了ldconfig缓存;仍然不可能得到与Fedora的正确链接。
我会感激任何提示，在哪里可以找到我的问题的根源。
$经过多次尝试，下面是使用英特尔MKL和ICC构建R-cran的正确脚本：
$ b $ b ＃！ / bin / sh
source /opt/intel/compilers_and_libraries_2016.0.109/linux/bin/mklvars intel64
source /opt/intel/bin/compilervars.sh intel64
_icclibpath = /opt/intel/compilers_and_libraries_2016.0.109/linux/compiler/intel64/
_mkllibpath = $ {MKLROOT} / lib / intel64 /
MKL =-L $ {_ mkllibpath} -lmkl_rt -lpthread
export CC =icc
export CXX =icpc
export AR =xiar
export LD =xild
export F77 = ifort
export CFLAGS = - g -O3 -xHost -I $ {MKLROOT} / include
export CXXFLAGS = - g -O3 -xHost-I $ {MKLROOT} / include
export FFLAGS = - I $ {MKLROOT} / include
export FCFLAGS = - I $ {MKLROOT} / include
＃shared libs
./configure --with-blas =$ {MKL}--enable-R-shlib --enable-BLAS-shlib
＃static libs
＃。/ configure --with-blas =$ {MKL}--with-lapack
make -j4
注意：
- 该脚本正在为Parallel studio 2016写入。如果composerxe 2015，请更改路径
。
- libRlib和libRblas可以构建为共享或静态库。
- 可以添加更多选项进行配置。
- 是在脚本中源mklvars和compilervars，所以它不会
polluated你的shell环境一旦构建完成。
I have been scratching my head for more than a week, with no answer to my issue.I want to build R from cran source with Intel MKL1 as a shared library. Here is the small script I use to test my configuration:
#! /bin/sh
export MKL=/opt/intel/compilers_and_libraries_2016.0.109/linux/mkl
MKL=" -L${_mkllibpath} \
-Wl,--start-group \
-lmkl_gf_lp64 \
-lmkl_gnu_thread \
-lmkl_core \
-Wl,--end-group \
-lgomp -lpthread"
./configure --prefix=/usr \
--libdir=/usr/lib \
--datarootdir=/usr/share \
rsharedir=/usr/share/R/ \
rincludedir=/usr/include/R/ \
rdocdir=/usr/share/doc/R/ \
--with-blas="${MKL}" \
--with-lapack \
--enable-R-shlib
make -j4
This small script do the following:
- build R with gcc and gfortran on x86_64
- build R with gnu threads
- export the path to Intel MKL libraries
- dynamically link BLAS to intel MKL
Now the part where I start getting mad.On one system, Archlinux, the build will let me with the following output from ldd ran inside the build directory
$ ldd bin/exec/R
.....
libmkl_gf_lp64.so => /opt/intel/mkl/lib/intel64/libmkl_gf_lp64.so (0x00007f7707797000)
libmkl_core.so => /opt/intel/mkl/lib/intel64/libmkl_core.so (0x00007f7705c2a000)
libmkl_gnu_thread.so => /opt/intel/mkl/lib/intel64/libmkl_gnu_thread.so (0x00007f7704ed3000)
libimf.so => /opt/intel/lib/libimf.so (0x00007f7704814000)
libintlc.so.5 => /opt/intel/lib/libintlc.so.5 (0x00007f770284b000)
.......
This is exactly what I am looking for. Now, same script with Intel MKL installed in same path, run on Fedora22.
$ ldd bin/exec/R
linux-vdso.so.1 (0x00007ffe9a9c5000)
libR.so => /usr/lib64/R/lib/libR.so (0x00007f45d9b69000)
libgomp.so.1 => /lib64/libgomp.so.1 (0x00007f45d9947000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f45d972a000)
libc.so.6 => /lib64/libc.so.6 (0x00007f45d936a000)
libblas.so.3 => /lib64/libblas.so.3 (0x00007f45d9111000)
libgfortran.so.3 => /lib64/libgfortran.so.3 (0x00007f45d8de5000)
......
As seen, not links at all to Intel MKL.
I have played with all kinds of make options, with LD_PATHS, with linker options etc; I have checked environment varaibles; I have checked ldconfig cache; etc. Still impossible to get the correct linking with Fedora.
I would appreciate any hints, where to look at for finding the root of my issue.
解决方案 After many tries, below is the correct script to build R-cran with Intel MKL and ICC:
#! /bin/sh
source /opt/intel/compilers_and_libraries_2016.0.109/linux/bin/mklvars intel64
source /opt/intel/bin/compilervars.sh intel64
_icclibpath=/opt/intel/compilers_and_libraries_2016.0.109/linux/compiler/intel64/
_mkllibpath=${MKLROOT}/lib/intel64/
MKL=" -L${_mkllibpath} -lmkl_rt -lpthread"
export CC="icc"
export CXX="icpc"
export AR="xiar"
export LD="xild"
export F77="ifort"
export CFLAGS="-g -O3 -xHost -I${MKLROOT}/include"
export CXXFLAGS="-g -O3 -xHost -I${MKLROOT}/include"
export FFLAGS="-I${MKLROOT}/include"
export FCFLAGS="-I${MKLROOT}/include"
# shared libs
./configure --with-blas="${MKL}" --enable-R-shlib --enable-BLAS-shlib
# static libs
#./configure --with-blas="${MKL}" --with-lapack
make -j4
NOTE:
- the script is writen for Parallel studio 2016. Change pathaccordingly if composerxe 2015.
- libRlib and libRblas can be build as shared or static librairies.
- More options can be added to configure.
- Best is to source mklvars and compilervars in a script so it won'tpolluated your shell environment once the build is done.
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