[GE users] Rmpi under SGE

arnuschky arne.brutschy at ulb.ac.be
Fri Dec 17 11:48:32 GMT 2010


Hi,

yay, thanks a lot reuti, you're a star! Works fine!

Arne

On Fri, 2010-12-17 at 11:28 +0100, reuti wrote:
> Hi,
> 
> Am 17.12.2010 um 11:04 schrieb arnuschky:
> 
> > 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.
> 
> when Open MPI has a tight integration into SGE, I would assume SGE is configured to use "ssh". What is the output of `qconf -sconf`, there might be double entries?
> 
> http://marc.info/?l=npaci-rocks-discussion&m=126411729709528
> 
> If you want or must use ssh for sure, you need either passphraseless ssh keys (deprecated), or a hostbased authentication:
> 
> http://gridengine.sunsource.net/howto/hostbased-ssh.html
> 
> -- Reuti
> 
> 
> >        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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-- 
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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