RE: AMBER: Compiling Amber 7

From: Ross Walker <>
Date: Sat, 10 Feb 2007 09:11:54 -0800

Hi Dave,

> programs (i.e., sander)
> as a non-root user, I get I/O errors, permission denied, etc.
> Basically
> ...
> Once I know
> these details I can set the
> file permissions appropriately. Currently, MPI is set-up to
> be run by
> non-root users and of course
> we need to be able to run Amber7 in a non-root mode.

I would suggest you make a group called amber and add any users that will
run amber to this group. Then make the exe directory and all files in it
readable and executable by the amber group. You also need to make the dat
directory and its contents readable by the amber group. This should be all
you actually need. (obviously non-root users need access to mpirun etc). All
of the amber programs read and write from the directory the user is in when
they run the code (or if they overide it with command line arguments). Some
of the programs, such as Leap read from the dat directory.

The alternative is just to make everything under $AMBERHOME readable by the
amber group. And make the exe directory contents also executable by the the

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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Received on Sun Feb 11 2007 - 06:07:45 PST
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