[gmx-users] Re: Gromacs-GPU benchmark test killed after exhausting the memory

Szilárd Páll szilard.pall at cbr.su.se
Mon Mar 5 12:16:01 CET 2012

Hi Efrat,

It indeed looks like a memory leak.

Could you please file a bug on redmine.gromacs.org?


On Sun, Mar 4, 2012 at 12:21 PM, Efrat Exlrod <Efrat.Exlrod at biu.ac.il> wrote:
> Hi Szilard,
> Thanks for your reply.
> I used your script and I think it does look as a memory leak. Please look at the attached runchkmem.out
> Is it possible this problem exists in version 4.5.5 and was solved in version 4.6 you are using?
> When will version 4.6 be released?
> Thanks, Efrat
>>Message: 2
>>Date: Fri, 2 Mar 2012 14:46:25 +0100
>>From: Szil?rd P?ll <szilard.pall at cbr.su.se>
>>Subject: Re: [gmx-users] Gromacs-GPU benchmark test killed after
>>        exhausting      the memory
>>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>>        <CANnYEw7rxa0NZ2weuyMwHZUCMfm2K6jyYP1htWGHcBadTvdYuw at mail.gmail.com>
>>Content-Type: text/plain; charset="iso-8859-1"
>>First I thought that there might be a memory leak which could have
>>caused this if you ran for really long time. However, I've just ran
>>the very same benchmark (dhfr with PME) for one hour, monitored the
>>memory usage and I couldn't see any change whatsoever (see the plot
>>I've attached a script I used to monitor the memory usage, feel free
>>to use if you want check again.
>>On Wed, Feb 29, 2012 at 9:50 AM, Efrat Exlrod <Efrat.Exlrod at biu.ac.il> wrote:
>>> Hi,
>>> I have?Gromacs-GPU version 4.5.5 and?GTX 580.
>>> I ran?dhfr-solv-PME benchmark test (see below) and my run was killed after
>>> couple of hours?exhausting all the computer memory, including the swap (2G
>>> +?4G swap).
>>> Has anyone encountered this problem? What?is wrong?
>>> Thanks, Efrat
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