[gmx-users] Problem with OpenMP+MPI

[Justin Lemkul]

On 2/27/13 11:27 AM, jesmin jahan wrote:
> Thanks again Justin,
>
> I added
>
> cutoff-scheme       = group
>
> But still I am getting
>
> OpenMP threads have been requested with cut-off scheme Group, but
> these are only supported with cut-off scheme Verlet
>
> which really says, openmp threads are supported only in Verlet!
>

Then you need to run without OpenMP threads.

-Justin

> constraints         =  none
> integrator          =  md
> cutoff-scheme       = group
>
> pbc                 =  no
> ;verlet-buffer-drift = -1
> dt                  =  0.001
> nsteps              =  0
> ns_type             = simple
> comm-mode           = angular
> rlist               = 0
> rcoulomb            = 0
> rvdw                = 0
> nstlist             = 0
> rgbradii            = 0
> nstgbradii          = 1
> coulombtype         = cutoff
> vdwtype             = cutoff
> implicit_solvent    =  GBSA
> gb_algorithm        =  HCT ;
> sa_algorithm        =  None
> gb_dielectric_offset    = 0.02
>
> optimize_fft             = yes
> energygrps               = protein
>
> Best Regards,
> Jesmin
>
>
> On Wed, Feb 27, 2013 at 10:57 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 2/27/13 10:54 AM, jesmin jahan wrote:
>>>
>>> Many thanks to you Justin for your help.
>>>
>>> Now my .mdp file looks like:
>>>
>>> constraints         =  none
>>> integrator          =  md
>>>
>>> pbc                 =  no
>>> verlet-buffer-drift = -1
>>> dt                  =  0.001
>>> nsteps              =  0
>>> ns_type             = simple
>>> comm-mode           = angular
>>> rlist               = 0
>>> rcoulomb            = 0
>>> rvdw                = 0
>>> nstlist             = 0
>>> rgbradii            = 0
>>> nstgbradii          = 1
>>> coulombtype         = cutoff
>>> vdwtype             = cutoff
>>> implicit_solvent    =  GBSA
>>> gb_algorithm        =  HCT ;
>>> sa_algorithm        =  None
>>> gb_dielectric_offset    = 0.02
>>>
>>> optimize_fft             = yes
>>> energygrps               = protein
>>>
>>> And when I run mdrun, it says
>>>
>>> "OpenMP threads have been requested with cut-off scheme Group, but
>>> these are only supported with cut-off scheme Verlet"
>>>
>>> Now if I add
>>>
>>> cutoff-scheme       = Verlet
>>>
>>> It says
>>>
>>>    With Verlet lists only full pbc or pbc=xy with walls is supported
>>>
>>>     With Verlet lists nstlist should be larger than 0
>>>
>>>
>>> So, what is the solution??
>>>
>>
>> Use the group cutoff scheme rather than Verlet, otherwise we wind up right
>> back where we were before.
>>
>>
>>> Also,  you told me
>>>
>>> "Note that implicit solvent calculations can be run on no more than 2
>>> processors.  You'll get a fatal error if you try to use more."
>>>
>>> Is there any documentation for this? Can I cite you if I want to add
>>> this information in an article?
>>>
>>
>> It's a bug, listed on Redmine somewhere.  I doubt that requires any sort of
>> citation, but if anyone asks, there are discussions in the list archive and
>> on redmine.gromacs.org.
>>
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================