[gmx-users] error in the middle of running mdrun_mpi

Nizar Masbukhin nizar.fkub08 at gmail.com
Mon Oct 27 10:59:40 CET 2014 

and how to use that 2 cores? i think that would increase performace twice
as now i am running 1 core per replica.

On Mon, Oct 27, 2014 at 7:15 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 10/26/14 9:55 AM, Nizar Masbukhin wrote:
>
>> regarding gaining speed in implicit solvent simulation, i have tried to
>> parallelize using -ntmpi flag. However gromacs doesn't allow as i use
>> group
>> cutoff-scheme. Any recommendation how to parallelise implicit solvent
>> simulation? I do need parallelise my simulation. I have found the same
>> question in this mail list, one suggest use all-vs-all kernel which uses
>> zero cut-off.
>> This is my test run actually. I intend to run my simulation in cluster
>> computer.
>>
>>
> Unless the restriction was lifted at some point, implicit simulations
> won't run on more than 2 cores.  There were issues with constraints that
> led to the limitation.
>
> -Justin
>
>
>  On Sun, Oct 26, 2014 at 8:23 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 10/26/14 9:17 AM, Nizar Masbukhin wrote:
>>>
>>>  Thanks Justin.
>>>> I have increased the cutoff, and yeah thats work. There were no error
>>>> message anymore. The first 6 nanoseconds, i felt the simulation run
>>>> slower.
>>>> Felt so curious that  simulation run very fast the rest of time.
>>>>
>>>>
>>>>  Longer cutoffs mean there are more interactions to calculate, but the
>>> cutoffs aren't to be toyed with arbitrarily to gain speed.  They are a
>>> critical element of the force field itself, though in implicit solvent,
>>> it
>>> is common to increase (and never decrease) the cutoff values used in
>>> explicit solvent.  Physical validity should trump speed any day.
>>>
>>> -Justin
>>>
>>>
>>>   On Fri, Oct 24, 2014 at 7:37 PM, Justin Lemkul <jalemkul at vt.edu>
>>> wrote:
>>>
>>>>
>>>>
>>>>
>>>>> On 10/24/14 8:31 AM, Nizar Masbukhin wrote:
>>>>>
>>>>>   Thanks for yor reply, Mark.
>>>>>
>>>>>>
>>>>>>
>>>>>> At first i was sure that the problem was table-exension because when I
>>>>>> enlarge table-extension value, warning message didn't  appear anymore.
>>>>>> Besides, i have successfully minimized and equilibrated the system
>>>>>> (indicated by Fmax < emtol reached; and no error messages during
>>>>>> NVT&NPT
>>>>>> equilibration, except a warning that the Pcouple is turned off in
>>>>>> vacuum
>>>>>> system).
>>>>>>
>>>>>> However, the error message appeared without table-extension warning
>>>>>> makes
>>>>>> me doubt also about my system stability. Here is my mdp setting.
>>>>>> Please
>>>>>> tell me if there are any 'weird' setting, and also kindly
>>>>>> suggest/recommend
>>>>>> a better setting.
