Re: NAMD took more than 1 day on 36 cpu to complete 1ns simulation for a 77000 system

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Mon Nov 16 2020 - 11:13:36 CST

6 ns/day may indeed be reasonable, but that isn't 2 days for a 1ns test
run. Instead, a nanosecond should finish in ~4 hours, so this doesn't
square away with what you sent earlier. It has been a while since I've
used CPU-only builds of NAMD, but my recollection was that the point
where they stopped scaling was when you had about 500 atoms per core,
and that you'd max out with somewhere in the 10-30 ns/day at that point,
depending on how beefy the cores were. Depending on the exact processor
model, you may be able to benefit from ongoing work to bring NAMD to the
AVX-512 instruction set, which I know exists but do not know the current
state of play.

-Josh

On 11/16/20 10:05 AM, Seke Keretsu wrote:
> Dear JV,
>
> My command was : namd2 +p36 production.namd > prod.log 
>
> It’s currently showing near 6 ns/day approx on a 77000 atom. Is that
> reasonable based on your experience?
>
>
> On Tue, Nov 17, 2020 at 1:01 AM Josh Vermaas <joshua.vermaas_at_gmail.com
> <mailto:joshua.vermaas_at_gmail.com>> wrote:
>
> Hi Seke,
>
> What was your run command, and what does the log look like? For a
> system
> that small, 36 CPUs should easily get many nanoseconds of
> simulation in
> a day. What I suspect happened is that you didn't specify a +p
> argument
> to the NAMD executable, and the default is one processor. It is also
> *possible* that CHARMM-GUI adds some really poorly performing
> constraints, but I don't expect that to be the main problem.
>
> -Josh
>
> On 11/16/20 12:55 AM, Seke Keretsu wrote:
> > Dear Expert,
> >
> > I am performing a conventional MD simulation of a GPCR-ligand system
> > consisting approximately 77000 atoms. The 1 ns test run took about 2
> > days to complete on a  36 cpu machine (Centos7, intex xeon gold).
> >
> > I am not sure if this rate is expected.
> >
> > I wonder if using the parameters/configuration generated from
> > charmm-gui is slowing my production run. Could someone give an
> insight
> > into this.
> > Is there a way to speed up the simulation ?
> >
> > The system consisted of POPC, solvent and protein-ligand complex
> > totalling to about 77000 atoms.
> >
> > The input config file is given below:
> >
> > structure               step5_charmm2namd.psf
> > coordinates             step5_charmm2namd.pdb
> >
> > set temp                303.15;
> > outputName              step7_production; # base name for output
> from
> > this run
> >                                             # NAMD writes two
> files at
> > the end, final coord and vel
> >                                             # in the format of
> > first-dyn.coor and first-dyn.vel
> >
> > set inputname           step6.6_equilibration;
> > binCoordinates          $inputname.coor;    # coordinates from last
> > run (binary)
> > binVelocities           $inputname.vel;     # velocities from
> last run
> > (binary)
> > extendedSystem          $inputname.xsc;     # cell dimensions from
> > last run (binary)
> >
> > restartfreq             5000;               # 5000 steps = every
> 10ps
> > dcdfreq                 50000;
> > dcdUnitCell             yes;                # the file will contain
> > unit cell info in the style of
> >                                             # charmm dcd files. if
> > yes, the dcd files will contain
> >                                             # unit cell
> information in
> > the style of charmm DCD files.
> > xstFreq                 5000;               # XSTFreq: control how
> > often the extended systen configuration
> >                                             # will be appended
> to the
> > XST file
> > outputEnergies          5000;               # 5000 steps = every
> 10ps
> >                                             # The number of
> timesteps
> > between each energy output of NAMD
> > outputTiming            5000;               # The number of
> timesteps
> > between each timing output shows
> >                                             # time per step and time
> > to completion
> >
> > # Force-Field Parameters
> > paraTypeCharmm          on;                 # We're using charmm
> type
> > parameter file(s)
> >                                             # multiple
> definitions may
> > be used but only one file per definition
> > parameters              toppar/par_all36m_prot.prm
> > parameters              toppar/par_all36_na.prm
> > parameters              toppar/par_all36_carb.prm
> > parameters              toppar/par_all36_lipid.prm
> > parameters              toppar/par_all36_cgenff.prm
> > parameters              toppar/par_interface.prm
> > parameters              toppar/toppar_all36_nano_lig.str
> > parameters              toppar/toppar_all36_nanolig_patch.str
> > parameters              toppar/toppar_all36_synthetic_polymer.str
> > parameters            
>  toppar/toppar_all36_synthetic_polymer_patch.str
> > parameters              toppar/toppar_all36_polymer_solvent.str
> > parameters              toppar/toppar_water_ions.str
> > parameters              toppar/toppar_dum_noble_gases.str
> > parameters              toppar/toppar_ions_won.str
> > parameters              toppar/toppar_all36_prot_arg0.str
> > parameters            
>  toppar/toppar_all36_prot_c36m_d_aminoacids.str
> > parameters              toppar/toppar_all36_prot_fluoro_alkanes.str
> > parameters              toppar/toppar_all36_prot_heme.str
> > parameters              toppar/toppar_all36_prot_na_combined.str
> > parameters              toppar/toppar_all36_prot_retinol.str
> > parameters              toppar/toppar_all36_prot_modify_res.str
> > parameters              toppar/toppar_all36_na_nad_ppi.str
> > parameters              toppar/toppar_all36_na_rna_modified.str
> > parameters              toppar/toppar_all36_lipid_archaeal.str
> > parameters              toppar/toppar_all36_lipid_bacterial.str
> > parameters              toppar/toppar_all36_lipid_cardiolipin.str
> > parameters              toppar/toppar_all36_lipid_cholesterol.str
> > parameters              toppar/toppar_all36_lipid_dag.str
> > parameters              toppar/toppar_all36_lipid_inositol.str
> > parameters              toppar/toppar_all36_lipid_lps.str
