[gmx-users] very strange domain composition statistics
Jennifer Williams
Jennifer.Williams at ed.ac.uk
Fri Jul 31 19:01:04 CEST 2009
Quoting Jennifer Williams <Jennifer.Williams at ed.ac.uk>:
>
> Hi,
>
> Thanks for your input. Sorry I should have mentioned that I am using
> the latest version of gromacs (4.0.5).
>
> This morning I noticed that the strange domain decomp statistics are
> only produced when my simulations run on certain nodes. Below I have
> pasted the domain decomp statistics for the SAME .tpr file run on 2
> different nodes (each time using 6 nodes)- the first looks ok to me
> while the second produces crazy numbers.
>
> I have opened a call to computer support at my Uni to ask if there is
> some difference between the nodes and for now I specify that my
> simulations should run on certain nodes which I have checked are ok.
>
> I don't know if this is something to do with the way I compiled
> gromacs or the architecture. I did a standard installation and it
> seemed to run smoothly-no error messages. I have attached my config.log.
>
> If you have any ideas please let me know,
>
> Thanks
>
>
>
> D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
>
> av. #atoms communicated per step for force: 2 x 1967.2
> av. #atoms communicated per step for LINCS: 2 x 20.4
>
> Average load imbalance: 30.3 %
> Part of the total run time spent waiting due to load imbalance: 5.8 %
> Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 %
>
> NOTE: 5.8 % performance was lost due to load imbalance
> in the domain decomposition.
>
> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>
> Computing: Nodes Number G-Cycles Seconds %
> -----------------------------------------------------------------------
> Domain decomp. 6 100001 852.216 341.9 3.0
> Comm. coord. 6 1000001 594.411 238.5 2.1
> Neighbor search 6 100001 2271.294 911.2 7.9
> Force 6 1000001 5560.129 2230.5 19.3
> Wait + Comm. F 6 1000001 1216.171 487.9 4.2
> PME mesh 6 1000001 15071.432 6046.1 52.2
> Write traj. 6 1001 2.577 1.0 0.0
> Update 6 1000001 264.545 106.1 0.9
> Constraints 6 1000001 923.418 370.4 3.2
> Comm. energies 6 1000001 942.036 377.9 3.3
> Rest 6 1167.866 468.5 4.0
> -----------------------------------------------------------------------
> Total 6 28866.096 11580.0 100.0
> -----------------------------------------------------------------------
>
> Parallel run - timing based on wallclock.
>
> NODE (s) Real (s) (%)
> Time: 1930.000 1930.000 100.0
> 32:10
> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
> Performance: 51.737 6.922 44.767 0.536
> Finished mdrun on node 0 Fri Jul 31 13:05:01 2009
>
>
> D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
>
> av. #atoms communicated per step for force: 2 x 1969.0
> av. #atoms communicated per step for LINCS: 2 x 15.7
>
> Average load imbalance: 500.0 %
> Part of the total run time spent waiting due to load imbalance:
> 5822746112.0 %
> Steps where the load balancing was limited by -rdd, -rcon and/or -dds: X 9 %
>
> NOTE: 5822746112.0 % performance was lost due to load imbalance
> in the domain decomposition.
>
> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>
> Computing: Nodes Number G-Cycles Seconds %
> -----------------------------------------------------------------------
> Write traj. 6 1001 18443320128.890 43061.8 100.0
> Update 6 1000001 314.175 0.0 0.0
> Rest 6 9223372036.855 21534.9 50.0
> -----------------------------------------------------------------------
> Total 6 18443397799.336 43062.0 100.0
> -----------------------------------------------------------------------
>
> NOTE: 306 % of the run time was spent communicating energies,
> you might want to use the -nosum option of mdrun
>
> Parallel run - timing based on wallclock.
