[R-sig-hpc] Rmpi, lam, & Fedora 10
Hao Yu
hyu at stats.uwo.ca
Tue May 12 18:19:01 CEST 2009
When you install lam, make sure to enable shared lib. The default one is
static lib. Rmpi used to be OK with static mpi lib. Not any more.
Hao
Richard A. Bilonick wrote:
> I'm still working on getting Rmpi working on CentOS 5.3. At the same
> time, I thought I would try to install it on a dual opteron system with
> Fedora 10.
>
> I was able to install & boot lam and check to make sure it is working. I
> then installed Rmpi (telling it where to find things) and it compiled
> without any errors or warnings. So I'm making progress.
>
> However, when I start R (64-bit version 2.9.0) and load Rmpi I get:
>
>> library(Rmpi)
> Error in dyn.load(file, DLLpath = DLLpath, ...) :
> unable to load shared library
> '/usr/lib64/R/library/Rmpi/libs/Rmpi.so':
> libmpi.so.0: cannot open shared object file: No such file or directory
> Error in library(Rmpi) : .First.lib failed for 'Rmpi'
> Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi", .Platform
> $dynlib.ext, :
> dynamic/shared library '/usr/lib64/R/library/Rmpi/libs/Rmpi.so' was
> not loaded
>
>
> I'm not sure what the difference is between Rmpi.so and Rmpi.so.0.
>
> [goldy at dom libs]$ ll /usr/lib64/R/library/Rmpi/libs/Rmpi.so
> -rwxr-xr-x 1 root root 109431 2009-05-12
> 09:48 /usr/lib64/R/library/Rmpi/libs/Rmpi.so
>
> Any ideas on what went wrong and how to fix it?
>
> I've included the output from installing Rmpi below.
>
> Thanks.
>
> Rick B.
>
>
>
> [root at dom Download]# R CMD INSTALL Rmpi_0.5-7.tar.gz
> --configure-args=--with-mpi=/usr/lib64/lam
> * Installing to library \u2018/usr/lib64/R/library\u2019
> * Installing *source* package \u2018Rmpi\u2019 ...
> checking for gcc... gcc
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc accepts -g... yes
> checking for gcc option to accept ISO C89... none needed
> Try to find mpi.h ...
> Found in /usr/lib64/lam/include
> Try to find libmpi.so or libmpich.a
> Found libmpi in /usr/lib64/lam/lib
> Try to find liblam.so ...
> Found liblam in /usr/lib64/lam/lib
> checking for openpty in -lutil... yes
> checking for main in -lpthread... yes
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/lam/include -DMPI2 -DLAM -fPIC
> -I/usr/local/include -fpic -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c RegQuery.c -o
> RegQuery.o
> gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/lam/include -DMPI2 -DLAM -fPIC
> -I/usr/local/include -fpic -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c Rmpi.c -o Rmpi.o
> gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/lam/include -DMPI2 -DLAM -fPIC
> -I/usr/local/include -fpic -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c conversion.c -o
> conversion.o
> gcc -m64 -std=gnu99 -I/usr/include/R -DPACKAGE_NAME=\"\"
> -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\"
> -DPACKAGE_BUGREPORT=\"\" -I/usr/lib64/lam/include -DMPI2 -DLAM -fPIC
> -I/usr/local/include -fpic -O2 -g -pipe -Wall
> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m64 -mtune=generic -c internal.c -o
> internal.o
> gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o Rmpi.so RegQuery.o
> Rmpi.o conversion.o internal.o -L/usr/lib64/lam/lib -lmpi -llam -lutil
> -lpthread -fPIC -L/usr/lib64/R/lib -lR
> ** R
> ** demo
> ** inst
> ** preparing package for lazy loading
> ** help
> *** installing help indices
> >>> Building/Updating help pages for package 'Rmpi'
> Formats: text html latex example
> hosts text html latex
> internal text html latex
> mpi.abort text html latex
> mpi.apply text html latex example
> mpi.barrier text html latex
> mpi.bcast text html latex
> mpi.bcast.Robj text html latex
> mpi.bcast.cmd text html latex
> mpi.cart.coords text html latex example
> mpi.cart.create text html latex example
> mpi.cart.get text html latex example
> mpi.cart.rank text html latex example
> mpi.cart.shift text html latex example
> mpi.cartdim.get text html latex example
> mpi.comm text html latex example
> mpi.comm.disconnect text html latex
> mpi.comm.free text html latex
> mpi.comm.inter text html latex
> mpi.comm.set.errhandler text html latex
> mpi.comm.spawn text html latex
> mpi.const text html latex
> mpi.dims.create text html latex example
> mpi.exit text html latex
> mpi.finalize text html latex
> mpi.gather text html latex example
> mpi.gather.Robj text html latex example
> mpi.get.count text html latex
> mpi.get.processor.name text html latex
> mpi.get.sourcetag text html latex
> mpi.iapply text html latex
> mpi.info text html latex
> mpi.init.sprng text html latex
> mpi.intercomm.merge text html latex
> mpi.parSim text html latex
> mpi.parapply text html latex example
> mpi.probe text html latex
> mpi.realloc text html latex
> mpi.reduce text html latex
> mpi.remote.exec text html latex example
> mpi.scatter text html latex example
> mpi.scatter.Robj text html latex example
> mpi.send text html latex example
> mpi.send.Robj text html latex
> mpi.sendrecv text html latex example
> mpi.setup.rng text html latex
> mpi.spawn.Rslaves text html latex example
> mpi.universe.size text html latex
> mpi.wait text html latex
> ** building package indices ...
> * DONE (Rmpi)
> [root at dom Download]#
>
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