Re: [bug #7225] Test Suite Check: palmer.py -- September 28, 2006 - 18:18

The problem with this one is probably that the modelfree4 program is
not located in the system path.  I would still consider this a relax
bug as the RelaxError message is confusing and inaccurate.  The way I
would consider fixing this one is to add a number of steps prior to
executing the external binary:

1.  Check that the file specified by the binary keyword option exists
and is a file.
2.  Check that the file is executable.
3.  Test that the file is a binary file.
4.  Test that the binary is located in the system path.
5.  If not, test that the binary in in the current directory (not
important but may as well).

At each stage, if the test fails a RelaxError message should be
printed which describes the problem precisely.  All these steps could
be implemented in a function such as 'self.test_binary()' in the file
'io.py'.  This should be done for the Dasha, Molmol, Grace, and OpenDX
functions as well.  I'll attempt an implemention later (I don't have
SVN access on the machine).

Edward



On 9/28/06, Alex Hansen <NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:
> URL:
>   <http://gna.org/bugs/?7225>
>
>                  Summary: Test Suite Check:  palmer.py
>                  Project: relax
>             Submitted by: viochemist
>             Submitted on: Thursday 09/28/2006 at 13:06
>                 Category: None
>                 Priority: 5 - Normal
>                 Severity: 3 - Normal
>                   Status: None
>                  Privacy: Public
>              Assigned to: None
>          Originator Name:
>         Originator Email:
>              Open/Closed: Open
>                  Release: Other (missing version)
>         Operating System: None
>
>     _______________________________________________________
>
> Details:
>
> Please see https://mail.gna.org/public/relax-users/2006-09/msg00031.html
> for a full post.
>
>
> -- the stage is set to 2 in palmer.py, so I change that to 1
>
> $ python relax palmer.py
>
> It fails with this at the end:
>
> ...
> relax> palmer.execute(run='m1', dir=None, force=1, binary='modelfree4')
> RelaxError: Execution of the program Modelfree4 has failed.
>
> I figure it needs modelfree4 to be there so, I copy it from another
> directory into  the relax directory and try again
>
> $ python relax palmer.py
>
> ...
> relax> palmer.create(run='m1', dir=None, force=0, binary='modelfree4',
> diff_search='none', sims=0, sim_type='pred', trim=0, steps=20,
> constraints=1, nucleus='15N', atom1='N', atom2='H')
> RelaxError: The file 'm1/mfin' already exists.  Set the force flag to 1 to
> overwrite.
>
> Oh yeah, modelfree doesn't like writing over things ... try again with force
> = 1
>
> $ python relax palmer.py
>
> ...
> relax> palmer.execute(run='m1', dir=None, force=1, binary='modelfree4')
> RelaxError: Execution of the program Modelfree4 has failed.
>
>
>
>
>
>
>     _______________________________________________________
>
> Reply to this item at:
>
>   <http://gna.org/bugs/?7225>
>
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