[gmx-users] Re: why it is so slow

Justin Lemkul jalemkul at vt.edu
Fri Nov 2 18:10:28 CET 2012

On 11/2/12 12:54 PM, Albert wrote:
> On 11/02/2012 05:48 PM, Justin Lemkul wrote:
>> That system is not small, it's rather large.  Are you sure each replica is
>> really running on 24 processors?  It occurred to me that there was a problem
>> in 4.5.4 that was fixed for 4.5.5, but the "fix" was really just a workaround,
>> allowing a maximum of 2 processors if GBSA calculations were invoked in parallel:
>> http://redmine.gromacs.org/issues/777
>> Your log file will tell you for sure.
>> -Justin
> oh, My..... only 2 core for each GBSA jobs..... How about the 4.6?

No idea.  Hopefully the issue will be fixed, but I haven't been involved in the 
development of any of those features.  Again, check your log file - it will tell 
you how many processors are actually being used.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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