作者boshings (bo)
看板R_Language
標題[問題] Rmpi 安裝請教
時間Tue May 7 22:55:47 2019
[問題類型]:
程式諮詢
[軟體熟悉度]:
入門
[問題描述]:
我想在用國網中心HPC主機執行平行運算，Rmpi一直無法安裝成功。
嘗試了幾個環境模組仍然失敗。
1) gcc/6.3.0 2) intel/2018_u1 3)openmpi/gcc/64/1.10.3
[程式範例]:
> 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
[環境敘述]:
[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
[關鍵字]:
Rmpi
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1F：→ Wush978: 安裝 openmpi-devel 05/07 23:09
感謝W大回復，希望這次能順利~
※ 編輯: boshings (36.229.137.67), 05/07/2019 23:46:41
2F：→ celestialgod: 我用mpich2 安裝成功，openmpi沒成功過 05/09 00:00
3F：→ celestialgod: 安裝的時候記得要指定mpi type 05/09 00:02
4F：→ celestialgod: 網路上google找的到相關教學 05/09 00:02
5F：→ celestialgod: (系統是用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: 我好像沒用內建的install.packages成功過... 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 裡的 README 寫得很清楚 05/09 10:54