Hi!
I compiled LAMMPS with support for KOKKOS, CUDA, and ML-PACE.
cmake -C ../cmake/presets/kokkos-cuda.cmake \
-D PKG_ML-PACE=YES \
-D CMAKE_BUILD_TYPE=Release \
-D BUILD_MPI=OFF \
-D PKG_OPENMP=YES \
-D BUILD_OMP=ON \
-D PKG_KOKKOS=ON \
-D BUILD_KOKKOS=ON \
-D Kokkos_ENABLE_CUDA=ON \
-D Kokkos_ARCH_HOSTARCH=YES \
-D BUILD_SHARED_LIBS=OFF \
-D CMAKE_CXX_FLAGS="-static-libgcc -static-libstdc++ -fopenmp" \
-D CMAKE_EXE_LINKER_FLAGS="-static-libgcc -static-libstdc++ -L/usr/lib/gcc/x86_64-linux-gnu/12 -lgomp" \
../cmake
When running on a cluster I see the following error
ERROR: KOKKOS package requires fix minimize/kk (src/KOKKOS/min_kokkos.cpp:64)
Last input line: minimize 1.0e-4 1.0e-6 1000 10000
Part of the input file
#[ UNITS
units metal
boundary f f f
atom_style atomic/kk
atom_modify map array
newton off
neighbor 0.1 bin
neigh_modify delay 10
timestep 0.001
thermo ${echo_thermo_every_step}
#]
#[ Atom Definition & potential
read_data ${start_file}
pair_style hybrid/overlay/kk pace table linear 10000
pair_coeff * * pace c_ace.yace C
pair_coeff * * table d2.table D2 9.0
#]
min_style cg/kk
minimize 1.0e-4 1.0e-6 1000 10000
run 0
delete_atoms group removed_atoms
If I add fix kkmin all minimize/kk to the input file I see the following error:
ERROR: Unrecognized fix style 'minimize/kk' (src/modify.cpp:928)
Last input line: fix kkmin all minimize/kk
I use LAMMPS (2 Apr 2025)
I don’t think the problem is related to the bug you fixed. I’ve tried patching locally and making a new binary, but I still have the same problem.-sf kk before.
I’m also surprised that I don’t see minimize/kk in the output of the following command:
$ lmp -sf kk -h
* Minimize styles:
cg cg/kk fire/old fire hftn
quickmin sd
* Pair styles:
born born/omp buck buck/coul/cut buck/coul/cut/kk
buck/coul/cut/omp buck/kk buck/omp coul/cut
coul/cut/kk coul/cut/omp coul/debye coul/debye/kk coul/debye/omp
coul/dsf coul/dsf/kk coul/dsf/omp coul/wolf coul/wolf/kk
coul/wolf/omp meam/c reax reax/c mesont/tpm
hybrid hybrid/omp hybrid/kk hybrid/molecular
hybrid/molecular/omp hybrid/overlay hybrid/overlay/omp
hybrid/overlay/kk hybrid/scaled hybrid/scaled/omp
lj/cut lj/cut/coul/cut lj/cut/coul/cut/kk
lj/cut/coul/cut/omp lj/cut/kk lj/cut/omp lj/expand
lj/expand/kk lj/expand/omp morse morse/kk morse/omp
pace pace/extrapolation pace/extrapolation/kk
pace/kk soft soft/kk soft/omp table
table/kk table/omp yukawa yukawa/kk yukawa/omp
zbl zbl/kk zbl/omp zero
I was wrong. I remove this line fix 1 all minimize/kk and now all good. Thanks.
You cannot see the KOKKOS minimize fix because it is an internal fix and thus hidden.
When you use -sf kk then you should remove all /kk suffixes in the input.
