Hi,
On Tue, Nov 27, 2018 at 4:31 AM Peiyin Lee <peiyinlee...@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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