RE: AMBER: amber8 error installation

From: Ross Walker <>
Date: Tue, 28 Mar 2006 20:35:03 -0800

Dear John,

> > If you don't want to run Leap on your
> > cluster, not recommended anyway as you should build the
> inpcrd and prmtop on
> > a local machine and copy them to the cluster to run MD,
> then you can ignore
> > the error message.
> I'm surprised that running leap is not recommended.
> Almost all of our
> users tend to work on Windows, and they log into our cluster,
> use leap to
> build inpcrd and prmtop files, and then launch their jobs. I
> hardly see
> how it would be easier to install amber/leap on all the
> Windows machines
> and then copy files over. Maybe I'm missing something?

If this is the case then you can justify installing leap on the cluster. It
can be installed under windows using cygwin but is not necessarily straight
forward. My comment regarding users building the inpcrd and prmtop files on
the cluster head node is that it is generally not recommended practice to
use the login nodes of clusters for interactive use. Typically these nodes
are responsible for queue management, nfs serving, internet routing etc.
Hence loading them up with user processes can be detrimental to the
performance of the rest of the cluster. However, if you have things
configured so that users can get interactive sessions on individual compute
nodes then the above does not apply. However, it does of course lock a node
that could otherwise be used for computation. If, however your cluster is
only small and you only have a few users you probably don't need to worry
about such things.

In which case I would contact whoever has root on the machine and ask them
to install Byacc and the X11 development libraries, you will then be able to
build leap successfully.

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Sun Apr 02 2006 - 06:10:10 PDT
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