AMBER Archive (2006)

Subject: RE: AMBER: running sander on several nodes

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Sep 28 2006 - 12:37:28 CDT

> I input the following command:
> mpirun -np 4 $AMBERHOME/exe/sander -ng 2 -groupfile
> <$AMBERHOME/exe/sander -O -i md25000ps.in -o
> md25000ps.out -p epac1modeller.prmtop -c md1.rst -r
> md25000_md2.rst -x md25000ps_md2.mdcrd>
>
> and I got the following message:
> Missing name for redirect.

Get rid of the < and > brackets. I.e.

mpirun -np 4 $AMBERHOME/exe/sander -O -i md25000ps.in -o md25000ps.out -p
epac1modeller.prmtop -c md1.rst -r md25000_md2.rst -x md25000ps_md2.mdcrd

And also read the manual for the queuing system installed on your cluster
and the implementation of mpi that you are using.

All the best
Ross

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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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