[gmx-users] Gromacs and ssh problem

Bernhard Knapp bernhard.knapp at meduniwien.ac.at
Thu Feb 5 10:07:07 CET 2009


I installed Gromacs successfully on Fedora 8 nodes. Afterwards I ran a 
successful small simulation. Thereafter I moved the node to our 
server-room did the following:
- set ip adress, subnetmask and gateway
- changed the ssh port in /etc/ssh/sshd_config since we use port 
forwarding on our router and /usr/sbin/semanage port -a -t 
inetd_child_port_t -p tcp 5101
- changed the firewall settings to additionally allow the new port
- changed the hostname via hostname command

Then I started exactly the same simulation (same command, same data) as 
before (before the network configuration) and Gromacs comes up with:

ssh: quoVadis01: Name or service not known
A daemon (pid 5039) died unexpectedly with status 255 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 noticed that the job aborted, but has no info as to the process
that caused that situation.
mpirun: clean termination accomplished

How is possible that some network configurations screw up Gromacs? The 
simulation is running in parallel on the 4 local cores of the maschine 
no network interaction is necessary at all. Can anybody tell me where 
the problem is. The error message above is obviously incorrect since it 
was already working and the library paths are ok ...


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