>>>>>>
>>>>>>
>>>>>> *mdp file for Minimisation*
>>>>>>
>>>>>>
>>>>>> integrator = steep
>>>>>>
>>>>>> nsteps = 5000
>>>>>>
>>>>>> emtol = 200
>>>>>>
>>>>>> emstep = 0.01
>>>>>>
>>>>>> niter = 20
>>>>>>
>>>>>> nstlog = 1
>>>>>>
>>>>>> nstenergy = 1
>>>>>>
>>>>>> cutoff-scheme = group
>>>>>>
>>>>>> nstlist = 1
>>>>>>
>>>>>> ns_type = simple
>>>>>>
>>>>>> pbc = no
>>>>>>
>>>>>> rlist = 0.5
>>>>>>
>>>>>> coulombtype = cut-off
>>>>>>
>>>>>> rcoulomb = 0.5
>>>>>>
>>>>>> vdw-type = cut-off
>>>>>>
>>>>>> rvdw-switch = 0.8
>>>>>>
>>>>>> rvdw = 0.5
>>>>>>
>>>>>> DispCorr = no
>>>>>>
>>>>>> fourierspacing = 0.12
>>>>>>
>>>>>> pme_order = 6
>>>>>>
>>>>>> ewald_rtol = 1e-06
>>>>>>
>>>>>> epsilon_surface = 0
>>>>>>
>>>>>> optimize_fft = no
>>>>>>
>>>>>> tcoupl = no
>>>>>>
>>>>>> pcoupl = no
>>>>>>
>>>>>> free_energy = yes
>>>>>>
>>>>>> init_lambda = 0.0
>>>>>>
>>>>>> delta_lambda = 0
>>>>>>
>>>>>> foreign_lambda = 0.05
>>>>>>
>>>>>> sc-alpha = 0.5
>>>>>>
>>>>>> sc-power = 1.0
>>>>>>
>>>>>> sc-sigma  = 0.3
>>>>>>
>>>>>> couple-lambda0 = vdw
>>>>>>
>>>>>> couple-lambda1 = none
>>>>>>
>>>>>> couple-intramol = no
>>>>>>
>>>>>> nstdhdl = 10
>>>>>>
>>>>>> gen_vel = no
>>>>>>
>>>>>> constraints = none
>>>>>>
>>>>>> constraint-algorithm = lincs
>>>>>>
>>>>>> continuation = no
>>>>>>
>>>>>> lincs-order  = 12
>>>>>>
>>>>>> implicit-solvent = GBSA
>>>>>>
>>>>>> gb-algorithm = still
>>>>>>
>>>>>> nstgbradii = 1
>>>>>>
>>>>>> rgbradii = 0.5
>>>>>>
>>>>>> gb-epsilon-solvent = 80
>>>>>>
>>>>>> sa-algorithm = Ace-approximation
>>>>>>
>>>>>> sa-surface-tension = 2.05
>>>>>>
>>>>>>
>>>>>> *mdp file for NVT equilibration*
>>>>>>
>>>>>>
>>>>>> define = -DPOSRES
>>>>>>
>>>>>> integrator = md
>>>>>>
>>>>>> tinit = 0
>>>>>>
>>>>>> dt = 0.002
>>>>>>
>>>>>> nsteps = 250000
>>>>>>
>>>>>> init-step = 0
>>>>>>
>>>>>> comm-mode = angular
>>>>>>
>>>>>> nstcomm = 100
>>>>>>
>>>>>> bd-fric = 0
>>>>>>
>>>>>> ld-seed = -1
>>>>>>
>>>>>> nstxout = 1000
>>>>>>
>>>>>> nstvout = 50000
>>>>>>
>>>>>> nstfout = 50000
>>>>>>
>>>>>> nstlog = 100
>>>>>>
>>>>>> nstcalcenergy = 100
>>>>>>
>>>>>> nstenergy = 1000
>>>>>>
>>>>>> nstxtcout = 100
>>>>>>
>>>>>> xtc-precision = 1000
>>>>>>
>>>>>> xtc-grps = system
>>>>>>
>>>>>> energygrps = system
>>>>>>
>>>>>> cutoff-scheme= group
>>>>>>
>>>>>> nstlist                  = 1
>>>>>>
>>>>>> ns-type = simple
>>>>>>
>>>>>> pbc= no
>>>>>>
>>>>>> rlist= 0.5
>>>>>>
>>>>>> coulombtype = cut-off
>>>>>>
>>>>>> rcoulomb= 0.5
>>>>>>
>>>>>> vdw-type = Cut-off
>>>>>>
>>>>>> vdw-modifier = Potential-shift-Verlet
