AMBER Archive (2007)

Subject: RE: AMBER: Amber 9 source code permissions (UNCLASSIFIED)

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Oct 29 2007 - 17:18:50 CST

Hi Marty,
 
Yes this is a problem that I have come across myself and something that we
should really fix in later versions of Amber. That is that nothing in
$AMBERHOME/exe/ should depend on anything in $AMBERHOME/src/
 
I believe that the mm_pbsa script is the only thing that has such
dependencies so I would do:
 
cd $AMBERHOME/src/
chmod -R 755 mm_pbsa
 
The files don't strictly need to be executable in this directory but the
Examples directory and the underlying subdirectory do so you can either go
through manually and set all the files to be 644 and the directories 755 or
just do everything as 755.
 
Note something else you may want to do is create a group called Amber and
then make the directories / files 750 that way you can restrict access to
people who are only members of the Amber group.
 
For the moment though the above should solve the problem and I believe
(someone may correct me if I am wrong here) but the mm_pbsa portion of the
code is open source and so you are fine to make this directory publicly
accessible.
 
All the best
Ross
 
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|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Monaghan, Martin (Cont, ARL/CISD)
Sent: Monday, October 29, 2007 14:31
To: amber_at_scripps.edu
Subject: AMBER: Amber 9 source code permissions (UNCLASSIFIED)

Classification: UNCLASSIFIED
Caveats: NONE
  
Everyone,

I've installed Amber 9 on our Linux cluster and everything has been running
great but I have a user asking about a permissions error. The user is
trying to use the script in the exe/ directory called mm_pbsa.pl which has a
line in it that points to:

use strict;
use lib ("$ENV{AMBERHOME}/src/mm_pbsa");
use mm_pbsa_global qw(@GC_PAR);

Right now the permissions are set to:

193 l5> ll
total 896
drwx--x--x 3 monaghan cta 32768 2007-10-29 16:02 .
drwx--x--x 25 monaghan cta 32768 2007-08-15 11:40 ..
drwx--x--x 8 monaghan cta 32768 2006-04-03 21:33 Examples
-rwx--x--x 1 monaghan cta 23312 2006-04-03 19:35 make_crd_hg.f
-rwx--x--x 1 monaghan cta 1896 2006-04-03 19:35 Makefile
-rwx--x--x 1 monaghan cta 16904 2006-04-03 19:35 mm_pbsa_calceneent.pm
-rwx--x--x 1 monaghan cta 1650 2006-04-03 19:35 mm_pbsa_createcoords.pm
-rwx--x--x 1 monaghan cta 16458 2006-04-03 19:35 mm_pbsa_createinput.pm
-rwx--x--x 1 monaghan cta 2677 2006-04-03 19:35 mm_pbsa_global.pm
-rwx--x--x 1 monaghan cta 992 2006-04-03 19:35 mm_pbsa_output.txt
-rwx--x--x 1 monaghan cta 2146 2006-04-03 19:35 mm_pbsa.pl
-rwx--x--x 1 monaghan cta 16044 2006-04-03 19:35 mm_pbsa_readinput.pm
-rwx--x--x 1 monaghan cta 1036 2006-04-03 19:35 mm_pbsa_statistics.pl
-rwx--x--x 1 monaghan cta 54314 2006-04-03 19:35 mm_pbsa_statistics.pm
-rwx--x--x 1 monaghan cta 2183 2006-04-03 19:35 mm_pbsa_util.pm
-rwx--x--x 1 monaghan cta 241211 2006-04-03 19:35 molsurf.c
-rwx--x--x 1 monaghan cta 10140 2006-04-03 19:35 molsurf.h

I don't want to have the source code open to the users and not break the
license agreement so would it be best to set every file but the fortran and
C files to 755?

thanks

Marty Monaghan
Raytheon
ARL-MSRC
410-278-7457
  
Classification: UNCLASSIFIED
Caveats: NONE

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