[gmx-users] Strange MPI problems. . .

Carsten Kutzner ckutzne at gwdg.de
Mon Aug 10 09:52:53 CEST 2009


probably there is just a problem with node126 on your system.  
errors can occur if there is still another (dead?) job occupying the  
myrinet interface.
You should check for such jobs on the node, kill them, and if it still  
does not work,
reboot that node.

Alternatively, if you just submit the same job again (and it ends up  
on different nodes),
I would guess that it runs fine.


On Aug 10, 2009, at 4:58 AM, Marc Charendoff wrote:

> Hello,
>        I am trying to perform a position restrained MD run on our  
> school cluster on a system I have successfully run on before. The  
> only difference is that this new run uses the 43a1 force field (the  
> original used gmx). All my preprocessing has gone well, but when I  
> submit to the cluster, my log file shows the following:
> [node126:13068] Error in mx_open_endpoint (error Failure querying MX  
> driver(wrong driver?))
> [node126:13068] mca_btl_mx_init: mx_open_endpoint() failed with  
> status=1
> warning:regcache incompatible with malloc
> NODEID=0 argc=12
> NODEID=1 argc=12
> [node126][0,1,0][btl_tcp_endpoint.c: 
> 572:mca_btl_tcp_endpoint_complete_connect] connect() failed with  
> errno=113
> I immediately reran the old calculation (gmx) which worked just  
> fine. I should also note the my energy minimization run (43a1) on a  
> single processor ran ok. Any guidance anyone could provide would be  
> appreciated.
> Much Thanks,
> Marc
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Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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