>>>>>>
>>>>>> rvdw-switch= 0.8
>>>>>>
>>>>>> rvdw = 0.5
>>>>>>
>>>>>> table-extension = 500
>>>>>>
>>>>>> fourierspacing = 0.12
>>>>>>
>>>>>> fourier-nx  = 0
>>>>>>
>>>>>> fourier-ny = 0
>>>>>>
>>>>>> fourier-nz = 0
>>>>>>
>>>>>> implicit-solvent = GBSA
>>>>>>
>>>>>> gb-algorithm = still
>>>>>>
>>>>>> nstgbradii = 1
>>>>>>
>>>>>> rgbradii = 0.5
>>>>>>
>>>>>> gb-epsilon-solvent = 80
>>>>>>
>>>>>> sa-algorithm = Ace-approximation
>>>>>>
>>>>>> sa-surface-tension = 2.05
>>>>>>
>>>>>> tcoupl = v-rescale
>>>>>>
>>>>>> nsttcouple = -1
>>>>>>
>>>>>> nh-chain-length = 10
>>>>>>
>>>>>> print-nose-hoover-chain-variables = no
>>>>>>
>>>>>> tc-grps = system
>>>>>>
>>>>>> tau-t = 0.1
>>>>>>
>>>>>> ref-t = 298.00
>>>>>>
>>>>>> pcoupl = No
>>>>>>
>>>>>> pcoupltype = Isotropic
>>>>>>
>>>>>> nstpcouple = -1
>>>>>>
>>>>>> tau-p = 1
>>>>>>
>>>>>> refcoord-scaling = No
>>>>>>
>>>>>> gen-vel = yes
>>>>>>
>>>>>> gen-temp = 298.00
>>>>>>
>>>>>> gen-seed  = -1
>>>>>>
>>>>>> constraints= all-bonds
>>>>>>
>>>>>> constraint-algorithm = Lincs
>>>>>>
>>>>>> continuation = no
>>>>>>
>>>>>> Shake-SOR = no
>>>>>>
>>>>>> shake-tol = 0.0001
>>>>>>
>>>>>> lincs-order = 4
>>>>>>
>>>>>> lincs-iter = 1
>>>>>>
>>>>>> lincs-warnangle = 30
>>>>>>
>>>>>>
>>>>>> *mdp file for NPT equilibration*
>>>>>>
>>>>>>
>>>>>> define = -DPOSRES
>>>>>>
>>>>>> integrator = md
>>>>>>
>>>>>> tinit = 0
>>>>>>
>>>>>> dt = 0.002
>>>>>>
>>>>>> nsteps = 500000
>>>>>>
>>>>>> init-step = 0
>>>>>>
>>>>>> simulation-part = 1
>>>>>>
>>>>>> comm-mode = angular
>>>>>>
>>>>>> nstcomm = 100
>>>>>>
>>>>>> bd-fric = 0
>>>>>>
>>>>>> ld-seed = -1
>>>>>>
>>>>>> nstxout = 1000
>>>>>>
>>>>>> nstvout = 500000
>>>>>>
>>>>>> nstfout = 500000
>>>>>>
>>>>>> nstlog = 100
>>>>>>
>>>>>> nstcalcenergy = 100
>>>>>>
>>>>>> nstenergy = 1000
>>>>>>
>>>>>> nstxtcout = 100
>>>>>>
>>>>>> xtc-precision = 1000
>>>>>>
>>>>>> xtc-grps = system
>>>>>>
>>>>>> energygrps = system
>>>>>>
>>>>>> cutoff-scheme = group
>>>>>>
>>>>>> nstlist = 1
>>>>>>
>>>>>> ns-type = simple
>>>>>>
>>>>>> pbc = no
>>>>>>
>>>>>> rlist  = 0.5
>>>>>>
>>>>>> coulombtype= cut-off
>>>>>>
>>>>>> rcoulomb = 0.5
>>>>>>
>>>>>> vdw-type = Cut-off
>>>>>>
>>>>>> vdw-modifier = Potential-shift-Verlet
>>>>>>
>>>>>> rvdw-switch = 0.8
>>>>>>
>>>>>> rvdw= 0.5
>>>>>>
>>>>>> table-extension = 1
>>>>>>
>>>>>> fourierspacing = 0.12
>>>>>>
>>>>>> fourier-nx= 0
>>>>>>
>>>>>> fourier-ny = 0
>>>>>>
>>>>>> fourier-nz = 0
>>>>>>
>>>>>> implicit-solvent = GBSA
>>>>>>
>>>>>> gb-algorithm = still
