[R-sig-hpc] Error in library(Rmpi)

[Hao Yu]

If you are able to
./R CMD INSTALL /root/src/Rmpi/Rmpi_0.5-7.tar.gz
 --configure-args=--with-mpi=/usr/lam

I assume Lam is in /usr/lam. So its lib must be in /usr/lam/lib or
usr/lam/lib64. Modify R script and add
LD_LIBRARY_PATH=/usr/lam/lib64

right after the first two lines. Then run R CMD ldd again to see if all
libs are sourced properly.

Hao

Arash Fard wrote:
> Dear Hao,
>
> I recognized that Rmoi.so points to MPICH libraries by mistake, as you may
> see followed the result of "R CMD ldd path_to_Rmpi.so". It must be the
> cause
> of its wrong behavior at run time. May you please advise me how I can
> dictate the right pathe to LAM libraries at the installation time.
>
> Thank you,
> Arash
> Odum School of Ecology
> The University of Georgia
>
> [root at furcatus ~]# R CMD ldd /usr/local/lib64/R/library/Rmpi/libs/Rmpi.so
>         PIC => not found
>         libmpich-gnu.so.1 => /usr/lib64/MPICH/p4/gnu/libmpich-gnu.so.1
> (0x0000002a95697000)
>         libutil.so.1 => /lib64/libutil.so.1 (0x0000002a9586b000)
>         libpthread.so.0 => /lib64/tls/libpthread.so.0 (0x0000002a9596e000)
>         libc.so.6 => /lib64/tls/libc.so.6 (0x0000002a95a84000)
>         libX11.so.6 => /usr/X11R6/lib64/libX11.so.6 (0x0000002a95cbd000)
>         libbproc.so.2 => /usr/lib64/libbproc.so.2 (0x0000002a95eb6000)
>         libbeomap.so.0.1 => /usr/lib64/libbeomap.so.0.1
> (0x0000002a95fbd000)
>         libbeostat.so.0 => /usr/lib64/libbeostat.so.0 (0x0000002a960c0000)
>         libdl.so.2 => /lib64/libdl.so.2 (0x0000002a961c4000)
>         /lib64/ld-linux-x86-64.so.2 (0x000000552aaaa000)
>
>
> On Thu, Jul 16, 2009 at 9:53 AM, Hao Yu <hyu at stats.uwo.ca> wrote:
>
>> Did you turn on dynamic lib when you were installing lam? The default
>> was
>> static lib. Rmpi needs libmpi.so and liblam.so to work. Also use
>>             R CMD ldd path_to_Rmpi.so
>> to see if Rmpi finds all libs.
>>
>> Hao
>>
>> Arash Fard wrote:
>> > Hi,
>> > I successfully installed Rmpi_0.5-7 for R-2.9.1; the installation
>> command
>> > was:
>> >
>> > ./R CMD INSTALL /root/src/Rmpi/Rmpi_0.5-7.tar.gz
>> > --configure-args=--with-mpi=/usr/lam
>> >
>> > However, when I call it inside R, I face this error:
>> >
>> >> library(Rmpi)
>> > Error in dyn.load(file, DLLpath = DLLpath, ...) :
>> >   unable to load shared library
>> > '/usr/local/lib64/R/library/Rmpi/libs/Rmpi.so':
>> >   /usr/local/lib64/R/library/Rmpi/libs/Rmpi.so: undefined symbol:
>> > lam_mpi_double
>> > Error in library(Rmpi) : .First.lib failed for 'Rmpi'
>> > Error in dyn.unload(file.path(libpath, "libs", paste("Rmpi",
>> > .Platform$dynlib.ext,  :
>> >   dynamic/shared library
>> '/usr/local/lib64/R/library/Rmpi/libs/Rmpi.so'
>> > was
>> > not loaded
>> >
>> > Please be informed that the environmental variables that I have set
>> for
>> > LAM
>> > are:
>> > LD_LIBRARY_PATH=/usr/lib64/LAM/gnu:$LD_LIBRARY_PATH
>> > PATH=/usr/lam/bin/gnu:/usr/lam/bin:$PATH
>> > MANPATH=/usr/lam/share/man:$MANPATH
>> >
>> > The result for "lamboot -v" is:
>> > LAM 7.1.2/MPI 2 C++/ROMIO/bproc - Indiana University
>> >
>> > n-1<26696> ssi:boot:bproc: beomap now in use, ignoring boot schema
>> file
>> > n-1<26696> ssi:boot:bproc: found master node (scyld.localdomain).
>> > Skipping
>> > checks.
>> > n-1<26696> ssi:boot:bproc:vector: launching on nodes -1
>> > n-1<26696> ssi:boot:base:linear_windowed: booting n0
>> (scyld.localdomain)
>> > n-1<26696> ssi:boot:bproc: starting lamd on (scyld.localdomain)
>> >
>> > The result for "lamnodes" is:
>> > n0      master:1:origin,this_node
>> >
>> > The result for "lamexec C hostname" is:
>> > furcatus.ecology.uga.edu
>> >
>> > I also added LD_LIBRARY_PATH to R script, but it was useless. I would
>> > appreciate it if you could help me.
>> >
>> > Thank you,
>> > Arash
>> >
>> > Odum School of Ecology
>> > The University of Georgia
>> >
>> >       [[alternative HTML version deleted]]
>> >
>> > _______________________________________________
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>> > R-sig-hpc at r-project.org
>> > https://stat.ethz.ch/mailman/listinfo/r-sig-hpc
>> >
>>
>>
>> --
>> Department of Statistics & Actuarial Sciences
>> Fax Phone#:(519)-661-3813
>> The University of Western Ontario
>> Office Phone#:(519)-661-3622
>> London, Ontario N6A 5B7
>> http://www.stats.uwo.ca/faculty/yu
>>
>


-- 
Department of Statistics & Actuarial Sciences
Fax Phone#:(519)-661-3813
The University of Western Ontario
Office Phone#:(519)-661-3622
London, Ontario N6A 5B7
http://www.stats.uwo.ca/faculty/yu