[gmx-users] Gromacs 4 bug?

Bernhard Knapp bernhard.knapp at meduniwien.ac.at
Tue Dec 16 12:25:29 CET 2008

Hi Berk,

I continued the simulation and it works fine (for the next few hours). 
Then it gets stuck again. So it seems that the problem is not directly 
related to gromacs. But it seems the interaction between the operating 
system or the hardware does not work for a longer time.
We are using openSuse 11 and as hardware:  motherboard: MSI 7360 P35 
Neo-F, cpu: Intel Core 2 Quad Q9300, 4x 2.50GHz, ram: AENEON 2GB CL5 
AET860UD00-25D, hd: SEAGATE 750 GB SATAII 16MB 7200. Do you see any 
problems with that hardware? The simulations are running only on the 
local 4 cores in parallel (not over the network)


>Message: 1
>Date: Mon, 15 Dec 2008 12:16:18 +0100
>From: Berk Hess <gmx3 at hotmail.com>
>Subject: RE: Subject: Re: Re: [gmx-users] Gromacs 4 bug?
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <BLU134-W286BE7131CAB0B7743B5568EF40 at phx.gbl>
>Content-Type: text/plain; charset="iso-8859-1"
>If your simulations no longer produce output, but still run
>and there is no error or warning message,
>my guess would be that they are waiting for MPI communication.
>But the developers any many users are using 4.0 and I have
>not heard from problems like this, so I wonder if the problem
>could be somewhere else.
>Could you (or have your tried to) continue your simulation
>from the last checkpoint (mdrun option -cpi) before the hang,
>to see if it crashes quickly then?

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