[gmx-users] Problem with OpenMP+MPI

[jesmin jahan]

Dear Justin,

I want to compare the performance of MPI+OpenMP implementation of
Gromacs GB-energy with other MPI+X implementation of GB-energy.

So, my question is:
Is there any way to get sensible result for the implicit solvent
simulation using Gromacs that employs both MPI and OpenMP?
If yes, then what should be the parameter set?

Thanks for your time.

Best Regards,
Jesmin

On Wed, Feb 27, 2013 at 11:54 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
> 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
>
> ========================================
> --
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-- 
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.