Re: [AMBER-Developers] Backup file renaming?

From: Robert Duke <>
Date: Sat, 7 Mar 2009 15:27:21 -0500

Yes, I agree also with Ross. And even if it would work, it is a change in an
external interface (the .rst) file that is being done to slightly simplify a
programming issue (how to get to rename functionality from different
versions of fortran on different platforms). I don't believe that is a huge
deal, though the fortran vs. c strings issue can be a pain if you can't find
a fortran interface to rename functionality.
Regards - Bob
----- Original Message -----
From: "Ross Walker" <>
To: "'AMBER Developers Mailing List'" <>
Sent: Saturday, March 07, 2009 3:20 PM
Subject: RE: [AMBER-Developers] Backup file renaming?

> Hi Joe,
>> The one disadvantage is that Fortran doesn't have portable file
>> manipulation commands, so file RENAME and DELETE are non-standard and
>> may require C library functions.
>> An alternative approach is to have a single file that contains 2 sets of
>> restart data, written with direct access. You can write restart data to
>> the inactive half, then change the active flag last.
> I don't believe that this will work. The key is to avoid file corruption
> that occurs for example when a node dies (or the queuing system kills you)
> while the file is being written. This often results in corrupt files or
> files containing garbage. Sure one would hope that writing to different
> parts of the file would be fine and it probably would be if you were
> writing
> to the second half when it crashes but if you are writing to the first
> half
> I wouldn't expect the second half to remain intact. Especially seeing as
> most of the filesystems are things like Lustre etc which write things in
> chunks my expectation would be that you would loose a chunk of data and
> chances are this would overlap with the second part of the file.
> I think it is much safe and much much simpler from a user perspective (and
> completely maintains backwards compatibility) to just have the .rst and
> .rst.bak system with simple renaming. We just need to add the c routines
> to
> do this in src/lib and link it in. I'll probably try and do it next week
> if
> I get a chance.
> All the best
> Ross
> /\
> \/
> |\oss Walker
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
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Received on Sun Mar 08 2009 - 01:21:13 PST
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