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Why bother with performance?
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Software performance is the use of computational resources effectively to reduce runtime
Understanding performance is the best way of utilising your HPC resources efficiently
Performance can be measured by looking at flops, walltime, and CPU hours
There are many ways of enhancing performance, and there is no single ‘correct’ way. The performance of any software will vary depending on the tasks you want it to undertake.
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Connecting performance to hardware
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Benchmarking and Scaling
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Benchmarking is a way of assessing the performance of a program or set of programs
The log.lammps file shows important information about the timing, processor layout, etc. which you can use to record your benchmark
Scaling concerns the effective use of computational resources. Two types are typically discussed: strong scaling (where we increase the compute resources but keep the problem size the same) and weak scaling (where we increase the problem size in proportion to our increase of compute resources
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Bottlenecks in LAMMPS
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The best way to identify bottlenecks is to run different benchmarks on a smaller system and compare it to a representative system
Effective load balancing is being able to distribute an equal amount of work across processes
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Accelerating LAMMPS
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The five accelerator packages currently offered by LAMMPS are i) OPT, ii) USER-INTEL, iii) USER-OMP, iv) GPU, v) KOKKOS
KOKKOS is available for use on all types of hardware. Other accelerator packages are hardware specific
To invoke a package in LAMMPS, the notation is package <style> <arguments>, where style is the package you want to invoke
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Invoking KOKKOS
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KOKKOS with OpenMP
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The three command line switches, -k on, -sf kk and -pk kokkos are needed to run the KOKKOS package
Different values of the keywords neigh, newton, comm and binsize result in different runtimes
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KOKKOS with GPUs
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Knowing the capabilities of your host, device and if you can use a CUDA-aware MPI runtime is required before starting a GPU run
KOKKOS compares very well with the GPU package in double precision
KOKKOS aims to be performance portable and is worth pursuing because of this
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Limitations and Rules of Thumb
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{:auto_ids}
package-OPT
: As of *3Mar20* version of LAMMPS, the following list of functionalities are available
with the OPT package
| Pair styles |
| :---------------: |
|eam_alloy |
|eam_fs |
|eam |
|lj_charmm_coul_long|
|lj_cut_coul_long |
|lj_cut |
|lj_cut_tip4p_long |
|lj_long_coul_long |
|morse |
|ufm |
package-USER-INTEL
: As of *3Mar20* version of LAMMPS, the following list of functionalities are available
with the USER-INTEL package
| Pair styles | Bond styles | Angle styles | Improper styles | Dihedral styles | Fix styles | K-space styles | Integrator styles |
| :------------------ | :---------- | :----------- | :-------------- | :-------------- | :--------- | :------------- | :---------------- |
|airebo | fene | charmm | cvff | charmm | nve | pppm | verlet_lrt |
|airebo_morse | harmonic | harmonic | harmonic | fourier | nvt | pppm_disp | |
|buck_coul_cut | | | | harmonic | npt | | |
|buck_coul_long | | | | opls | nh | | |
|buck | | | | | nve_asphere| | |
|dpd | | | | | nvt_sllod | | |
|eam_alloy | | | | | | | |
|eam_fs | | | | | | | |
|eam | | | | | | | |
|gayberne | | | | | | | |
|lj_charmm_coul_charmm| | | | | | | |
|lj_charmm_coul_long | | | | | | | |
