在Ubuntu 16.04 VirtualBox上安装Rmpi [英] Installing Rmpi on Ubuntu 16.04 VirtualBox
问题描述
我在VM VirtualBox上创建了新的ubuntu-16.04.2-desktop-amd64计算机，并且希望能够将R环境与Rmpi一起使用.
I created a new ubuntu-16.04.2-desktop-amd64 machine on VM VirtualBox and I want to be able to use the R environment with Rmpi.
以下两种方法都给出类似的错误.
Both of the below approaches gives a similar error.
更新的简化的预构建二进制方法:
在安装Ubuntu后，我打开了一个终端并执行以下命令:
When Ubuntu had installed I opened a terminal and executed the following commands:
~$ sudo apt-get update
~$ sudo apt-get install openmpi-bin
~$ sudo apt-get install r-base
~$ sudo apt-get install r-cran-rmpi
~$ R
这打开了R终端，我调用了跟随函数，导致了错误:
This opened the R terminal and I invoking the follow function which resulted in an error:
> library(Rmpi)
libmpi.so: cannot open shared object file: No such file or directory
Error : .onLoad failed in loadNamespace() for 'Rmpi', details:
call: fun(libname, pkgname)
error: Cannot start MPI_Init(). Exit
Error: package or namespace load failed for ‘Rmpi’
我尝试过的替代方法包括使用本地OpenMPI安装和使用R函数install.packages安装Rmpi软件包(请参见下文).这些都导致了相同的错误.
Alternative approaches that I have attempted include using a local OpenMPI installation and using the R function install.packages to install the Rmpi package (see below). These all resulted in the same error.
我还尝试通过将~$ sudo apt-get install mpich替换为上述过程中的第二个命令来使用MPICH(包括使用R函数安装软件包)，这会导致更加繁重的运行时错误.
I have also tried using MPICH by substituting ~$ sudo apt-get install mpich as the second command in the above procedure (including using the R function for installing the package) which results in an even more onerous runtime error.
有人知道我做错了什么或者我可以解决该安装错误吗?
Does anyone know what I have done wrong or what I can do to resolve this installation error?
或者，是否有人能够使用任何Linux发行版或具有预安装组件的映像成功地使用Rmpi安装VirtualBox计算机?
Or alternatively, have anyone been able to successfully install a VirtualBox machine with Rmpi using any Linux distro or an image with pre-installed components?
原始本地安装方法:
Original local installation approach:
I have followed the instructions on this blog to download OpenMPI version 2.1.0, compile and install it. However when I try to install the package in R with:
> install.packages("Rmpi", configure.args =
c("--with-Rmpi-include=/home/jormunr/openmpi/include",
"--with-Rmpi-libpath=/home/jormunr/openmpi/lib",
"--with-Rmpi-type=OPENMPI",
"--with-mpi=/home/jormunr/openmpi/"))
出现以下错误
Error: .onLoad failed in loadNamespace() for 'Rmpi', details:
call: dyn.load(file, DLLpath = DLLpath, ...)
error: unable to load shared object '/home/jormunr/R/x86_64-pc-linux-gnu-library/3.2/Rmpi/libs/Rmpi.so':
libmpi.so.20: cannot open shared object file: No such file or directory
Error: loading failed
Execution halted
ERROR: loading failed
我可以看到'libmpi.so.20'文件位于我作为安装参数之一提供的/home/jormunr/openmpi/lib中.
I can see that the 'libmpi.so.20' file is in the /home/jormunr/openmpi/lib that I provided as one of the parameter to the installation.
推荐答案
[免责声明:我不是Linux专家，只具有用户级技能.专家的任何贡献或纠正将不胜感激.]
[Disclaimer: I am not a Linux expert and merely have user level skills. Any contributions or corrections from an expert will be greatly appreciated.]
预构建二进制方法
尽管尝试了各种方法来安装预构建的二进制文件，但我没有设法使该选项起作用.这涉及在终端中执行命令"sudo apt-get install r-cran-rmpi"以安装r-cran-rmpi预先构建的软件包，该软件包还将自动安装列出的先决条件libopenmpi1.10软件包.但是，似乎文件'libmpi.so'没有包含在libopenmpi1.10包中，而是Rmpi库期望的，这会在R环境中导致找不到该文件的错误.
Although trying various ways to install the prebuilt binaries I did not manage to get this option to work. This involved executing in the terminal the command 'sudo apt-get install r-cran-rmpi' to install the r-cran-rmpi prebuilt packages which also automatically installs the libopenmpi1.10 package that is a listed prerequisite. However, it appears that the file 'libmpi.so' is not included in the libopenmpi1.10 package but expected by the Rmpi library which causes an error in the R environment that it cannot find this file.
本地安装方法
本地安装最终成功，但进行了一些修改.我使用默认设置创建了一个新的ubuntu-16.04.2-desktop-amd64 VirtualBox映像，但默认设置为2048MB内存和32GB硬盘空间.安装后，我打开了一个终端并执行了
The local installation did eventually succeed with a few amendments. I created a new ubuntu-16.04.2-desktop-amd64 VirtualBox image with default settings, except for 2048MB of memory and 32GB of hard drive space. When installed I opened a terminal and executed the commands from the Jovinge Lab website with the inclusion of the penultimate command which amends the run-time link editor's path and enables the install.package() function of R to find the 'libmpi.so' file. (also changed the version to 1.10.6 as this is the latest version release of version 1 – see below for version 2)
~$ cd /home/jormunr
~$ wget https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.2.tar.gz
~$ tar -zxvf openmpi-1.10.6.tar.gz
~$ cd openmpi-1.10.2
~$ ./configure --prefix=/home/jormunr
~$ make
~$ make install
~$ sudo apt-get install r-base
~$ export LD_LIBRARY_PATH=/home/jormunr/lib:$LD_LIBRARY_PATH
~$ R
这将打开R终端，我调用了该函数:
This opens an R terminal and I invoked the function:
> install.packages("Rmpi", configure.args =
+ c("--with-Rmpi-include=/home/jormunr/include/",
+ "--with-Rmpi-libpath=/home/jormunr/lib/",
+ "--with-Rmpi-type=OPENMPI",
+ "--with-mpi=/home/jormunr/"))
现在执行此操作没有错误，我可以使用以下R语句对其进行测试:
This now executed without errors and I could test it with the following R statements:
> library("Rmpi")
> mpi.spawn.Rslaves()
master (rank 0, comm. 1) of size 2 is running on: Valhalla
slave1 (rank 1, comm. 1) of size 2 is running on: Valhalla
> mpi.close.Rslaves()
[1] 1
> mpi.quit()
当我尝试使用OpenMPI版本2.1.0进行此过程时，安装成功完成，但是上述测试存在问题； mpi.spawn.Rslaves()函数已完成，但mpi.close.Rslaves()未完成–从未返回，并且终端被挂起.
When I tried this process with the OpenMPI Version 2.1.0 the installation completed successfully but the above test had issues; the mpi.spawn.Rslaves() function completed but mpi.close.Rslaves() did not complete – it never returned and the terminal was left hanging.
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