[gmx-users] Gromacs 4 bug?

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 16 13:13:11 CET 2008

Bernhard Knapp wrote:
> 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)
> Bernhard
You could try to force the MPI implementation to use TCP/IP rather than 
shared memory, which I assume is the default.
>> 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"
>> Hi,
>> 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?
>> Berk
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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