作者boshings (bo)
看板R_Language
标题[问题] Rmpi 安装请教
时间Tue May 7 22:55:47 2019
[问题类型]:
程式谘询
[软体熟悉度]:
入门
[问题描述]:
我想在用国网中心HPC主机执行平行运算，Rmpi一直无法安装成功。
尝试了几个环境模组仍然失败。
1) gcc/6.3.0 2) intel/2018_u1 3)openmpi/gcc/64/1.10.3
[程式范例]:
> install.packages("Rmpi")
Installing package into ‘
/home/u1/ee/R/x86_64-redhat-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL '
https://cran.mtu.edu/src/contrib/Rmpi_0.6-9.tar.gz'
Content type 'application/x-gzip' length 106745 bytes (104 KB)
==================================================
downloaded 104 KB
* installing *source* package ‘Rmpi’ ...
** package ‘Rmpi’ successfully unpacked and MD5 sums checked
checking for gcc... gcc -m64 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -m64 -std=gnu99 accepts -g... yes
checking for gcc -m64 -std=gnu99 option to accept ISO C89... none needed
checking for pkg-config... /usr/bin/pkg-config
checking if pkg-config knows about OpenMPI... no
checking how to run the C preprocessor... gcc -m64 -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking mpi.h usability... yes
checking mpi.h presence... yes
checking for mpi.h... yes
Trying to find libmpi.so or libmpich.a ...
checking for main in -lmpi... no
libmpi not found. exiting...
ERROR: configuration failed for package ‘Rmpi’
* removing ‘/home/u1/ee/R/x86_64-redhat-linux-gnu-library/3.5/Rmpi’
The downloaded source packages are in
‘/tmp/RtmpcVbC04/downloaded_packages’
Warning message:
In install.packages("Rmpi") :
installation of package ‘Rmpi’ had non-zero exit status
[环境叙述]:
[ee@clogin1 ~]$ module list
Currently Loaded Modulefiles:
1) openmpi/gcc/64/1.10.3
> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.5.2
[关键字]:
Rmpi
--
※ 发信站: 批踢踢实业坊(ptt.cc), 来自: 36.229.137.67
※ 文章网址: https://webptt.com/cn.aspx?n=bbs/R_Language/M.1557240953.A.5E4.html
1F：→ Wush978: 安装 openmpi-devel 05/07 23:09
感谢W大回复，希望这次能顺利~
※ 编辑: boshings (36.229.137.67), 05/07/2019 23:46:41
2F：→ celestialgod: 我用mpich2 安装成功，openmpi没成功过 05/09 00:00
3F：→ celestialgod: 安装的时候记得要指定mpi type 05/09 00:02
4F：→ celestialgod: 网路上google找的到相关教学 05/09 00:02
5F：→ celestialgod: (系统是用centos 7) 05/09 00:05
6F：→ celestialgod: PS: 用wget先抓下套件tar.gz 再用R CMD INSTALL 05/09 00:06
7F：→ celestialgod: 我好像没用内建的install.packages成功过... 05/09 00:06
8F：→ clickhere: 找出 mpi.h 和 libmpi.so 的 path 05/09 10:51
9F：→ clickhere: 用 R CMD INSTALL Rmpi*.tar.g --configure-args=" 05/09 10:53
10F：→ clickhere: --with-Rmpi-include=...path.to.mpi.h 05/09 10:53
11F：→ clickhere: --with-Rmpi-libpath=...path.to.libmpi.so" 05/09 10:54
12F：→ clickhere: Rmpi 里的 README 写得很清楚 05/09 10:54