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Subject: Re: [OMPI users] [Fwd: Re: open mpi on non standard ssh port]
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2009-03-18 16:55:22


It means you started the jobs ok (via ssh) but Open MPI wasn't able to
open TCP sockets between the two MPI processes. Open MPI needs to be
able to communicate via random TCP ports between its MPI processes.

On Mar 18, 2009, at 8:39 AM, Bernhard Knapp wrote:

> Hey again,
>
> I tried to build a work around via port redirection: iptables -t
> nat -A PREROUTING -i eth1 -p tcp --dport 22 -j REDIRECT --to-port 5101
>
>
> If I do that then I can start the job:
>
> mpirun -np 2 -machinefile /home/bknapp/scripts/machinefile.txt
> mdrun -np 2 -nice 0 -s 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.tpr -
> o 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.trr -c
> 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.pdb -g
> 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.log -e
> 1fyt_PKYVKQNTLELAT_bindingRegionsOnly.md.edr -v
> bknapp_at_192.168.0.104's password:
> NNODES=2, MYRANK=0, HOSTNAME=quoVadis01
> NNODES=2, MYRANK=1, HOSTNAME=quoVadis04
>
> but it comes up with "[quoVadis01][[24802,1],0][btl_tcp_endpoint.c:
> 631:mca_btl_tcp_endpoint_complete_connect] connect() failed: No
> route to host (113)". The CPUs are calculating on both (physically
> different machines) but unfortunately no results are written ...
>
> Was the port redirection of 22 not enough or is there another problem?
>
> thx
> Bernhard
>
>
>
>
>
> -------- Original Message --------
> Subject:
> Re: open mpi on non standard ssh port
> Date:
> Wed, 18 Mar 2009 09:19:18 +0100
> From:
> Bernhard Knapp <bernhard.knapp_at_[hidden]>
> To:
> users_at_[hidden]
> References:
> <mailman.2006.1237281160.6040.users_at_[hidden]>
>
>
> come on, it must be somehow possible to use openmpi not on port
> 22!? ;-)
>
> >
> >------------------------------
> >
> >Message: 3
> >Date: Tue, 17 Mar 2009 09:45:29 +0100
> >From: Bernhard Knapp <bernhard.knapp_at_[hidden]>
> >Subject: [OMPI users] open mpi on non standard ssh port
> >To: users_at_[hidden]
> >Message-ID: <49BF6329.8090802_at_[hidden]>
> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >
> >Hi
> >
> >I want to start a gromacs simulation on a small cluster where non
> >standard ports are used for ssh. If I just use a "normal"
> maschinelist
> >file (with the ips of the nodes), consequently, the following error
> >comes up:
> >ssh: connect to host 192.168.0.103 port 22: Connection refused
> >
> >I guess that I need to somehow tell him to use the other ports. I
> tried
> >it in the following way (maschinelist file):
> >192.168.0.101 -p 5101
> >192.168.0.102 -p 5102
> >192.168.0.103 -p 5103
> >192.168.0.104 -p 5104
> >
> >But it seems this is not the correct way to specifiy the port:
> >Open RTE detected a parse error in the hostfile:
> > /home/bknapp/scripts/machinefile.txt
> >It occured on line number 1 on token 5:
> > -p
> >
> >How can I tell him to use port 5101 on machine 192.168.0.101?
> >May be the question is stupid but I could not find a solution via
> google
> >or search function ...
> >
> >cheers
> >Bernhard
> >
> >
> >
> >
>
>
> --
> Dipl.-Ing. (FH) Bernhard Knapp
> Univ.-Ass.postgrad.
> Unit for Medical Statistics and Informatics - Section for Biomedical
> Computersimulation and Bioinformatics
> Medical University of Vienna - General Hospital
> Spitalgasse 23 A-1090 WIEN / AUSTRIA
> Room: BT88 - 88.03.712
> Phone: +43(1) 40400-6673
> _______________________________________________
> users mailing list
> users_at_[hidden]
> http://www.open-mpi.org/mailman/listinfo.cgi/users

-- 
Jeff Squyres
Cisco Systems