Re: AMBER: mpirun Permission denied.

From: David Watson <>
Date: Tue, 30 Dec 2008 23:04:40 -0600

Also, you should check to make sure that you have ssh configured
properly to use public/private key pairs, then use a combination of
ssh-agent and ssh-add as described in their manual pages if you wish
to use a passphrase on your private-key, which would probably be a
good idea.

In case this is all new to you, I would suggest reading the
documentation for openssh, particularly the requirements for
permissions on your home directory and ~/.ssh directory and the files
that should reside there. Another command that could be of use in this
regard is ssh-keygen to generate an rsa or dsa keypair in the first

Once you can successfully ssh without having to type in a passphrase,
you should be able to do multiprocessor runs.

If you are using the mpich2 implementation, you may need to run
mpdboot before this as well, but that's getting too far ahead at the

On Dec 30, 2008, at 8:32 PM, Jackie. J. Shen wrote:

> 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£º
>> 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
>> -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 - 01:22:43 PST
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