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@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
List-Post: users@lists.open-mpi.org
Date: Wed, 18 Mar 2009 09:19:18 +0100
From: Bernhard Knapp <bernhard.kn...@meduniwien.ac.at>
To: us...@open-mpi.org
References: <mailman.2006.1237281160.6040.us...@open-mpi.org>
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.kn...@meduniwien.ac.at>
Subject: [OMPI users] open mpi on non standard ssh port
To: us...@open-mpi.org
Message-ID: <49bf6329.8090...@meduniwien.ac.at>
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
