[gmx-users] Gromacs 2018.3 Exceeding Memory Issue

Tue Nov 27 17:27:07 CET 2018

Hi,

A 21K atom simulation uses essentially no memory at all for actual GROMACS
workload. That plus all the supporting stuff for all the related processes
in a node will fit easily in 1GB of memory. Just ask for that :-) I'm not
sure what units slurm is using for reporting the memory over-use.

Mark

On Tue, Nov 27, 2018 at 4:53 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/27/18 10:43 AM, Peiyin Lee wrote:
> > Hi, Mark,
> >
> >     Thank you for all the suggestions! Regarding to the memory limit it
> > should be around 118 GB. The cluster I am using has 20 cores per node
> and 6
> > GB of memory space per code. That's why I think it is strange for my job
> to
> > exceed the large memory limit. Right now I have checked my mdp file and
> > submission file and couldn't see any possible reason that causes this
> large
> > memory usage issue. Do you have suggestions on other places to look at?
>
> Probably the most applicable attribute is the number of atoms in the
> system.
>
> -Justin
>
> > Thank you so much for your help.
> >
> > Regards,
> > Peiyin
> >
> > On Tue, Nov 27, 2018 at 2:50 AM Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> On Tue, Nov 27, 2018 at 4:31 AM Peiyin Lee <peiyinlee329 at gmail.com>
> wrote:
> >>
> >>> Hi, all GROMACS users,
> >>>
> >>>     I am trying to run jobs with Gromacs 2018.3 version and constantly
> >> got a
> >>> memory exceeding error. The system I ran is an all-atom system with
> 21073
> >>> atoms. The largest file that is estimated to be generated is around 5.8
> >> GB.
> >> Estimate sizes of disk files don't matter here.
> >>
> >>
> >>> My jobs got constantly killed after running for only around 15 minutes
> >> and
> >>> got an error message like this: "slurmstepd: error: Job 12381762
> exceeded
> >>> memory limit (123122052 > 122880000), being killed". I have tried
> using a
> >>>
> >> 128MB is pretty tiny these days - no compute node will have less than
> 1GB
> >> physical memory, so I suggest to ask for that.
> >>
> >> GROMACS should never leak memory as the simulation progresses - if you
> >> think you are seeing that (e.g. with slightly larger memory limit, slurm
> >> interrupts a bit later) then we would like to see a bug report at
> >> https://redmine.gromacs.org
> >>
> >>
> >>> larger memory specification (12GB/core) but it would take too long to
> >> wait
> >>> and I don't think my job really uses that many memories. I have
> attached
> >> my
> >>> .mdp file as below:
> >>> "title = NVT Production Run for Trpzip4 in pure H2O
> >>>
> >>> define =        ; position restrain the protein
> >>>
> >>> ; Run parameters
> >>>
> >>> integrator = md ; leap-frog integrator
> >>>
> >>> nsteps = 50000000 ; 0.002 * 50000 = 100000 ps (100 ns)
> >>>
> >>> dt     = 0.002 ; 2 fs
> >>>
> >>> ; Output control
> >>>
> >>> nstenergy = 10000 ; save energies every 20 ps
> >>>
> >>> nstlog = 10000 ; update log file every 20 ps
> >>>
> >>> nstxout-compressed = 10000      ; 20ps
> >>>
> >>> compressed-x-precision = 200   ; 0.05
> >>>
> >>> compressed-x-grps       = System
> >>>
> >>> ; Bond parameters
> >>>
> >>> continuation = yes     ; Restarting after NVT
> >>>
> >>> 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 cels
> >>>
> >>> nstlist = 5     ; 10 fs
> >>>
> >>> rlist = 1.2 ; short-range neighborlist cutoff (in nm)
> >>>
> >>> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
> >>>
> >>> rvdw = 1.2 ; short-range van der Waals 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
> >>>
> >>> ; Temperature coupling is on
> >>>
> >>> tcoupl = V-rescale         ; More accurate thermostat
> >>>
> >>> tc-grps = Protein SOL NA        ; 2 coupling groups - more accurate
> >>>
> >> Off topic, but it is not good practice to couple ions separately. Did
> you
> >> perhaps follow some tutorial that we can ask the author to fix?
> >>
> >>
> >>> tau_t = 0.5 0.5 0.5        ; time constant, in ps
> >>>
> >>> ref_t = 400 400  400     ; reference temperature, one for each group,
> in
> >> K
> >>> ; Pressure coupling is on
> >>>
> >>> pcoupl = No      ; Pressure coupling on in NPT
> >>>
> >>> pcoupltype = isotropic     ; uniform scaling of x-y box vectors,
> >>> independent z
> >>>
> >>> tau_p = 5.0         ; time constant, in ps
> >>>
> >>> ref_p = 1.0         ; reference pressure, x-y, z (in bar)
> >>>
> >>> compressibility = 4.5e-5 ; isothermal compressibility, bar^-1
> >>>
> >>> ; Periodic boundary conditions
> >>>
> >>> pbc     = xyz ; 3-D PBC
> >>>
> >>> ; Dispersion correction
> >>>
> >>> DispCorr = EnerPres ; account for cut-off vdW scheme
> >>>
> >>> ; Velocity generation
> >>> gen_vel = no ; Velocity generation is off"
> >>> and the command I used to run was "mpirun -np 80 gmx_mpi mdrun -npme 16
> >>> -noappend -s md.tpr -c md.gro -e md.edr -x md.xtc -cpi md.cpt -cpo
> md.cpt
> >>> -g md.log".
> >>
> >> Looks fine. I encourage everybody to use the default file names, and
> >> organize their projects into natural groups for the infrastructure, like
> >> directories. Renaming them doesn't add value and makes your life more
> >> complicated when you're doing restarts.
> >>
> >> Mark
> >>
> >>
> >>> This is my first time posting so please excuse anything that's
> >>> unclear. I will try to clarify if needed. Any help is greatly
> >> appreciated!
> >>> Regards,
> >>> Peiyin Lee
> >>> --
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>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
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