[gmx-developers] Error with octahedral box and domain decomposition in CVS-version

[Berk Hess]

Hi,

It seems that in your group lots of people are using a CVS version of 
nearly a year ago.
This is VERY BAD.
There have been loads of bugs in the initial CVS versions. Most bugs 
were minor
things, but there were some major ones, such as the one you experienced.
The developers have been using certain versions, but we knew which 
versions were
more or less reliable. Since a few months there have been no real problems.

So I would immediately update to the current version.
Please tell your group members to do so as well.

Berk.


Jochen Hub wrote:
> Hi Berk,
>
> thanks for the quick reply. You were right, the error does NOT occur 
> in a recent Version (3.3.99_development_20080208). I was using an oder 
> CVS-Version (3.3.99_development_20070618) from last summer.
>
> thanks again,
> Jochen
>
> Berk Hess wrote:
>> Hi,
>>
>> Since you mention the current CVS version, I assume you are using an 
>> old version.
>> From when is that version?
>> There have been loads of bugs in CVS, but we are using the current 
>> version
>> without problems.
>>
>> Berk.
>>
>> Jochen Hub wrote:
>>> Hi,
>>>
>>> when running a octahedral system of 31779 atoms on 16 or 8 CPUs with 
>>> domain decomposition I am getting the errors like shown below. Is 
>>> that a known problem or has it even been fixed in the current  CVS 
>>> version? Should I submit a bugzilla? Playing with the -dd parameters 
>>> or switching -dbl on an off did not help. Btw, the charge group 
>>> which seems to move too rapidly is always a water molecule. The 
>>> system (protein+water+ions) is OK, it is runnig without problems in 
>>> gromacs 3.3.1.
>>>
>>> Cheers, Jochen
>>>
>>>
>>> Making 3D domain decomposition 2 x 2 x 2
>>> starting mdrun 'Protein'
>>> 100000000 steps, 200000.0 ps.
>>>
>>> step 0
>>>
>>> Step 30:
>>> The charge group starting at atom 21975 moved more than the cut-off 
>>> (1.000000) in direction x
>>> distance out of cell -1.110520
>>> Old coordinates:    0.602    1.641    0.007
>>> New coordinates:   -1.668    4.849    5.566
>>> Old cell boundaries in direction x:    0.000    3.257
>>> New cell boundaries in direction x:    0.000    3.225
>>> -------------------------------------------------------
>>> Program mdrun, VERSION 3.3.99_development_20070618
>>> Source code file: domdec.c, line: 1806
>>>
>>> Fatal error:
>>> A charge group move too far between two domain decomposition steps
>>> -------------------------------------------------------
>>>
>>>
>>>
>>
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