>
> NODE (s) Real (s) (%)
> Time: 7177.000 7177.000 100.0
> 1h59:37
> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
> Performance: 13.907 1.861 12.038 1.994
> Finished mdrun on node 0 Thu Jul 30 01:47:05 2009
>
>
>
>
>
>
>
>
>
>
> Quoting Berk Hess <gmx3 at hotmail.com>:
>
>>
>>
>>
>>> Date: Fri, 31 Jul 2009 07:49:49 +0200
>>> From: spoel at xray.bmc.uu.se
>>> To: gmx-users at gromacs.org
>>> Subject: Re: [gmx-users] very strange domain composition statistics
>>>
>>> Mark Abraham wrote:
>>>> Jennifer Williams wrote:
>>>>> Hi ,
>>>>>
>>>>> I am having some problems when running in parallel. Although my jobs
>>>>> run to completion I am getting some worrying domain decomposition
>>>>> statistics in particular the average load imbalance and the
>>>>> performance loss due to load imbalance see below:
>>>>
>>>> Please report your GROMACS version number. If it's not the latest
>>>> (4.0.5), then you should probably update and see if it's a problem that
>>>> may have been fixed between those releases. You might also try it
>>>> without your freeze groups, especially if they dominate the system.
>>>
>>> In addition, you do not specify how may processors you used, nor the
>>> division over processors that mdrun makes and not the expected
>>> performance either. From the numbers below it seems like you used 1 or 2
>>> processors at most. The large number is definitely erroneous though.
>>>
>>
>> For the cycle count table the number of processors seems to be 6.
>>
>> It seems that the cycle counters have overflowed.
>> On what kind of architecture with what kind of compilers are you
>> running this?
>>
>> Berk
>>
>>>>
>>>>> D O M A I N D E C O M P O S I T I O N S T A T I S T I C S
>>>>>
>>>>> av. #atoms communicated per step for force: 2 x 1974.8
>>>>> av. #atoms communicated per step for LINCS: 2 x 15.2
>>>>>
>>>>> Average load imbalance: 500.0 %
>>>>> Part of the total run time spent waiting due to load imbalance:
>>>>> 4246403072.0 %
>>>>> Steps where the load balancing was limited by -rdd, -rcon and/or
>>>>> -dds: X 9 %
>>>>>
>>>>> NOTE: 4246403072.0 % performance was lost due to load imbalance
>>>>> in the domain decomposition.
>>>>>
>>>>> R E A L C Y C L E A N D T I M E A C C O U N T I N G
>>>>>
>>>>> Computing: Nodes Number G-Cycles Seconds %
>>>>> -----------------------------------------------------------------------
>>>>> Write traj. 6 1001 18443320139.164 42130.9 100.0
>>>>> Update 6 1000001 18442922984.491 42130.0 100.0
>>>>> Rest 6 9223372036.855 21069.4 50.0
>>>>> -----------------------------------------------------------------------
>>>>> Total 6 18446422611.669 42138.0 100.0
>>>>> -----------------------------------------------------------------------
>>>>>
>>>>> NOTE: 305 % of the run time was spent communicating energies,
>>>>> you might want to use the -nosum option of mdrun
>>>>>
>>>>> Parallel run - timing based on wallclock.
>>>>>
>>>>> NODE (s) Real (s) (%)
>>>>> Time: 7023.000 7023.000 100.0
>>>>> 1h57:03
>>>>> (Mnbf/s) (GFlops) (ns/day) (hour/ns)
>>>>> Performance: 14.214 1.902 12.302 1.951
>>>>> Finished mdrun on node 0 Wed Jul 29 23:47:18 2009
>>>>>
>>>>>
>>>>>
>>>>> Below is my .mdp file: I am using the PME but not having much of a
>>>>> feel for how to set the options under Spacing for the PME/PPPM FFT
>>>>> grid, I left these as the default values. Could this be where the
>>>>> trouble lies?
>>>>>
>>>>> My cut-off cannot be larger than 0.9 as my unit cell is only 18.2A in
>>>>> one direction.
>>>>>
>>>>> How do I choose values for PME/PPPM? Ie what kind of values to use for
>>>>> nx, ny and nz ?
>>>>
>>>> See manual section 3.17.5
>>>>
>>>>> I read that they should be divisible by npme to get the best
>>>>> performance. Is npme the pme_order in the .mdp file? If not where do I
>>>>> set this parameter?
>>>>
>>>> No, -npme is a command line parameter to mdrun. Roughly speaking, things
>>>> that have a material effect on the physics are specified in the .mdp
>>>> file, and things that either require external file(names) to be supplied
>>>> or which only affect the implementation of the physics are specified on
>>>> the command line.
