Provided by: gromacs-data_2020.1-1_all 
NAME
gmx-tune_pme - Time mdrun as a function of PME ranks to optimize settings
SYNOPSIS
gmx tune_pme [-s [<.tpr>]] [-cpi [<.cpt>]] [-table [<.xvg>]]
[-tablep [<.xvg>]] [-tableb [<.xvg>]]
[-rerun [<.xtc/.trr/...>]] [-ei [<.edi>]] [-p [<.out>]]
[-err [<.log>]] [-so [<.tpr>]] [-o [<.trr/.cpt/...>]]
[-x [<.xtc/.tng>]] [-cpo [<.cpt>]]
[-c [<.gro/.g96/...>]] [-e [<.edr>]] [-g [<.log>]]
[-dhdl [<.xvg>]] [-field [<.xvg>]] [-tpi [<.xvg>]]
[-tpid [<.xvg>]] [-eo [<.xvg>]] [-px [<.xvg>]]
[-pf [<.xvg>]] [-ro [<.xvg>]] [-ra [<.log>]]
[-rs [<.log>]] [-rt [<.log>]] [-mtx [<.mtx>]]
[-swap [<.xvg>]] [-bo [<.trr/.cpt/...>]] [-bx [<.xtc>]]
[-bcpo [<.cpt>]] [-bc [<.gro/.g96/...>]] [-be [<.edr>]]
[-bg [<.log>]] [-beo [<.xvg>]] [-bdhdl [<.xvg>]]
[-bfield [<.xvg>]] [-btpi [<.xvg>]] [-btpid [<.xvg>]]
[-bdevout [<.xvg>]] [-brunav [<.xvg>]] [-bpx [<.xvg>]]
[-bpf [<.xvg>]] [-bro [<.xvg>]] [-bra [<.log>]]
[-brs [<.log>]] [-brt [<.log>]] [-bmtx [<.mtx>]]
[-bdn [<.ndx>]] [-bswap [<.xvg>]] [-xvg <enum>]
[-mdrun <string>] [-np <int>] [-npstring <enum>]
[-ntmpi <int>] [-r <int>] [-max <real>] [-min <real>]
[-npme <enum>] [-fix <int>] [-rmax <real>]
[-rmin <real>] [-[no]scalevdw] [-ntpr <int>]
[-steps <int>] [-resetstep <int>] [-nsteps <int>]
[-[no]launch] [-[no]bench] [-[no]check]
[-gpu_id <string>] [-[no]append] [-[no]cpnum]
[-deffnm <string>]
DESCRIPTION
For a given number -np or -ntmpi of ranks, gmx tune_pme systematically times gmx mdrun with various
numbers of PME-only ranks 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 gmx tune_pme together with other options for gmx mdrun as needed.
gmx tune_pme needs to call gmx mdrun and so requires that you specify how to call mdrun with the argument
to the -mdrun parameter. Depending how you have built GROMACS, values such as 'gmx mdrun', 'gmx_d mdrun',
or 'mdrun_mpi' might be needed.
The program that runs MPI programs can be set in the environment variable MPIRUN (defaults to 'mpirun').
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" Note that in such cases it is normally necessary to
compile and/or run gmx tune_pme without MPI support, so that it can call the MPIRUN program.
Before doing the actual benchmark runs, gmx tune_pme will do a quick check whether gmx mdrun works as
expected with the provided parallel settings if the -check option is activated (the default). Please
call gmx tune_pme with the normal options you would pass to gmx mdrun and add -np for the number of ranks
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.
gmx 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 somewhat 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 ranks; 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
accuracy 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:
gmx tune_pme -np 64 -s protein.tpr -launch
After calling gmx 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.
Basic support for GPU-enabled mdrun exists. Give a string containing the IDs of the GPUs that you wish to
use in the optimization in the -gpu_id command-line argument. This works exactly like mdrun -gpu_id, does
not imply a mapping, and merely declares the eligible set of GPU devices. gmx-tune_pme will construct
calls to mdrun that use this set appropriately. gmx-tune_pme does not support -gputasks.
