Note:
libmpi.dylib: cannot open shared object file: No such file or directory
Linux does not have .dylib's: Darwin (part of Mac OS X) does.
This is not an R question (it seems to be about your MPI installation)
and you need to discuss it with the package maintainer (see the posting
quide).
Hi all,
I am trying to install the Rmpi package in R and, while the installation
itself works, it breaks down when trying to load the library. I think it
has something to do with shared vs static loading of helper libraries,
or the order in which shared libraries are loaded, but I am not sure.
R
Kristian,
> Another update: I ditched the pre-installed version of openmpi and
> installed openmpi from source (./configure --without-openib).
A very reasonable approach. Remembering my own struggles with SuSE years
ago, I did not dare to propose that procedure.
> Compiling and running your tes
Another update: I ditched the pre-installed version of openmpi and
installed openmpi from source (./configure --without-openib).
Compiling and running your test programme gives me the following error:
unger@zytosrv01dmi:~/R_projects/OS> ./mtest
[zytosrv01dmi:6094] *** An error occurred in MPI_Sen
Hi Hugo
One step closer! I added the path to libmpi to ld.so.conf and ran ldconfig
(see
http://www.linuxforums.org/forum/programming-scripting/80405-linking-shared
-libraries.html).
Compiling the code you sent me works but running the file gets stuck with
the following message:
./mtest
librdmacm
Dear Kristian,
please run exactly
mpicc mtest.c -o mtest
If you really need it, add -v separately. mpicc is nothing but a compiler
wrapper.
The "-o" switch specifies the outfile name, which has to follow immediately
after "-o",
with or without a blank character in between. I'm
Dear Hugo
I ran the command with the verbose switch and get the following output:
> mpicc mtest.c -ov mtest
mtest: In function `_start':
/usr/src/packages/BUILD/glibc-2.11.1/csu/../sysdeps/x86_64/elf/start.S:65:
multiple definition of `_start'
/usr/lib64/gcc/x86_64-suse-linux/4.3/../../../../lib6
Kristian,
these are the usual problems with binary distributions.
Regarding
> --with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include
and configure output
> checking for mpi.h... no
... so does "/usr/lib64/mpi/gcc/openmpi/include" really exist? At least,
that appears to b
Thanks Hugo.
I am pretty sure openmpi is installed:
# zypper se openmpi
Loading repository data...
Reading installed packages...
S | Name | Summary | Type
--+---+-+---
i | openmpi | A powerful implementaio
Kristian,
I just tried that particular command here on a Gentoo system with
openmpi-1.5.3 installed, because I wondered why the Rmpi configure
script tests for "main" function in a shared library ...
But I got a completly different output from configure. While the
linker succeeds here, the pa
Thank you very much Hugo. Using the command as suggested results exactly
the same error:
# R CMD INSTALL
--configure-args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openmpi/include
--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64
--with-Rmpi-type=OPENMPI" Rmpi_0.5-4.tar.gz
* installing to library
Hmm,
looks like there was a trailing blank after the backslash and before end of
line,
resulting in --with-Rmpi-libpath possibly not recognised:
> \--with-Rmpi-libpath=/usr/lib64/mpi/gcc/openmpi/lib64 \
I also doubt there is real need to escape newlines within a string. But another
possib
Hi there
I am trying to install Rmpi (version 0.5-4) on our 8-core SUSE Linux
Enterprise Server 11 SP1. I read all I could find about Rmpi installation
but still cannot get it working.
Here the last command that I used:
R CMD INSTALL
--configure.args="--with-Rmpi-include=/usr/lib64/mpi/gcc/openm
Hi guys,
I'm trying to install Rmpi on the slave nodes of my cluster. The
installation seems to work with no errors or warnings using this
command:
R CMD INSTALL
--configure-args="--with-Rmpi-include=/usr/lib64/openmpi/1.3.2-gcc/include
--with-Rmpi-libpath=/usr/lib64/openmpi/1.3.2-gcc/lib
--with
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