>>>>
>>>> Mark
>>>>
>>>>> Much appreciated,
>>>>>
>>>>> Jenny
>>>>>
>>>>>
>>>>>
>>>>> ; VARIOUS PREPROCESSING OPTIONS
>>>>> ; Preprocessor information: use cpp syntax.
>>>>> ; e.g.: -I/home/joe/doe -I/home/mary/hoe
>>>>> include = -I../top
>>>>> ; e.g.: -DI_Want_Cookies -DMe_Too
>>>>> define =
>>>>>
>>>>> ; RUN CONTROL PARAMETERS
>>>>> integrator = md
>>>>> ; Start time and timestep in ps
>>>>> tinit = 0
>>>>> dt = 0.001
>>>>> nsteps = 1000000
>>>>> ; For exact run continuation or redoing part of a run
>>>>> ; Part index is updated automatically on checkpointing (keeps files
>>>>> separate)
>>>>> simulation_part = 1
>>>>> init_step = 0
>>>>> ; mode for center of mass motion removal
>>>>> comm-mode = linear
>>>>> ; number of steps for center of mass motion removal
>>>>> nstcomm = 1
>>>>> ; group(s) for center of mass motion removal
>>>>> comm-grps =
>>>>>
>>>>> ; LANGEVIN DYNAMICS OPTIONS
>>>>> ; Friction coefficient (amu/ps) and random seed
>>>>> bd-fric = 0
>>>>> ld-seed = 1993
>>>>>
>>>>> ; ENERGY MINIMIZATION OPTIONS
>>>>> ; Force tolerance and initial step-size
>>>>> emtol =
>>>>> emstep =
>>>>> ; Max number of iterations in relax_shells
>>>>> niter =
>>>>> ; Step size (ps^2) for minimization of flexible constraints
>>>>> fcstep =
>>>>> ; Frequency of steepest descents steps when doing CG
>>>>> nstcgsteep =
>>>>> nbfgscorr =
>>>>>
>>>>> ; TEST PARTICLE INSERTION OPTIONS
>>>>> rtpi =
>>>>>
>>>>> ; OUTPUT CONTROL OPTIONS
>>>>> ; Output frequency for coords (x), velocities (v) and forces (f)
>>>>> nstxout = 1000
>>>>> nstvout = 1000
>>>>> nstfout = 0
>>>>> ; Output frequency for energies to log file and energy file
>>>>> nstlog = 1000
>>>>> nstenergy = 1000
>>>>> ; Output frequency and precision for xtc file
>>>>> nstxtcout = 1000
>>>>> xtc-precision = 1000
>>>>> ; This selects the subset of atoms for the xtc file. You can
>>>>> ; select multiple groups. By default all atoms will be written.
>>>>> xtc-grps =
>>>>> ; Selection of energy groups
>>>>> energygrps =
>>>>>
>>>>> ; NEIGHBORSEARCHING PARAMETERS
>>>>> ; nblist update frequency
>>>>> nstlist =
>>>>> ; ns algorithm (simple or grid)
>>>>> ns_type = grid
>>>>> ; Periodic boundary conditions: xyz, no, xy
>>>>> pbc = xyz
>>>>> periodic_molecules = yes
>>>>> ; nblist cut-off
>>>>> rlist = 0.9
>>>>>
>>>>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>>>>> ; Method for doing electrostatics
>>>>> coulombtype = PME
>>>>> rcoulomb-switch = 0
>>>>> rcoulomb = 0.9
>>>>> ; Relative dielectric constant for the medium and the reaction field
>>>>> epsilon_r =
>>>>> epsilon_rf =
>>>>>
>>>>> ; Method for doing Van der Waals
>>>>> vdw-type = Cut-off
>>>>> ; cut-off lengths
>>>>> rvdw-switch = 0
>>>>> rvdw = 0.9
>>>>> ; Apply long range dispersion corrections for Energy and Pressure
>>>>> DispCorr = No
>>>>> ; Extension of the potential lookup tables beyond the cut-off
>>>>> table-extension =
>>>>> ; Seperate tables between energy group pairs
>>>>> energygrp_table =
>>>>>
>>>>>
>>>>> ; Spacing for the PME/PPPM FFT grid
>>>>> fourierspacing = 0.12
>>>>> ; FFT grid size, when a value is 0 fourierspacing will be used
>>>>> fourier_nx = 0
>>>>> fourier_ny = 0
>>>>> fourier_nz = 0
>>>>> ; EWALD/PME/PPPM parameters