OPTIONS
Options to specify input files:
-s [<.tpr>] (topol.tpr)
Portable xdr run input file
-cpi [<.cpt>] (state.cpt) (Optional)
Checkpoint file
-table [<.xvg>] (table.xvg) (Optional)
xvgr/xmgr file
-tablep [<.xvg>] (tablep.xvg) (Optional)
xvgr/xmgr file
-tableb [<.xvg>] (table.xvg) (Optional)
xvgr/xmgr file
-rerun [<.xtc/.trr/...>] (rerun.xtc) (Optional)
Trajectory: xtc trr cpt gro g96 pdb tng
-ei [<.edi>] (sam.edi) (Optional)
ED sampling input
Options to specify output files:
-p [<.out>] (perf.out)
Generic output file
-err [<.log>] (bencherr.log)
Log file
-so [<.tpr>] (tuned.tpr)
Portable xdr run input file
-o [<.trr/.cpt/...>] (traj.trr)
Full precision trajectory: trr cpt tng
-x [<.xtc/.tng>] (traj_comp.xtc) (Optional)
Compressed trajectory (tng format or portable xdr format)
-cpo [<.cpt>] (state.cpt) (Optional)
Checkpoint file
-c [<.gro/.g96/...>] (confout.gro)
Structure file: gro g96 pdb brk ent esp
-e [<.edr>] (ener.edr)
Energy file
-g [<.log>] (md.log)
Log file
-dhdl [<.xvg>] (dhdl.xvg) (Optional)
xvgr/xmgr file
-field [<.xvg>] (field.xvg) (Optional)
xvgr/xmgr file
-tpi [<.xvg>] (tpi.xvg) (Optional)
xvgr/xmgr file
-tpid [<.xvg>] (tpidist.xvg) (Optional)
xvgr/xmgr file
-eo [<.xvg>] (edsam.xvg) (Optional)
xvgr/xmgr file
-px [<.xvg>] (pullx.xvg) (Optional)
xvgr/xmgr file
-pf [<.xvg>] (pullf.xvg) (Optional)
xvgr/xmgr file
-ro [<.xvg>] (rotation.xvg) (Optional)
xvgr/xmgr file
-ra [<.log>] (rotangles.log) (Optional)
Log file
-rs [<.log>] (rotslabs.log) (Optional)
Log file
-rt [<.log>] (rottorque.log) (Optional)
Log file
-mtx [<.mtx>] (nm.mtx) (Optional)
Hessian matrix
-swap [<.xvg>] (swapions.xvg) (Optional)
xvgr/xmgr file
-bo [<.trr/.cpt/...>] (bench.trr)
Full precision trajectory: trr cpt tng
-bx [<.xtc>] (bench.xtc)
Compressed trajectory (portable xdr format): xtc
-bcpo [<.cpt>] (bench.cpt)
Checkpoint file
-bc [<.gro/.g96/...>] (bench.gro)
Structure file: gro g96 pdb brk ent esp
-be [<.edr>] (bench.edr)
Energy file
-bg [<.log>] (bench.log)
Log file
-beo [<.xvg>] (benchedo.xvg) (Optional)
xvgr/xmgr file
-bdhdl [<.xvg>] (benchdhdl.xvg) (Optional)
xvgr/xmgr file
-bfield [<.xvg>] (benchfld.xvg) (Optional)
xvgr/xmgr file
-btpi [<.xvg>] (benchtpi.xvg) (Optional)
xvgr/xmgr file
-btpid [<.xvg>] (benchtpid.xvg) (Optional)
xvgr/xmgr file
-bdevout [<.xvg>] (benchdev.xvg) (Optional)
xvgr/xmgr file
-brunav [<.xvg>] (benchrnav.xvg) (Optional)
xvgr/xmgr file
-bpx [<.xvg>] (benchpx.xvg) (Optional)
xvgr/xmgr file
-bpf [<.xvg>] (benchpf.xvg) (Optional)
xvgr/xmgr file
-bro [<.xvg>] (benchrot.xvg) (Optional)
xvgr/xmgr file
-bra [<.log>] (benchrota.log) (Optional)
Log file
-brs [<.log>] (benchrots.log) (Optional)
Log file
-brt [<.log>] (benchrott.log) (Optional)
Log file
-bmtx [<.mtx>] (benchn.mtx) (Optional)
Hessian matrix
-bdn [<.ndx>] (bench.ndx) (Optional)
Index file
-bswap [<.xvg>] (benchswp.xvg) (Optional)
xvgr/xmgr file
Other options:
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-mdrun <string>
Command line to run a simulation, e.g. 'gmx mdrun' or 'mdrun_mpi'
-np <int> (1)
Number of ranks to run the tests on (must be > 2 for separate PME ranks)
-npstring <enum> (np)
Name of the $MPIRUN option that specifies the number of ranks to use ('np', or 'n'; use 'none' if
there is no such option): np, n, 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 ranks to test with
-min <real> (0.25)
Min fraction of PME ranks 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, subset
-fix <int> (-2)
If >= -1, do not vary the number of PME-only ranks, 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 (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 <int> (1000)
Take timings for this many steps in the benchmark runs
-resetstep <int> (1500)
Let dlb equilibrate this many steps before timings are taken (reset cycle counters after this many
steps)
-nsteps <int> (-1)
If non-negative, perform this many steps in the real run (overwrites nsteps from .tpr, add .cpt
steps)
-[no]launch (no)
Launch the real simulation after optimization
-[no]bench (yes)
Run the benchmarks or just create the input .tpr files?
-[no]check (yes)
Before the benchmark runs, check whether mdrun works in parallel
-gpu_id <string>
List of unique GPU device IDs that are eligible for use
-[no]append (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 (no)
Keep and number checkpoint files (launch only)
-deffnm <string>
Set the default filenames (launch only)
SEE ALSO
gmx(1)
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2020, GROMACS development team