[R] Rmpi installation over MPICH
Sean Davis
sdavis2 at mail.nih.gov
Fri Jun 17 14:35:48 CEST 2005
This is a rather obscure question, I realize. I have written to the
package author but have not heard back as of yet. I have read the
README in the package, as well, but it didn't give me enough detail to
diagnose the problems that I am having. (I did edit out the LAM-MPI
check in zzz.R.in.)
I am working to install Rmpi on top of MPICH on a beowulf cluster.
Below is the output of the install command (which seems to go OK and
then the start of the R session, which fails. I was hoping someone
with some experience installing Rmpi on MPICH could give me some help
with doing so.
Any help would be greatly appreciated....
Sean
[sdavis at beowulf Rmpi]$ R CMD INSTALL
--configure-args=--with-mpi=/opt/lib32/usr/lib
--library='/home/sdavis/R/library' ../Rmpi_0.4-9.tar.gz
* Installing *source* package 'Rmpi' ...
Try to find mpi.h ...
checking for gcc... gcc
checking for C compiler default output... 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 ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for egrep... 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
Try to find libmpi ...
checking for main in -lmpi... yes
Try to find liblam ...
checking for main in -llam... no
liblam not found. Probably not LAM-MPI
checking for openpty in -lutil... yes
checking for main in -lpthread... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating R/zzz.R
** libs
gcc -I/usr/lib/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\"
-DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1
-DHAVE_UNISTD_H=1 -I/usr/local/include -fPIC -O2 -g -pipe
-march=i386 -mcpu=i686 -c conversion.c -o conversion.o
gcc -I/usr/lib/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\"
-DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1
-DHAVE_UNISTD_H=1 -I/usr/local/include -fPIC -O2 -g -pipe
-march=i386 -mcpu=i686 -c internal.c -o internal.o
gcc -I/usr/lib/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\"
-DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1
-DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1
-DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1
-DHAVE_UNISTD_H=1 -I/usr/local/include -fPIC -O2 -g -pipe
-march=i386 -mcpu=i686 -c Rmpi.c -o Rmpi.o
gcc -shared -L/usr/local/lib -o Rmpi.so conversion.o internal.o Rmpi.o
-lmpi -lutil -lpthread
** R
** demo
** inst
** preparing package for lazy loading
** help
>>> 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.barrier text html latex
mpi.bcast text html latex
mpi.bcast.Robj text html latex
mpi.bcast.cmd text html latex
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.exit text html latex
mpi.finalize text html latex
mpi.gather text html latex
mpi.get.count text html latex
mpi.get.processor.name text html latex
mpi.get.sourcetag text html latex
mpi.info text html latex
mpi.init.sprng text html latex
mpi.intercomm.merge text html latex
mpi.parallel.sim text html latex
mpi.probe text html latex
mpi.reduce text html latex
mpi.remote.exec text html latex
mpi.scatter text html latex
mpi.send text html latex
mpi.send.Robj text html latex
mpi.sendrecv text html latex example
mpi.spawn.Rslaves text html latex
mpi.universe.size text html latex
** building package indices ...
* DONE (Rmpi)
[sdavis at beowulf Rmpi]$ mpirun -np 1 R
R : Copyright 2005, The R Foundation for Statistical Computing
Version 2.1.0 (2005-04-18), ISBN 3-900051-07-0
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for a HTML browser interface to help.
Type 'q()' to quit R.
> library('Rmpi',lib='~/R/library')
Rmpi version: 0.4-9
Rmpi is an interface (wrapper) to MPI APIs
with interactive R slave functionalities.
See `library (help=Rmpi)' for details.
unable to load shared library
'/home/sdavis/R/library/Rmpi/libs/Rmpi.so':
/home/sdavis/R/library/Rmpi/libs/Rmpi.so: cannot open shared object
file: No such file or directory
In addition: Warning message:
Cannot start LAM/MPI. Exit in: f(libname, pkgname)
Error in library("Rmpi", lib = "~/R/library") :
.First.lib failed for 'Rmpi'
Error in dyn.unload(x) : dynamic/shared library
'/home/sdavis/R/library/Rmpi/libs/Rmpi.so' was not loaded
>
And the library file is there....
[sdavis at beowulf libs]$ ls -la
-rwxr-xr-x 1 sdavis sdavis 46756 Jun 15 17:51 Rmpi.so
[sdavis at beowulf libs]$ pwd
/home/sdavis/R/library/Rmpi/libs
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