>>>>>>
>>>>>> nstgbradii = 1
>>>>>>
>>>>>> rgbradii = 0.5
>>>>>>
>>>>>> gb-epsilon-solvent = 80
>>>>>>
>>>>>> sa-algorithm = Ace-approximation
>>>>>>
>>>>>> sa-surface-tension = 2.05
>>>>>>
>>>>>> tcoupl  = Nose-Hoover
>>>>>>
>>>>>> tc-grps = system
>>>>>>
>>>>>> tau-t  = 0.1
>>>>>>
>>>>>> ref-t = 298.00
>>>>>>
>>>>>> pcoupl = parrinello-rahman
>>>>>>
>>>>>> pcoupltype = Isotropic
>>>>>>
>>>>>> tau-p   = 1.0
>>>>>>
>>>>>> compressibility   = 4.5e-5
>>>>>>
>>>>>> ref-p   = 1.0
>>>>>>
>>>>>> refcoord-scaling = No
>>>>>>
>>>>>> gen-vel   = no
>>>>>>
>>>>>> gen-temp = 298.00
>>>>>>
>>>>>> gen-seed   = -1
>>>>>>
>>>>>> constraints  = all-bonds
>>>>>>
>>>>>> constraint-algorithm   = Lincs
>>>>>>
>>>>>> continuation  = yes
>>>>>>
>>>>>> Shake-SOR  = no
>>>>>>
>>>>>> shake-tol  = 0.0001
>>>>>>
>>>>>> lincs-order = 4
>>>>>>
>>>>>> lincs-iter   = 1
>>>>>>
>>>>>> lincs-warnangle  = 30
>>>>>>
>>>>>>
>>>>>> *mdp file for MD*
>>>>>>
>>>>>>
>>>>>> integrator  = md
>>>>>>
>>>>>> tinit = 0
>>>>>>
>>>>>> dt  = 0.001
>>>>>>
>>>>>> nsteps = 500000000 ; 1 us
>>>>>>
>>>>>> init-step = 0
>>>>>>
>>>>>> simulation-part= 1
>>>>>>
>>>>>> comm-mode  = Angular
>>>>>>
>>>>>> nstcomm = 100
>>>>>>
>>>>>> comm-grps = system
>>>>>>
>>>>>> bd-fric  = 0
>>>>>>
>>>>>> ld-seed = -1
>>>>>>
>>>>>> nstxout  = 10000
>>>>>>
>>>>>> nstvout  = 0
>>>>>>
>>>>>> nstfout   = 0
>>>>>>
>>>>>> nstlog  = 10000
>>>>>>
>>>>>> nstcalcenergy = 10000
>>>>>>
>>>>>> nstenergy = 10000
>>>>>>
>>>>>> nstxtcout  = 0
>>>>>>
>>>>>> xtc-precision  = 1000
>>>>>>
>>>>>> xtc-grps  = system
>>>>>>
>>>>>> energygrps  = system
>>>>>>
>>>>>> cutoff-scheme  = group
>>>>>>
>>>>>> nstlist  = 10
>>>>>>
>>>>>> ns-type  = simple
>>>>>>
>>>>>> pbc   = no
>>>>>>
>>>>>> rlist    = 0.5
>>>>>>
>>>>>> coulombtype    = cut-off
>>>>>>
>>>>>> rcoulomb  = 0.5
>>>>>>
>>>>>> vdw-type  = Cut-off
>>>>>>
>>>>>> vdw-modifier  = Potential-shift-Verlet
>>>>>>
>>>>>> rvdw-switch = 0.8
>>>>>>
>>>>>> rvdw  = 0.5
>>>>>>
>>>>>> DispCorr = No
>>>>>>
>>>>>> table-extension  = 500
>>>>>>
>>>>>> fourierspacing = 0.12
>>>>>>
>>>>>> fourier-nx  = 0
>>>>>>
>>>>>> fourier-ny = 0
>>>>>>
>>>>>> fourier-nz = 0
>>>>>>
>>>>>> implicit-solvent = GBSA
>>>>>>
>>>>>> ;implicit-solvent = GBSA
>>>>>>
>>>>>> gb-algorithm = still
>>>>>>
>>>>>> nstgbradii = 1
>>>>>>
>>>>>> rgbradii = 0.5
>>>>>>
>>>>>> gb-epsilon-solvent = 80
>>>>>>
>>>>>> sa-algorithm = Ace-approximation
>>>>>>
>>>>>> sa-surface-tension = 2.05
>>>>>>
>>>>>> tcoupl = v-rescale
>>>>>>
>>>>>> nsttcouple = -1