|lj_cut_coul_long | | | | | | | |
|lj_cut | | | | | | | |
|lj_long_coul_long | | | | | | | |
|rebo | | | | | | | |
|sw | | | | | | | |
|tersoff | | | | | | | |
package-USER-OMP
: As of *3Mar20* version of LAMMPS, the following list of functionalities are available
with the USER-OMP package
| Pair styles | | | | | |
| :------------------ | :-------------------- | :---------------------------- | :--------------------- | :------------------- | :---------------------- |
|adp |agni |airebo_morse |airbo |beck |born_coul_long |
|born_coul_msm |born_coul_wolf |born |brownian |brownian_poly |buck_coul_cut |
|buck_coul_long |buck_coul_msm |buck_long_coul_long |buck |colloid |comb |
|coul_cut |coul_cut_soft |coul_debye |coul_diel |coul_dsf |coul_long |
|coul_long_soft |coul_msm |coul_wolf |dpd |dpd_tstat |eam_alloy |
|eam_cd |eam_fs |eam |edip |eim |gauss_cut |
|gauss |gayberne |gran_hertz_history |gran_hooke_history |gran_hooke |hbond_dreiding_lj |
|hbond_dreiding_morse |lj96_cut |lj_charmm_coul_charmm_implicit |lj_charmm_coul_charmm |lj_charmm_coul_long |lj_charmm_coul_long_soft |
|lj_charmm_coul_msm |lj_class2_coul_cut |lj_class2_coul_long |lj_class2 |lj_cubic |lj_cut_coul_cut |
|lj_cut_coul_cut_soft |lj_cut_coul_debye |lj_cut_coul_dsf |lj_cut_coul_long |lj_cut_coul_long_soft |lj_cut_coul_msm |
|lj_cut_coul_wolf |lj_cut_dipole_cut |lj_cut |lj_cut_soft |lj_cut_thole_long |lj_cut_tip4p_cut |
|lj_cut_tip4p_long |lj_cut_tip4p_long_soft |lj_expand |lj_gromacs_coul_gromacs |lj_gromacs |lj_long_coul_long |
|lj_long_tip4p_long |lj_sdk_coul_long |lj_sdk_coul_msm |lj_sdk |lj_sf_dipole_sf |lj_smooth_linear |
|lj_smooth_linear |lj_smooth |lubricate |lubricate_poly |meam_spline |morse |
|morse_smooth_linear |nm_cut_coul_cut |nm_cut_coul_long |nm_cut |peri_lps |peri_pmb |
|reaxc |rebo |resquared |soft |sw |table |
|tersoff_mod_c |tersoff_mod |tersoff |tersoff_table |tersoff_zbl |tip4p_cut |
|tip4p_long |tip4p_long_soft |umf |vashishta |vashishta_table |yukawa_colloid |
|yukawa |zbl | | | | |
| Bond styles | Angle styles | Improper styles | Dihedral styles | Fix styles | | K-space styles |
| :----------------- | :--------------- | :-------------- | :--------------- | :------------ | :---------- |:--------------- |
| class2 | charmm | class2 | charmm | gravity | nvt_sllod | pppm_cg |
| fene_expand | class2 | cossq | class2 | neigh_history | nvt_sphere | pppm_disp |
| fene | cosine_delta | cvff | cosine_shift_exp | nh_asphere | peri_neigh | pppm_disp_tip4p |
| gromos | cosine | fourier | fourier | nh | qeq_comb | pppm |
| harmonic | cosine_periodic | harmonic | harmonic | nh_sphere | qeq_reax | pppm_tip4p |
| harmonic_shift_cut | cosine_shift_exp | ring | helix | nph_asphere | rigid_nh | |
| harmonic_shift | cosine_shift | umbrella | multi_harmonic | nph | rigid_nph | |
| morse | cosine_squared | | nharmonic | nph_sphere | rigid_npt | |
| nonlinear | dipole | | opls | npt_asphere | rigid_nve | |
| quartic | fourier | | quadratic | npt | rigid_nvt | |
| table | fourier_simple | | table | npt_sphere | rigid | |
| | harmonic | | | nve | rigid_small | |
| | quartic | | | nve_sphere | | |
| | sdk | | | nvt_asphere | | |
| | table | | | nvt | | |
package-GPU
: As of *3Mar20* version of LAMMPS, the following list of functionalities are
available with the GPU package
| | | Pair styles | | | K-space style |
| :----------------- | :------------------ | :--------------- | :------------------ | :----------------- | :------------ |
| beck | born_coul_long_cs |born_coul_long | born_coul_wolf_cs |born_coul_wolf | pppm |
| born | buck_coul_cut |buck_coul_long | buck |colloid | |
| coul_cut | coul_debye |coul_dsf | coul_long_cs |coul_long | |
| dpd | dpd_tstat |eam_alloy | eam_fs |eam | |
| gauss | gayberne |lj96_cut | lj_charmm_coul_long |lj_class2_coul_long | |
| lj_class2 | lj_cubic |lj_cut_coul_cut | lj_cut_coul_deby |lj_cut_coul_dsf | |
| lj_cut_coul_long | lj_cut_coul_msm |lj_cut_dipole_cut | lj_cut_dipole_long |lj_cut | |
| lj_cut_tip4p_long | lj_expand_coul_long |lj_expand | lj_gromacs |lj_sdk_coul_long | |
| lj_sdk | lj_sf_dipole_sf |mie_cut | morse |resquared | |
| soft | sw |table | tersoff |tersoff_mod | |
| tersoff_zbl | ufm |vashishta | yukawa_colloid |yukawa | |
| zbl | | | | | |