Re: [AMBER-Developers] Backup file renaming?

From: Robert Duke <>
Date: Fri, 6 Mar 2009 11:34:58 -0500

Oops, sorry. I take it back, in that you gave an example of mapping content
in vmd (sorry, I scanned the mail too quickly). But still, the objection
only applies if you were to actually HAVE to use the .bak, in which case you
would probably rename it. And anything else you would come up with as a
mechanism is basically an extension-based backup name (.0, .1, .foo, .bar),
so there is not a lot in the way of options here. You can get into atomic
file write mechs, but really anything you do is going to consist of creating
a tmp and switching the name (even if you are using some atomic write
capability in an OS, and I have not looked recently at what is exposed to do
this in extant api's).
Regards - Bob
----- Original Message -----
From: "Carlos Simmerling" <>
To: "AMBER Developers Mailing List" <>
Sent: Friday, March 06, 2009 11:20 AM
Subject: Re: [AMBER-Developers] Backup file renaming?

> this does restrict file names for users, and the extension can be
> really useful (for example, using .rst7 for quick identification of
> type in vmd)
> On Fri, Mar 6, 2009 at 11:12 AM, Daniel Roe <>
> wrote:
>> Hi all,
>> On Fri, Mar 6, 2009 at 11:02 AM, Ross Walker <>
>> wrote:
>>> What you suggest might be a good way to address this assuming it is
>>> portable
>>> across all machine types - although it might be slightly overcomplicated
>>> for
>>> what we need here. I think just a single restart + .bak is suitable to
>>> fix
>>> the majority of crash issues. The key is to do it in a way that doesn't
>>> hurt
>>> performance - I.e. copying the current restart file to .bak then
>>> overwriting
>>> the .rst file is probably safest in terms of recovering from a crash
>>> with an
>>> intact restart file but is not good for performance. Renaming may be
>>> very
>>> fast and in the noise and is probably good enough to avoid corrupting
>>> the
>>> restart file if it crashes while that is happening.
>> Why not just have two fixed restart files, <restart name>.0 and
>> <restart name>.1, and alternate between the two.
>> No copying, no renaming, and you'll know which is more recent since
>> the time is written out at the top.
>> -Dan
>> --
>> Daniel R. Roe, Ph.D.
>> Research Chemist
>> National Institute of Standards and Technology
>> 100 Bureau Drive, Stop 8443
>> Gaithersburg, MD 20899-8443
>> (301) 975-8741
>> _______________________________________________
>> AMBER-Developers mailing list
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Received on Sun Mar 08 2009 - 01:10:15 PST
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