>>>>>>
>>>>>> nh-chain-length = 10
>>>>>>
>>>>>> print-nose-hoover-chain-variables = no
>>>>>>
>>>>>> tc-grps = system
>>>>>>
>>>>>> tau-t  = 0.1
>>>>>>
>>>>>> ref-t = 298.00
>>>>>>
>>>>>> pcoupl = No
>>>>>>
>>>>>> pcoupltype = Isotropic
>>>>>>
>>>>>> nstpcouple = -1
>>>>>>
>>>>>> tau-p  = 1
>>>>>>
>>>>>> refcoord-scaling = No
>>>>>>
>>>>>> gen-vel = no
>>>>>>
>>>>>> gen-temp = 298.00
>>>>>>
>>>>>> gen-seed  = -1
>>>>>>
>>>>>> constraints  = none
>>>>>>
>>>>>> constraint-algorithm = Lincs
>>>>>>
>>>>>> continuation = yes
>>>>>>
>>>>>> Shake-SOR = no
>>>>>>
>>>>>> shake-tol = 0.0001
>>>>>>
>>>>>> lincs-order = 4
>>>>>>
>>>>>> lincs-iter = 1
>>>>>>
>>>>>> lincs-warnangle = 30
>>>>>>
>>>>>> morse = no
>>>>>>
>>>>>> free-energy = yes
>>>>>>
>>>>>> couple-lambda0 = vdw-q
>>>>>>
>>>>>> couple-lambda1= vdw-q
>>>>>>
>>>>>> couple-intramol = no
>>>>>>
>>>>>> init-lambda = 0
>>>>>>
>>>>>> delta-lambda = 0.1
>>>>>>
>>>>>> nstdhdl  = 50
>>>>>>
>>>>>> calc-lambda-neighbors  = 1
>>>>>>
>>>>>> dhdl-print-energy = no
>>>>>>
>>>>>> sc-alpha = 0
>>>>>>
>>>>>> sc-power= 1
>>>>>>
>>>>>> sc-r-power  = 6
>>>>>>
>>>>>> sc-sigma= 0.3
>>>>>>
>>>>>> sc-coul = no
>>>>>>
>>>>>> separate-dhdl-file = yes
>>>>>>
>>>>>> dhdl-derivatives  = yes
>>>>>>
>>>>>> dh_hist_size  = 0
>>>>>>
>>>>>> dh_hist_spacing = 0.1
>>>>>>
>>>>>>
>>>>>>   You need to simplify significantly to determine what the issue is.
>>>>>>
>>>>> You're
>>>>> using (1) very short cutoffs, (2) free energy, and (3) implicit
>>>>> solvent.
>>>>> Any combination of those might be causing the problem you're having.
>>>>> Generally, extra long cutoffs are used in implicit environments.  Try a
>>>>> "normal" run without the free energy code going and see if that
>>>>> improves
>>>>> the situation.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
>>>>>
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at http://www.gromacs.org/
>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>
>>>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>> * For (un)subscribe requests visit
>>>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>  --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
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>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
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>
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>



-- 
Thanks
My Best Regards, Nizar
Medical Faculty of Brawijaya University

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