AMBER Archive (2009)

Subject: RE: [AMBER] Error in using Amber

From: Ross Walker (
Date: Thu Feb 26 2009 - 00:03:12 CST

Hi Sri,

This suggests that perhaps you do not have write permission to the directory
in which the output file is being created. Or that the file exists already
and you do not have permission to overwrite it.

You should check this - also make sure that each of the nodes running the
calculation in the parallel run mount the same file system and also have
relevant permissions to read and write to these files.

Can you run the calculation okay in serial?

All the best

> -----Original Message-----
> From: [] On
> Behalf Of sri noraima othman
> Sent: Wednesday, February 25, 2009 7:27 PM
> To:
> Subject: [AMBER] Error in using Amber
> Dear Amber experts,
> I am test sander.MPI using amber9 in SGI cluster.
> I tried the command below and I got the error output further blow.
> I have no idea how to fix this matter.
> Could anyone share your idea?
> mpirun -stats cl1n001,cl1n002,cl1n003,cl1n004 8
> /usr/local/amber9/exe/sander.MPI -O -i
> /home/amberadm/Amber/
> -o /home/amberadm/Amber/polyAT.out -p
> /home/amberadm/Amber/polyAT_vac.prmtop
> -c /home/amberadm/Amber/polyAT_vac.inpcrd -x
> /home/amberadm/Amber/polyAT_gb_init_min.crd
> -e /home/amberadm/Amber/polyAT_gb_init_min.en -inf
> /home/amberadm/Amber/
> -r /home/amberadm/Amber/polyAT_gb_init_min.rst
> Error: Unit 6 Error on OPEN: /home/amberadm/Amber/polyAT.out
> That I need to manually create output file or just let the command do
> that?
> Waiting for your reply.
> Thank you.
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