Main Table of Contents

Fri 29 Aug 2014


For a given number -np or -ntmpi of processors/threads, this program systematically times mdrun with various numbers of PME-only nodes and determines which setting is fastest. It will also test whether performance can be enhanced by shifting load from the reciprocal to the real space part of the Ewald sum. Simply pass your .tpr file to g_tune_pme together with other options for mdrun as needed.

Which executables are used can be set in the environment variables MPIRUN and MDRUN. If these are not present, 'mpirun' and 'mdrun' will be used as defaults. Note that for certain MPI frameworks you need to provide a machine- or hostfile. This can also be passed via the MPIRUN variable, e.g.

export MPIRUN="/usr/local/mpirun -machinefile hosts"

Please call g_tune_pme with the normal options you would pass to mdrun and add -np for the number of processors to perform the tests on, or -ntmpi for the number of threads. You can also add -r to repeat each test several times to get better statistics.

g_tune_pme can test various real space / reciprocal space workloads for you. With -ntpr you control how many extra .tpr files will be written with enlarged cutoffs and smaller Fourier grids respectively. Typically, the first test (number 0) will be with the settings from the input .tpr file; the last test (number ntpr) will have the Coulomb cutoff specified by -rmax with a somwhat smaller PME grid at the same time. In this last test, the Fourier spacing is multiplied with rmax/rcoulomb. The remaining .tpr files will have equally-spaced Coulomb radii (and Fourier spacings) between these extremes. Note that you can set -ntpr to 1 if you just seek the optimal number of PME-only nodes; in that case your input .tpr file will remain unchanged.

For the benchmark runs, the default of 1000 time steps should suffice for most MD systems. The dynamic load balancing needs about 100 time steps to adapt to local load imbalances, therefore the time step counters are by default reset after 100 steps. For large systems (>1M atoms), as well as for a higher accuarcy of the measurements, you should set -resetstep to a higher value. From the 'DD' load imbalance entries in the md.log output file you can tell after how many steps the load is sufficiently balanced. Example call:

g_tune_pme -np 64 -s protein.tpr -launch

After calling mdrun several times, detailed performance information is available in the output file perf.out. Note that during the benchmarks, a couple of temporary files are written (options -b*), these will be automatically deleted after each test.

If you want the simulation to be started automatically with the optimized parameters, use the command line option -launch.


-p perf.out Output Generic output file
-err bencherr.log Output Log file
-so tuned.tpr Output Run input file: tpr tpb tpa
-s topol.tpr Input Run input file: tpr tpb tpa
-o traj.trr Output Full precision trajectory: trr trj cpt
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi state.cpt Input, Opt. Checkpoint file
-cpo state.cpt Output, Opt. Checkpoint file
-c confout.gro Output Structure file: gro g96 pdb etc.
-e ener.edr Output Energy file
-g md.log Output Log file
-dhdl dhdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tabletf tabletf.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-tableb table.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-tpid tpidist.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo edsam.xvg Output, Opt. xvgr/xmgr file
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-px pullx.xvg Output, Opt. xvgr/xmgr file
-pf pullf.xvg Output, Opt. xvgr/xmgr file
-ro rotation.xvg Output, Opt. xvgr/xmgr file
-ra rotangles.log Output, Opt. Log file
-rs rotslabs.log Output, Opt. Log file
-rt rottorque.log Output, Opt. Log file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file
-bo bench.trr Output Full precision trajectory: trr trj cpt
-bx bench.xtc Output Compressed trajectory (portable xdr format)
-bcpo bench.cpt Output Checkpoint file
-bc bench.gro Output Structure file: gro g96 pdb etc.
-be bench.edr Output Energy file
-bg bench.log Output Log file
-beo benchedo.xvg Output, Opt. xvgr/xmgr file
-bdhdl benchdhdl.xvg Output, Opt. xvgr/xmgr file
-bfield benchfld.xvg Output, Opt. xvgr/xmgr file
-btpi benchtpi.xvg Output, Opt. xvgr/xmgr file
-btpid benchtpid.xvg Output, Opt. xvgr/xmgr file
-bjo bench.gct Output, Opt. General coupling stuff
-bffout benchgct.xvg Output, Opt. xvgr/xmgr file
-bdevout benchdev.xvg Output, Opt. xvgr/xmgr file
-brunav benchrnav.xvg Output, Opt. xvgr/xmgr file
-bpx benchpx.xvg Output, Opt. xvgr/xmgr file
-bpf benchpf.xvg Output, Opt. xvgr/xmgr file
-bro benchrot.xvg Output, Opt. xvgr/xmgr file
-bra benchrota.log Output, Opt. Log file
-brs benchrots.log Output, Opt. Log file
-brt benchrott.log Output, Opt. Log file
-bmtx benchn.mtx Output, Opt. Hessian matrix
-bdn bench.ndx Output, Opt. Index file

Other options

-[no]h bool no Print help info and quit
-[no]version bool no Print version info and quit
-nice int 0 Set the nicelevel
-xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none
-np int 1 Number of nodes to run the tests on (must be > 2 for separate PME nodes)
-npstring enum -np Specify the number of processors to $MPIRUN using this string: -np, -n or none
-ntmpi int 1 Number of MPI-threads to run the tests on (turns MPI & mpirun off)
-r int 2 Repeat each test this often
-max real 0.5 Max fraction of PME nodes to test with
-min real 0.25 Min fraction of PME nodes to test with
-npme enum auto Within -min and -max, benchmark all possible values for -npme, or just a reasonable subset. Auto neglects -min and -max and chooses reasonable values around a guess for npme derived from the .tpr: auto, all or subset
-fix int -2 If >= -1, do not vary the number of PME-only nodes, instead use this fixed value and only vary rcoulomb and the PME grid spacing.
-rmax real 0 If >0, maximal rcoulomb for -ntpr>1 (rcoulomb upscaling results in fourier grid downscaling)
-rmin real 0 If >0, minimal rcoulomb for -ntpr>1
-[no]scalevdw bool yes Scale rvdw along with rcoulomb
-ntpr int 0 Number of .tpr files to benchmark. Create this many files with different rcoulomb scaling factors depending on -rmin and -rmax. If < 1, automatically choose the number of .tpr files to test
-steps step 1000 Take timings for this many steps in the benchmark runs
-resetstep int 100 Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many steps)
-simsteps step -1 If non-negative, perform this many steps in the real run (overwrites nsteps from .tpr, add .cpt steps)
-[no]launch bool no Launch the real simulation after optimization
-[no]bench bool yes Run the benchmarks or just create the input .tpr files?
-[no]append bool yes Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names (for launch only)
-[no]cpnum bool no Keep and number checkpoint files (launch only)