I have no problem with the latest develop branch using this simplified input:
units lj
atom_style atomic/kk
lattice fcc 0.8442
region box block 0 2 0 2 0 2
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 3.0 2131513 loop geom
pair_style hybrid/overlay/kk lj/cut/kk 2.5 morse/kk 2.5
pair_coeff 1 1 lj/cut/kk 0.5 1.0
pair_coeff 1 1 morse/kk 50.0 2.0 1.5
neighbor 0.3 bin
neigh_modify every 20 delay 0 check no one 100000 page 10000000
fix 1 all nve/kk
thermo 5
min_style cg/kk
minimize 1.0e-4 1.0e-6 1000 10000
run_style verlet/kk
run 0
Here is the output from ./lmp -h:
Large-scale Atomic/Molecular Massively Parallel Simulator - 2 Apr 2025 - Development
Git info (molecule-refactor-for-json / patch_2Apr2025-455-g9941d9132c-modified)
Usage example: ./lmp -var t 300 -echo screen -in in.alloy
[...]
OS: Linux "Fedora Linux 42 (Adams)" 6.14.8-300.fc42.x86_64 x86_64
Compiler: GNU C++ 15.1.1 20250521 (Red Hat 15.1.1-2) with OpenMP 4.5
C++ standard: C++17
Embedded fmt library version: 10.2.0
Embedded JSON class version: 3.12.0
MPI v4.1: MPICH Version: 4.2.2
MPICH Release date: Wed Jul 3 09:16:22 AM CDT 2024
MPICH ABI: 16:2:4
Accelerator configuration:
GPU package API: HIP
GPU package precision: mixed
KOKKOS package API: OpenMP Serial
KOKKOS package precision: double
Kokkos library version: 4.6.0
OPENMP package API: OpenMP
OPENMP package precision: double
OpenMP standard: OpenMP 4.5
Compatible GPU present: yes
FFT information:
FFT precision = double
FFT engine = mpiFFT
FFT library = KISS
KOKKOS FFT engine = mpiFFT
KOKKOS FFT library = KISS
Active compile time flags:
-DLAMMPS_GZIP
-DLAMMPS_PNG
-DLAMMPS_JPEG
-DLAMMPS_FFMPEG
-DLAMMPS_CURL
-DLAMMPS_SMALLBIG
sizeof(smallint): 32-bit
sizeof(imageint): 32-bit
sizeof(tagint): 32-bit
sizeof(bigint): 64-bit
Available compression formats:
Extension: .gz Command: gzip
Extension: .bz2 Command: bzip2
Extension: .zst Command: zstd
Extension: .xz Command: xz
Extension: .lzma Command: xz
Extension: .lz4 Command: lz4
Installed packages:
AMOEBA ASPHERE AWPMD BOCS BODY BPM BROWNIAN CG-DNA CG-SPICA CLASS2 COLLOID
COLVARS COMPRESS CORESHELL DIELECTRIC DIFFRACTION DIPOLE DPD-BASIC DPD-MESO
DPD-REACT DPD-SMOOTH DRUDE EFF ELECTRODE EXTRA-COMMAND EXTRA-COMPUTE
EXTRA-DUMP EXTRA-FIX EXTRA-MOLECULE EXTRA-PAIR FEP GPU GRANULAR H5MD
INTERLAYER KIM KOKKOS KSPACE LATBOLTZ LEPTON MACHDYN MANIFOLD MANYBODY MC MDI
MEAM MESONT MGPT MISC ML-HDNNP ML-IAP ML-PACE ML-POD ML-QUIP ML-RANN ML-SNAP
ML-UF3 MOFFF MOLECULE MOLFILE NETCDF OPENMP OPT ORIENT PERI PHONON PLUGIN
PLUMED POEMS PTM PYTHON QEQ QTB REACTION REAXFF REPLICA RHEO RIGID SHOCK SMTBQ
SPH SPIN SRD TALLY UEF VORONOI YAFF
List of individual style options included in this LAMMPS executable
* Atom styles:
