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 <jalem...@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.abra...@gmail.com> > > wrote: > > > >> 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 > >>> -- > >>> 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-requ...@gromacs.org. > >>> > >> -- > >> 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-requ...@gromacs.org. > >> > > -- > ================================================== > > 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 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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