This is actually an MPI issue, not an Amber issue. Several MPI
implementations require you to start a daemon in order for it to work
properly. Common examples are MPICH2 (older versions), which required you
to launch an mpd process (mpdboot) before running an MPI program, and
LAM/MPI, which requires lamboot. Based on your email, it appears that you
installed LAM/MPI with Amber 10 (so all of the binaries and everything are
in the AMBERHOME/exe directory). However, your error message below
suggests that $AMBERHOME/exe is not in your PATH. In this instance, you
actually have to provide the full path to your executables.
For instance:
$AMBERHOME/exe/lamboot
$AMBERHOME/exe/mpirun -np 2 $AMBERHOME/exe/sander.MPI -ng 2 ...
HTH,
Jason
On Sat, Nov 12, 2011 at 10:01 AM, leila karami <karami.leila1.gmail.com>wrote:
> when I use lamboot or lamnodes command,
>
> -bash: lamboot: command not found.
>
>
> but in exe and bin directory, there are lamboot, lamnodes, lamd and mpirun.
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Nov 12 2011 - 08:00:04 PST
