Trouble using Rmpi after successful installation
Okay I've actually managed to sort this error by creating a simlink to libmpi.so.0 in another directory: ln -s /usr/lib64/openmpi/1.3.2-gcc/lib/libmpi.so.0 /usr/lib64/R/lib/ Unfortunately this has led to another error:
library(Rmpi)
[syd:25489] mca: base: components_open: component timer / linux open function failed [syd:25583] mca: base: components_open: component timer / linux open function failed librdmacm: couldn't read ABI version. librdmacm: assuming: 4 libibverbs: Fatal: couldn't read uverbs ABI version. CMA: unable to open /dev/infiniband/rdma_cm -------------------------------------------------------------------------- WARNING: Failed to open "OpenIB-cma" [DAT_INTERNAL_ERROR:]. This may be a real error or it may be an invalid entry in the uDAPL Registry which is contained in the dat.conf file. Contact your local System Administrator to confirm the availability of the interfaces in the dat.conf file. -------------------------------------------------------------------------- I think this has something to do with the fact that I'm trying to install Rmpi on the slave image, i.e. I do a "chroot /cm/images/default-image" before running the installation. I do need to install this on the slave image also right? As I said it installed fine on the master node? Thanks, Paul
On Tue, Apr 27, 2010 at 12:40 PM, Sean Davis <sdavis2 at mail.nih.gov> wrote:
On Tue, Apr 27, 2010 at 7:23 AM, Paul Geeleher <paulgeeleher at gmail.com> wrote:
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-Rmpi-type=OPENMPI" Rmpi_0.5-8.tar.gz
This has worked for me in the past: CC=mpicc R CMD INSTALL --clean Rmpi_..... However, I haven't tried it very recently. Sean
But when I attempt to load Rmpi I get the following error:
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 wonder does anybody have an ideas as to what might be wrong here?
It seemed to install just fine on my master node by the way.
Thanks,
Paul.
--
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com
--
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland
--
www.bioinformaticstutorials.com
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Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com