Re: [AMBER-Developers] Update question

From: Carlos Simmerling <>
Date: Fri, 6 Mar 2009 07:04:27 -0500

I know this was a problem on SGI machines under IRIX, since it would
often crash the job. I agree with Ross, best to be safe.

On Thu, Mar 5, 2009 at 6:30 PM, Ross Walker <> wrote:
> 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
> Ross
>> -----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 Sun Mar 08 2009 - 01:07:35 PST
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