AMBER Archive (2009)

Subject: RE: [AMBER] MM_PBSA not successful

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Aug 16 2009 - 13:15:42 CDT

> yes I am using a cluser machine
> When I try to run /u0/z/zz217/USG/amber/9.0/exe/pbsa -O -i pbsa.in
> -o pbsa_com.1.out -c ./snapshot_com.crd.1 -p ./GNNQQNYMYRSB.prmtop
>
> I got
>
> mikre_at_nid00092:~/PRION/MMPBSA> /u0/z/zz217/USG/amber/9.0/exe/pbsa -O
> -i pbsa.in -o pbsa_com.1.out -c ./snapshot_com.crd.1 -p
> ./GNNQQNYMYRSB.prmtop
> Illegal instruction

This almost certainly means you are using an executable which was built for
a different architecture (or chip version) than the machine you are running
on. Most likely it was built on a newer Intel or AMD chip than you have in
the node you are running on. You will need to compile a new version of AMBER
for the architecture of your cluster nodes. If you do not know how to do
this I would suggest talking with whoever manages your cluster who should
appreciate why the executable you have does not match the node architecture.

All the best
Ross

/\
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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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