[gmx-users] Problem with OpenMP+MPI

[jesmin jahan]

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!

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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-- 
Jesmin Jahan Tithi
PhD Student, CS
Stony Brook University, NY-11790.