amoeba angle angle/kk atomic atomic/kk
body bond bond/kk bpm/sphere charge
charge/kk dielectric dipole dipole/kk dpd
dpd/kk edpd electron ellipsoid full
full/kk hybrid hybrid/kk line mdpd
molecular molecular/kk oxdna peri rheo
rheo/thermal smd sph sphere sphere/kk
spin spin/kk tdpd template tri
wavepacket
* Integrate styles:
respa respa/omp verlet verlet/kk verlet/split
* Minimize styles:
cg cg/kk fire/old fire hftn
quickmin sd spin spin/cg spin/lbfgs
* Pair styles:
adp adp/kk adp/omp agni agni/omp
aip/water/2dm aip/water/2dm/opt airebo airebo/morse
airebo/morse/omp airebo/omp amoeba amoeba/gpu
atm awpmd/cut beck beck/gpu beck/omp
body/nparticle body/rounded/polygon body/rounded/polyhedron
bop born born/coul/dsf born/coul/dsf/cs
born/coul/long born/coul/long/cs born/coul/long/cs/gpu
born/coul/long/gpu born/coul/long/omp born/coul/msm
born/coul/msm/omp born/coul/wolf born/coul/wolf/cs
born/coul/wolf/cs/gpu born/coul/wolf/gpu
born/coul/wolf/omp born/gauss born/gpu born/omp
bpm/spring brownian brownian/kk brownian/omp brownian/poly
brownian/poly/omp buck buck6d/coul/gauss/dsf
buck6d/coul/gauss/long buck/coul/cut buck/coul/cut/gpu
buck/coul/cut/kk buck/coul/cut/omp buck/coul/long
buck/coul/long/cs buck/coul/long/gpu
buck/coul/long/kk buck/coul/long/omp buck/coul/msm
buck/coul/msm/omp buck/gpu buck/kk
buck/long/coul/long buck/long/coul/long/omp buck/mdf
buck/omp colloid colloid/gpu colloid/omp comb
comb3 comb/omp cosine/squared coul/ctip coul/cut
coul/cut/dielectric coul/cut/global coul/cut/global/omp
coul/cut/gpu coul/cut/kk coul/cut/omp coul/cut/soft
coul/cut/soft/omp coul/debye coul/debye/gpu coul/debye/kk
coul/debye/omp coul/diel coul/diel/omp coul/dsf coul/dsf/gpu
coul/dsf/kk coul/dsf/omp coul/exclude coul/long coul/long/cs
coul/long/cs/gpu coul/long/dielectric coul/long/gpu
coul/long/kk coul/long/omp coul/long/soft coul/long/soft/omp
coul/msm coul/msm/omp coul/shield coul/slater/cut coul/slater/long
coul/slater/long/gpu coul/streitz coul/tt coul/wolf
coul/wolf/cs coul/wolf/kk coul/wolf/omp meam/c reax
reax/c mesont/tpm dispersion/d3 dpd
dpd/coul/slater/long dpd/coul/slater/long/gpu dpd/ext
dpd/ext/kk dpd/ext/omp dpd/ext/tstat dpd/ext/tstat/kk
dpd/ext/tstat/omp dpd/fdt dpd/fdt/energy
dpd/fdt/energy/kk dpd/gpu dpd/kk dpd/omp
dpd/tstat dpd/tstat/gpu dpd/tstat/kk dpd/tstat/omp drip
dsmc e3b eam eam/alloy eam/alloy/gpu
eam/alloy/kk eam/alloy/omp eam/alloy/opt eam/cd eam/cd/old
eam/fs eam/fs/gpu eam/fs/kk eam/fs/omp eam/fs/opt
eam/gpu eam/he eam/kk eam/omp eam/opt
edip edip/multi edip/omp edpd edpd/gpu
eff/cut eim eim/omp exp6/rx exp6/rx/kk
extep gauss gauss/cut gauss/cut/omp gauss/gpu
gauss/omp gayberne gayberne/gpu gayberne/omp
gran/hertz/history gran/hertz/history/omp gran/hooke