>>>>> pme_order =
>>>>> ewald_rtol = 1e-05
>>>>> ewald_geometry = 3d
>>>>> epsilon_surface = 0
>>>>> optimize_fft = yes
>>>>>
>>>>>
>>>>>
>>>>> ; OPTIONS FOR WEAK COUPLING ALGORITHMS
>>>>> ; Temperature coupling
>>>>> tcoupl = nose-hoover
>>>>> ; Groups to couple separately
>>>>> tc-grps = System
>>>>> ; Time constant (ps) and reference temperature (K)
>>>>> tau_t = 0.1
>>>>> ref_t = 150
>>>>>
>>>>> ; Pressure coupling
>>>>> Pcoupl = No
>>>>> Pcoupltype =
>>>>> ; Time constant (ps), compressibility (1/bar) and reference P (bar)
>>>>> tau-p =
>>>>> compressibility =
>>>>> ref-p =
>>>>> ; Scaling of reference coordinates, No, All or COM
>>>>> refcoord_scaling = no
>>>>> ; Random seed for Andersen thermostat
>>>>> andersen_seed =
>>>>>
>>>>> ; GENERATE VELOCITIES FOR STARTUP RUN
>>>>> gen_vel = yes
>>>>> gen_temp = 150
>>>>> gen_seed = 173529
>>>>>
>>>>> ; OPTIONS FOR BONDS
>>>>> constraints = none
>>>>> ; Type of constraint algorithm
>>>>> constraint-algorithm = Lincs
>>>>> ; Do not constrain the start configuration
>>>>> continuation = no
>>>>> ; Use successive overrelaxation to reduce the number of shake iterations
>>>>> Shake-SOR = no
>>>>> ; Relative tolerance of shake
>>>>> shake-tol = 0.0001
>>>>> ; Highest order in the expansion of the constraint coupling matrix
>>>>> lincs-order = 4
>>>>> ; Number of iterations in the final step of LINCS. 1 is fine for
>>>>> ; normal simulations, but use 2 to conserve energy in NVE runs.
>>>>> ; For energy minimization with constraints it should be 4 to 8.
>>>>> lincs-iter = 1
>>>>> ; Lincs will write a warning to the stderr if in one step a bond
>>>>> ; rotates over more degrees than
>>>>> lincs-warnangle = 30
>>>>> ; Convert harmonic bonds to morse potentials
>>>>> morse = no
>>>>>
>>>>> ; ENERGY GROUP EXCLUSIONS
>>>>> ; Pairs of energy groups for which all non-bonded interactions are
>>>>> excluded
>>>>> energygrp_excl =
>>>>>
>>>>> ; WALLS
>>>>> ; Number of walls, type, atom types, densities and box-z scale factor
>>>>> for Ewald
>>>>> nwall = 0
>>>>> wall_type = 9-3
>>>>> wall_r_linpot = -1
>>>>> wall_atomtype =
>>>>> wall_density =
>>>>> wall_ewald_zfac = 3
>>>>>
>>>>>
>>>>> ; Non-equilibrium MD stuff
>>>>> acc-grps =
>>>>> accelerate =
>>>>> freezegrps = SI_O
>>>>> freezedim = Y Y Y
>>>>> cos-acceleration = 0
>>>>> deform =
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
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>>>
>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
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>>
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>
>
>
> Dr. Jennifer Williams
> Institute for Materials and Processes
> School of Engineering
> University of Edinburgh
> Sanderson Building
> The King's Buildings
> Mayfield Road
> Edinburgh, EH9 3JL, United Kingdom
> Phone: ++44 (0)131 650 4 861
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
Dr. Jennifer Williams
Institute for Materials and Processes
School of Engineering
University of Edinburgh
Sanderson Building
The King's Buildings
Mayfield Road
Edinburgh, EH9 3JL, United Kingdom
Phone: ++44 (0)131 650 4 861
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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