[GE users] Rmpi under SGE

arnuschky arne.brutschy at ulb.ac.be
Fri Dec 17 10:04:23 GMT 2010


Hi,

we're having massive problems using Rmpi with OpenMPI under SGE. OpenMPI
is tested and works fine. We're submittig one master Rscript, which is
in turn spawning the required slaves using Rmpi. Unfortunately, this
fails:
        
        $ cat testRmpi.e3480556
        Warning: Permanently added 'compute-1-13.local' (RSA) to the list of known hosts.
        Warning: Permanently added 'compute-1-10.local' (RSA) to the list of known hosts.
        Warning: Permanently added 'compute-1-11.local' (RSA) to the list of known hosts.
        Warning: Permanently added 'compute-1-12.local' (RSA) to the list of known hosts.
        Warning: Permanently added 'compute-1-14.local' (RSA) to the list of known hosts.
        Permission denied, please try again.
        Permission denied, please try again.
        Permission denied (publickey,gssapi-with-mic,password).
        Permission denied, please try again.
        Permission denied, please try again.
        Permission denied (publickey,gssapi-with-mic,password).
        Permission denied, please try again.
        Permission denied, please try again.
        Permission denied, please try again.
        Permission denied (publickey,gssapi-with-mic,password).
        Permission denied, please try again.
        Permission denied (publickey,gssapi-with-mic,password).
        Permission denied, please try again.
        Permission denied, please try again.
        Permission denied (publickey,gssapi-with-mic,password).
        --------------------------------------------------------------------------
        A daemon (pid 26953) died unexpectedly with status 129 while attempting
        to launch so we are aborting.
        
        There may be more information reported by the environment (see above).
        
        This may be because the daemon was unable to find all the needed shared
        libraries on the remote node. You may set your LD_LIBRARY_PATH to have the
        location of the shared libraries on the remote nodes and this will
        automatically be forwarded to the remote nodes.
        --------------------------------------------------------------------------
        mpirun: clean termination accomplished
        
We're using openmpi-1.3.3 (--with-sge) and SGE V62u4.

Any hint's on what's going wrong here?

Cheers,
Arne

-- 
Arne Brutschy
Ph.D. Student                    Email    arne.brutschy(AT)ulb.ac.be
IRIDIA CP 194/6                  Web      iridia.ulb.ac.be/~abrutschy
Universite' Libre de Bruxelles   Tel      +32 2 650 2273
Avenue Franklin Roosevelt 50     Fax      +32 2 650 2715
1050 Bruxelles, Belgium          (Fax at IRIDIA secretary)

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