R 和 nvblas.dynlib（在 mac 上）

Question

我通过 CRAN. I also have openblas installed via homebrew 在 mac 上安装了 R。我可以按如下方式在 BLAS 实现之间切换：

参考 blas（我认为是 netlib）：

ln -sf /Library/Frameworks/R.framework/Resources/lib/libRblas.0.dylib /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib

vecLib（Apple 的 BLAS）：

 ln -sf /System/Library/Frameworks/Accelerate.framework/Frameworks/vecLib.framework/Versions/Current/libBLAS.dylib /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib

openblas（通过自制软件提供）：

brew link openblas --force
ln -sf /usr/local/lib/libopenblas.dylib /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib

在 3 个选项中，openblas 似乎是最快的选项（尽管 vecLib 紧随其后）。

不过，我想尝试更多的力量：

我installed CUDA 6.5 from NVIDIA。这会将一堆文件下载到 /Developer/NVIDIA/，并将其中一些文件 link 下载到 /usr/local/cuda。我在 ~/.profile:

中设置了我的 cuda 环境变量

export PATH="/usr/local/cuda/bin:$PATH"
export LD_LIBRARY_PATH="/usr/local/cuda/lib:$LD_LIBRARY_PATH"
export CUDA_ROOT="/usr/local/cuda/bin"
export CUDA_HOME="/usr/local/cuda"
export NVBLAS_CONFIG_FILE="/Users/me/nvblas.conf"

然后我创建了一个包含以下条目的“/Users/me/nvblas.conf”：

NVBLAS_CPU_BLAS_LIB /usr/local/lib/libopenblas.dylib
NVBLAS_GPU_LIST ALL0
NVBLAS_TILE_DIM 2048
NVBLAS_AUTOPIN_MEM_ENABLED

理论上，对于 nvblas.dylib.

中未包含的 BLAS 函数，这应该将 nvblas.dylib 指向 libopenblas.dylib

到目前为止一切顺利。接下来就是linkR对nvblas.dylib:

ln -sf /usr/local/cuda/lib/libnvblas.dylib /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib

然而，当我启动 R 时，似乎 libRlapack.dylib 无法找到它正在寻找的所有 BLAS 函数：

me:~ me$ R
[NVBLAS] Using devices :0 
[NVBLAS] Config parsed

R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Library/Frameworks/R.framework/Versions/3.1/Resources/library/stats/libs/stats.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.1/Resources/library/stats/libs/stats.so, 6): Symbol not found: _dasum_
  Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libRlapack.dylib
  Expected in: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libRblas.dylib
 in /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libRlapack.dylib
During startup - Warning message:
package ‘stats’ in options("defaultPackages") was not found

openblas 本身运行良好，并提供了 R 正在寻找的所有功能，所以我认为错误是 libnvblas.dylib 没有正确地回退到 libopenblas.dylib.

无论 CPU BLAS 我将 libnvblas.dylib 指向 (netlib、vecLib、openblas) 是什么，都会发生这种情况。谁能帮我解决这个错误？是否还有其他我需要添加到我的路径或 link 以使 libnvblas.dylib 在 mac?

上正确使用 R

相关错误大概是：

Symbol not found: _dasum_
Referenced from: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libRlapack.dylib
Expected in: /Library/Frameworks/R.framework/Versions/3.1/Resources/lib/libRblas.dylib

在我看来 nvblas 没有转发 _dasum_ 到 openblas。

/编辑：

otool -L /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib

产量：

/Library/Frameworks/R.framework/Resources/lib/libRblas.dylib:
    @rpath/libnvblas.6.5.dylib (compatibility version 0.0.0, current version 6.5.14)
    @rpath/libcublas.6.5.dylib (compatibility version 0.0.0, current version 6.5.14)
    /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 635.21.0)
    /usr/lib/libstdc++.6.dylib (compatibility version 7.0.0, current version 52.0.0)
    /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 159.1.0)

Answer 1

我遇到了和你一样的问题。在 OSX 下覆盖库而不是替换 R.framework 中的库为我解决了问题：

$ DYLD_FORCE_FLAT_NAMESPACE=y DYLD_INSERT_LIBRARIES=/Developer/NVIDIA/CUDA-7.0/lib/libnvblas.7.0.dylib R

R 和 nvblas.dynlib（在 mac 上）

R and nvblas.dynlib (on a mac)

cuda

r

blas

openblas

nvblas