[gmx-users] MPI error in gromacs 4.6, more Errors
Ankita Naithani
ankitanaithani at gmail.com
Mon Mar 24 12:57:17 CET 2014
Hi, so I modified my mdp file which now looks like the following:
title = production MD
; Run parameters
integrator = md ; leap-frog algorithm
;nsteps = 20000000 ; 0.005 * 20000000 = 100000 ps or 100 ns
;nsteps = 200000 ; 0.005 * 200000 = 1 ns
;dt = 0.005 ; 5 fs
nsteps = 33333333 ; 0.003 * 33333333 = 100000 ps or 100 n
dt = 0.003 ; 3 fs
; Output control
nstxout = 0 ; save coordinates every 2 ps
nstvout = 0 ; save velocities every 2 ps
nstxtcout = 1000 ; xtc compressed trajectory output every 5 ps
nstenergy = 1000 ; save energies every 5 ps
nstlog = 1000 ; update log file every 5 ps
; Bond parameters
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 25 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
rlistlong = 1.0 ; long-range neighborlist cutoff (in nm)
cutoff-scheme = Verlet
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
nstcomm = 10 ; remove com every 10 steps
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more
accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 318 318 ; reference temperature, one for each group,
in K
; Pressure coupling is off
pcoupl = berendsen ; Berendsen thermostat
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 1.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = yes ; Velocity generation is on
gen_temp = 318 ; reference temperature, for protein in K
--------------------------------------------------
But, when I try to generate the tpr file on the cluster itself using
gromacs 4.6.3, I get the following error:
NOTE 1 [file md3.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
NOTE 2 [file md3.mdp]:
nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Generated 3403 of the 3403 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 3403 of the 3403 1-4 parameter combinations
Segmentation fault
Can anyone please suggest further?
Kind regards,
Ankita
On Mon, Mar 24, 2014 at 11:48 AM, Ankita Naithani
<ankitanaithani at gmail.com>wrote:
> Hi Pavan,
> Thank you for your response. I am trying to generate the tpr file with the
> following parameter;
> ; Neighborsearching
> ns_type = grid ; search neighboring grid cells
> nstlist = 5 ; 25 fs
> rlist = 1.0 ; short-range neighborlist cutoff (in nm)
> rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
> rlistlong = 1.0 ; long-range neighborlist cutoff (in nm)
> cutoff-scheme = Verlet
>
> But, I get a warning of Unknown left-hand 'cutoff-scheme' in parameter
> file.
>
>
> On Mon, Mar 24, 2014 at 11:26 AM, Pavan Kumar <kumar.pavan006 at gmail.com>wrote:
>
>> Hello Ankita
>> You have to just include the following line in your mdp file
>> cutoff-scheme=Verlet
>> And run your grompp with the modfied mdp file to generate tpr file and
>> then
>> mdrun.
>> Hope this doesn't give you the same error
>>
>>
>> On Mon, Mar 24, 2014 at 4:47 PM, Ankita Naithani
>> <ankitanaithani at gmail.com>wrote:
>>
>> > Hi,
>> >
>> > I am trying to run a simulation of my protein (monomer ~500 residues). I
>> > had few questions and erors regarding the same.
>> > I have previously run the simulation of the apo form of the same protein
>> > using Gromacs 4.5.5 which was available at the cluster facility I was
>> using
>> > and also which is installed in my system. However, when I tried to run
>> the
>> > holo form, I got error :
>> > Fatal error:
>> > 11 particles communicated to PME node 106 are more than 2/3 times the
>> > cut-off out of the domain decomposition cell of their charge group in
>> > dimension y.
>> > This usually means that your system is not well equilibrated.
>> > For more information and tips for troubleshooting, please check the
>> GROMACS
>> > website at http://www.gromacs.org/Documentation/Errors
>> >
>> > This I figured out could be solved using a lower timestep as my previous
>> > timestep was 4fs and now I have reduced it to 3fs which should work fine
>> > now.
