RE: [AMBER-Developers] Update question

From: Ross Walker <>
Date: Thu, 5 Mar 2009 15:30:00 -0800

Hi Lachele,

This is 'in my experience' operating system dependent. In theory replacing
the executable with another one while that executable is running should not
cause a problem. I.e. the executable that was present has been loaded into
memory. However, this is not always true and certainly isn't true in the
case of shared libraries like MKL etc. If you link these shared and then
change them during a run you can all sorts of problems.

The same can be true of the executable. I have certainly seen problems in
the past on IBM AIX where replacing the executable would ultimately crash
the job since IBM didn't necessarily load the entire executable into memory.
I have not seen this problem on Linux although that does not of course mean
it doesn't exist.

Short answer is if the job is still running okay you are probably fine. I
doubt it will give the wrong answer because you moved / updated / removed
the executable but rather would just crash with some error.

In general when running very long runs (where I don't want to keep
restarting etc) I place the statically linked executable in the same
directory as my run script. That way I don't inadvertently modify it.

All the best

> -----Original Message-----
> From: [mailto:amber-developers-
>] On Behalf Of Lachele Foley
> Sent: Thursday, March 05, 2009 3:14 PM
> To: AMBER Developers Mailing List
> Subject: [AMBER-Developers] Update question
> I'm pretty sure the answer to this is "it shouldn't cause trouble", but a
> user asked me, so I want to be sure.
> Let's say someone is running a really long job using amber11's sander or
> pmemd or some other routine likely to be run for a really long time. Is
> there any chance that updating amber11 will cause any trouble for that
> run? I think no. I think these programs, like most others, find all the
> data they need at the start, and the executable is loaded into active
> memory, and the version of the program on the disk is ignored thereafter
> until the program is called again. Yes? No?
> :-) Lachele
> --
> B. Lachele Foley, PhD '92,'02
> Assistant Research Scientist
> Complex Carbohydrate Research Center, UGA
> 706-542-0263
> _______________________________________________
> AMBER-Developers mailing list

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Received on Fri Mar 06 2009 - 01:25:55 PST
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