[R] Rmpi installation over MPICH

From: Sean Davis <sdavis2_at_mail.nih.gov>
Date: Fri 17 Jun 2005 - 22:35:48 EST


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@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

R : Copyright 2005, The R Foundation for Statistical Computing Version 2.1.0 (2005-04-18), ISBN 3-900051-07-0

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 > 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@beowulf libs]$ ls -la
-rwxr-xr-x 1 sdavis sdavis 46756 Jun 15 17:51 Rmpi.so
[sdavis@beowulf libs]$ pwd
/home/sdavis/R/library/Rmpi/libs



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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Jun 17 22:46:16 2005

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