Re: AMBER: mpirun Permission denied.

From: Jackie. J. Shen <>
Date: Wed, 31 Dec 2008 10:32:17 +0800

Hi Andrew

In cluster, you may define the nodes where you want to perform MD. Such as:

$MPI_HOME/bin/mpirun -np 2 -machinefile [HOSTFILE] ..........

Also, you should give the full path to MPIRUN.

Hope it help.
Jackie. J. Shen

>Sent£º2008-12-25 14:52:51
>Subject£ºAMBER: mpirun Permission denied.

>Dear amber users,
>I'm trying to run Amber8 on cluster through ssh. It runs fine on cluster server's but when I use mpi I get an error:
>$ mpirun -np 2 -nolocal /data/soft/amber8/exe/sander -O -i -o polyAT_vac_md1_12Acut.out - c polyAT_gb_init_min.rst -p polyAT_vac.prmtop -r polyAT_gb_md1_12Acut.rst -x polyAT_gb_md1_12Acut.mdcrd
>Permission denied.
>Is it because of some wrong flags or I need to ask administrator to change permissions?
>Best regards,
>The AMBER Mail Reflector
>To post, send mail to
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> to

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Received on Wed Dec 31 2008 - 01:21:50 PST
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