Hi Andrew
In cluster, you may define the nodes where you want to perform MD. Such as:
$MPI_HOME/bin/mpirun -np 2 -machinefile [HOSTFILE] ..........
Also, you should give the full path to MPIRUN.
Hope it help.
Jackie. J. Shen
2008-12-31
-----------------------Original-------------------------
>From£ºdrugdesign
>Sent£º2008-12-25 14:52:51
>To£ºamber.scripps.edu
>Cc£º
>Subject£ºAMBER: mpirun Permission denied.
>>
>Dear amber users,
>I'm trying to run Amber8 on cluster through ssh. It runs fine on cluster server's but when I use mpi I get an error:
>$ mpirun -np 2 -nolocal /data/soft/amber8/exe/sander -O -i polyAT_gb_md1_12Acut.in -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,
>Andrew
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Received on Wed Dec 31 2008 - 01:21:50 PST