gran/hooke/history gran/hooke/history/kk
gran/hooke/history/omp gran/hooke/omp granular gw
gw/zbl harmonic/cut harmonic/cut/omp
hbond/dreiding/lj hbond/dreiding/lj/angleoffset
hbond/dreiding/lj/angleoffset/omp hbond/dreiding/lj/omp
hbond/dreiding/morse hbond/dreiding/morse/angleoffset
hbond/dreiding/morse/angleoffset/omp hbond/dreiding/morse/omp
hdnnp hippo hippo/gpu hybrid hybrid/omp
hybrid/kk hybrid/molecular hybrid/molecular/omp
hybrid/overlay hybrid/overlay/omp hybrid/overlay/kk
hybrid/scaled hybrid/scaled/omp ilp/graphene/hbn
ilp/graphene/hbn/opt ilp/tmd ilp/tmd/opt kim
kolmogorov/crespi/full kolmogorov/crespi/z lcbop
lebedeva/z lennard/mdf lepton lepton/coul lepton/coul/omp
lepton/omp lepton/sphere lepton/sphere/omp line/lj
list lj96/cut lj96/cut/gpu lj96/cut/omp
lj/charmm/coul/charmm lj/charmm/coul/charmm/gpu
lj/charmm/coul/charmm/implicit lj/charmm/coul/charmm/implicit/kk
lj/charmm/coul/charmm/implicit/omp lj/charmm/coul/charmm/kk
lj/charmm/coul/charmm/omp lj/charmm/coul/long
lj/charmm/coul/long/gpu lj/charmm/coul/long/kk
lj/charmm/coul/long/omp lj/charmm/coul/long/opt
lj/charmm/coul/long/soft lj/charmm/coul/long/soft/omp
lj/charmm/coul/msm lj/charmm/coul/msm/omp
lj/charmmfsw/coul/charmmfsh lj/charmmfsw/coul/long
lj/charmmfsw/coul/long/kk lj/class2 lj/class2/coul/cut
lj/class2/coul/cut/kk lj/class2/coul/cut/omp
lj/class2/coul/cut/soft lj/class2/coul/long
lj/class2/coul/long/cs lj/class2/coul/long/gpu
lj/class2/coul/long/kk lj/class2/coul/long/omp
lj/class2/coul/long/soft lj/class2/gpu lj/class2/kk lj/class2/omp
lj/class2/soft lj/cubic lj/cubic/gpu lj/cubic/omp lj/cut
lj/cut/coul/cut lj/cut/coul/cut/dielectric lj/cut/coul/cut/dielectric/omp
lj/cut/coul/cut/gpu lj/cut/coul/cut/kk
lj/cut/coul/cut/omp lj/cut/coul/cut/soft
lj/cut/coul/cut/soft/gpu lj/cut/coul/cut/soft/omp
lj/cut/coul/debye lj/cut/coul/debye/dielectric
lj/cut/coul/debye/dielectric/omp lj/cut/coul/debye/gpu
lj/cut/coul/debye/kk lj/cut/coul/debye/omp lj/cut/coul/dsf
lj/cut/coul/dsf/gpu lj/cut/coul/dsf/kk
lj/cut/coul/dsf/omp lj/cut/coul/long
lj/cut/coul/long/cs lj/cut/coul/long/dielectric
lj/cut/coul/long/dielectric/omp lj/cut/coul/long/gpu
lj/cut/coul/long/kk lj/cut/coul/long/omp
lj/cut/coul/long/opt lj/cut/coul/long/soft
lj/cut/coul/long/soft/gpu lj/cut/coul/long/soft/omp lj/cut/coul/msm
lj/cut/coul/msm/dielectric lj/cut/coul/msm/gpu
lj/cut/coul/msm/omp lj/cut/coul/wolf
lj/cut/coul/wolf/omp lj/cut/dipole/cut
lj/cut/dipole/cut/gpu lj/cut/dipole/cut/kk
lj/cut/dipole/cut/omp lj/cut/dipole/long
lj/cut/dipole/long/gpu lj/cut/gpu lj/cut/kk lj/cut/omp
lj/cut/opt lj/cut/soft lj/cut/soft/omp lj/cut/sphere
lj/cut/sphere/omp lj/cut/thole/long
lj/cut/thole/long/omp lj/cut/tip4p/cut