>> > However, after producing the tpr file for production run in my GROMACS
>> > 4.5.5, I realised that the grant for the cluster facility is over and
>> the
>> > new clusters which I am trying to set up the same protein for support
>> only
>> > gromacs 4.6. I am trying to run the code in these clusters and I get he
>> > following error:
>> >
>> >
>> > -------------------------------------------------------
>> > Program mdrun_mpi, VERSION 4.6.3
>> > Source code file: /home/gromacs-4.6.3/src/kernel/runner
>> > .c, line: 824
>> >
>> > Fatal error:
>> > OpenMP threads have been requested with cut-off scheme Group, but these
>> are
>> > only
>> > supported with cut-off scheme Verlet
>> > For more information and tips for troubleshooting, please check the
>> GROMACS
>> > website at http://www.gromacs.org/Documentation/Errors
>> >
>> >
>> ---------------------------------------------------------------------------------
>> >
>> > 1. I wanted help with my mdp options to make it compatible.
>> > 2. Since my pevious calculations were based on gromacs 4.5.5, switching
>> to
>> > gromacs 4.6, would that break the continuity of the run or would that
>> bring
>> > about differences in the way the trajectories would be analysed?
>> >
>> >
>> > Below, is my mdp file
>> > title = production MD
>> > ; Run parameters
>> > integrator = md ; leap-frog algorithm
>> > nsteps = 33333333 ; 0.003 * 33333333 = 100000 ps or 100 n
>> > dt = 0.003 ; 3 fs
>> > ; Output control
>> > nstxout = 0 ; save coordinates every 2 ps
>> > nstvout = 0 ; save velocities every 2 ps
>> > nstxtcout = 1000 ; xtc compressed trajectory output every 5 ps
>> > nstenergy = 1000 ; save energies every 5 ps
>> > nstlog = 1000 ; update log file every 5 ps
>> > energygrps = Protein ATP
>> > ; Bond parameters
>> > constraint_algorithm = lincs ; holonomic constraints
>> > constraints = all-bonds ; all bonds (even heavy atom-H bonds)
>> > constrained
>> > lincs_iter = 1 ; accuracy of LINCS
>> > lincs_order = 4 ; also related to accuracy
>> > ; Neighborsearching
>> > ns_type = grid ; search neighboring grid cells
>> > nstlist = 5 ; 25 fs
>> > rlist = 1.0 ; short-range neighborlist cutoff (in nm)
>> > rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
>> > rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
>> > rlistlong = 1.0 ; long-range neighborlist cutoff (in nm)
>> > ; Electrostatics
>> > coulombtype = PME ; Particle Mesh Ewald for long-range
>> > electrostatics
>> > pme_order = 4 ; cubic interpolation
>> > fourierspacing = 0.16 ; grid spacing for FFT
>> > nstcomm = 10 ; remove com every 10 steps
>> > ; Temperature coupling is on
>> > tcoupl = V-rescale ; modified Berendsen thermostat
>> > tc-grps = Protein Non-Protein ; two coupling groups - more
>> > accurate
>> > tau_t = 0.1 0.1 ; time constant, in ps
>> > ref_t = 318 318 ; reference temperature, one for each
>> group,
>> > in K
>> > ; Pressure coupling is off
>> > pcoupl = berendsen ; Berendsen thermostat
>> > pcoupltype = isotropic ; uniform scaling of box vectors
>> > tau_p = 1.0 ; time constant, in ps
>> > ref_p = 1.0 ; reference pressure, in bar
>> > compressibility = 4.5e-5 ; isothermal compressibility of water,
>> bar^-1
>> > ; Periodic boundary conditions
>> > pbc = xyz ; 3-D PBC
>> > ; Dispersion correction
>> > DispCorr = EnerPres ; account for cut-off vdW scheme
>> > ; Velocity generation
>> > gen_vel = yes ; Velocity generation is on
>> > gen_temp = 318 ; reference temperature, for protein in K
>> >
>> >
>> >
>> >
>> > Kind regards--
>> > Ankita Naithani
>> > --
>> > Gromacs Users mailing list
>> >
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>>
>>
>>
>> --
>> Cheers
>> Pavan
>> --
>> Gromacs Users mailing list
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>
>
>
> --
> Ankita Naithani
>
--
Ankita Naithani
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