> > parameters              toppar/toppar_all36_lipid_miscellaneous.str
> > parameters              toppar/toppar_all36_lipid_model.str
> > parameters              toppar/toppar_all36_lipid_prot.str
> > parameters              toppar/toppar_all36_lipid_sphingo.str
> > parameters              toppar/toppar_all36_lipid_yeast.str
> > parameters              toppar/toppar_all36_lipid_hmmm.str
> > parameters              toppar/toppar_all36_lipid_detergent.str
> > parameters              toppar/toppar_all36_lipid_ether.str
> > parameters              toppar/toppar_all36_carb_glycolipid.str
> > parameters              toppar/toppar_all36_carb_glycopeptide.str
> > parameters              toppar/toppar_all36_carb_imlab.str
> > parameters              toppar/toppar_all36_label_spin.str
> > parameters              toppar/toppar_all36_label_fluorophore.str
> > parameters              ../unk/unk.prm   # Custom topology and
> > parameter files for UNK
> > source                  step5_charmm2namd.str
> >
> > # These are specified by CHARMM
> > exclude                 scaled1-4           # non-bonded exclusion
> > policy to use "none,1-2,1-3,1-4,or scaled1-4"
> >                                             # 1-2: all atoms pairs
> > that are bonded are going to be ignored
> >                                             # 1-3: 3 consecutively
> > bonded are excluded
> >                                             # scaled1-4: include all
> > the 1-3, and modified 1-4 interactions
> >                                             # electrostatic
> scaled by
> > 1-4scaling factor 1.0
> >                                             # vdW special 1-4
> > parameters in charmm parameter file.
> > 1-4scaling              1.0
> > switching               on
> > vdwForceSwitching       yes;                # New option for
> > force-based switching of vdW
> >                                             # if both switching and
> > vdwForceSwitching are on CHARMM force
> >                                             # switching is used for
> > vdW forces.
> >
> > # You have some freedom choosing the cutoff
> > cutoff                  12.0;               # may use smaller, maybe
> > 10., with PME
> > switchdist              10.0;               # cutoff - 2.
> >                                             # switchdist - where you
> > start to switch
> >                                             # cutoff - where you
> stop
> > accounting for nonbond interactions.
> >                                             # correspondence in
> charmm:
> >                                             # (cutnb,ctofnb,ctonnb =
> > pairlistdist,cutoff,switchdist)
> > pairlistdist            16.0;               # stores the all the
> pairs
> > with in the distance it should be larger
> >                                             # than cutoff( + 2.)
> > stepspercycle           20;                 # 20 redo pairlists
> every
> > ten steps
> > pairlistsPerCycle       2;                  # 2 is the default
> >                                             # cycle represents the
> > number of steps between atom reassignments
> >                                             # this means every
> 20/2=10
> > steps the pairlist will be updated
> >                          
> > # Integrator Parameters
> > timestep                2.0;                # fs/step
> > rigidBonds              all;                # Bound constraint all
> > bonds involving H are fixed in length
> > nonbondedFreq           1;                  # nonbonded forces
> every step
> > fullElectFrequency      1;                  # PME every step
> >
> > wrapWater               on;                 # wrap water to
> central cell
> > wrapAll                 on;                 # wrap other
> molecules too
> > if { $boxtype == "hexa" } {
> > wrapNearest             on;                 # use for
> non-rectangular
> > cells (wrap to the nearest image)
> > } else {
> > wrapNearest             off;                # use for
> non-rectangular
> > cells (wrap to the nearest image)
> > }
> >
> > # PME (for full-system periodic electrostatics)
> > PME                     yes;
> > PMEInterpOrder          6;                  # interpolation order
> > (spline order 6 in charmm)
> > PMEGridSpacing          1.0;                # maximum PME grid
> space /
> > used to calculate grid size
> >
> > # Constant Pressure Control (variable volume)
> > useGroupPressure        yes;                # use a hydrogen-group
> > based pseudo-molecular viral to calcualte pressure and
> >                                             # has less
> fluctuation, is
> > needed for rigid bonds (rigidBonds/SHAKE)
> > useFlexibleCell         yes;                # yes for anisotropic
> > system like membrane
> > useConstantRatio        yes;                # keeps the ratio of the
> > unit cell in the x-y plane constant A=B
> >
> > langevinPiston          on;                 # Nose-Hoover Langevin
> > piston pressure control
> > langevinPistonTarget    1.01325;            # target pressure in bar
> > 1atm = 1.01325bar
> > langevinPistonPeriod    50.0;               # oscillation period in
> > fs. correspond to pgamma T=50fs=0.05ps
> >                                             # f=1/T=20.0(pgamma)
> > langevinPistonDecay     25.0;               # oscillation decay
> time.
> > smaller value correspons to larger random
> >                                             # forces and increased
> > coupling to the Langevin temp bath.
> >                                             # Equall or smaller than
> > piston period
> > langevinPistonTemp      $temp;              # coupled to heat bath
> >
> > # Constant Temperature Control
> > langevin                on;                 # langevin dynamics
> > langevinDamping         1.0;                # damping coefficient of
> > 1/ps (keep low)
> > langevinTemp            $temp;              # random noise at
> this level
> > langevinHydrogen        off;                # don't couple bath to
> > hydrogens
> > # run
> > numsteps                500000;             # 1ns run stops when
> this
> > step is reached
> > run                     500000;             # 1ns
> >
> >
> > Thank you.
> >
> > Sincerely,
> > seke keretsu
> >
>

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