lj/cut/tip4p/cut/omp lj/cut/tip4p/long
lj/cut/tip4p/long/gpu lj/cut/tip4p/long/omp
lj/cut/tip4p/long/opt lj/cut/tip4p/long/soft
lj/cut/tip4p/long/soft/omp lj/expand lj/expand/coul/long
lj/expand/coul/long/gpu lj/expand/coul/long/kk lj/expand/gpu
lj/expand/kk lj/expand/omp lj/expand/sphere
lj/expand/sphere/omp lj/gromacs lj/gromacs/coul/gromacs
lj/gromacs/coul/gromacs/kk lj/gromacs/coul/gromacs/omp lj/gromacs/gpu
lj/gromacs/kk lj/gromacs/omp lj/long/coul/long
lj/long/coul/long/dielectric lj/long/coul/long/omp
lj/long/coul/long/opt lj/long/dipole/long
lj/long/tip4p/long lj/long/tip4p/long/omp lj/mdf
lj/pirani lj/pirani/omp lj/relres lj/relres/omp lj/sf/dipole/sf
lj/sf/dipole/sf/gpu lj/sf/dipole/sf/omp lj/smooth
lj/smooth/gpu lj/smooth/linear lj/sf
lj/smooth/linear/omp lj/sf/omp lj/smooth/omp lj/spica
lj/sdk lj/spica/coul/long lj/sdk/coul/long
lj/spica/coul/long/gpu lj/sdk/coul/long/gpu
lj/spica/coul/long/kk lj/sdk/coul/long/kk
lj/spica/coul/long/omp lj/sdk/coul/long/omp
lj/spica/coul/msm lj/sdk/coul/msm lj/spica/coul/msm/omp
lj/sdk/coul/msm/omp lj/spica/gpu lj/sdk/gpu lj/spica/kk
lj/sdk/kk lj/spica/omp lj/sdk/omp lj/switch3/coulgauss/long
local/density lubricate lubricateU lubricateU/poly lubricate/omp
lubricate/poly lubricate/poly/omp mdpd mdpd/gpu
mdpd/rhosum meam meam/kk meam/ms meam/ms/kk
meam/spline meam/spline/omp meam/sw/spline mesocnt mesocnt/viscous
mgpt mie/cut mie/cut/gpu mliap mliap/kk
mm3/switch3/coulgauss/long momb morse morse/gpu
morse/kk morse/omp morse/opt morse/smooth/linear
morse/smooth/linear/omp morse/soft multi/lucy multi/lucy/rx
multi/lucy/rx/kk nb3b/harmonic nb3b/screened nm/cut
nm/cut/coul/cut nm/cut/coul/cut/omp nm/cut/coul/long
nm/cut/coul/long/omp nm/cut/omp nm/cut/split oxdna2/coaxstk
oxdna2/dh oxdna2/excv oxdna/coaxstk oxrna2/coaxstk oxdna/excv
oxdna/hbond oxdna2/hbond oxdna/stk oxdna2/stk oxdna/xstk
oxdna2/xstk oxrna2/dh oxrna2/excv oxrna2/hbond oxrna2/stk
oxrna2/xstk pace pace/extrapolation
pace/extrapolation/kk pace/kk pedone pedone/omp
peri/eps peri/lps peri/lps/omp peri/pmb peri/pmb/omp
peri/ves pod pod/kk polymorphic python
quip rann reaxff reaxff/kk reaxff/omp
rebo rebo/omp rebomos rebomos/omp resquared
resquared/gpu resquared/omp rheo rheo/solid saip/metal
saip/metal/opt sdpd/taitwater/isothermal smatb smatb/single
smd/hertz smd/tlsph smd/tri_surface smd/ulsph smtbq
snap snap/kk soft soft/gpu soft/kk
soft/omp sph/heatconduction sph/heatconduction/gpu
sph/idealgas sph/lj sph/lj/gpu sph/rhosum sph/taitwater
sph/taitwater/gpu sph/taitwater/morris spin/dipole/cut
spin/dipole/long spin/dmi spin/exchange
spin/exchange/biquadratic spin/magelec spin/neel srp
srp/react sw sw/angle/table sw/gpu sw/kk
sw/mod sw/mod/omp sw/omp table table/gpu
table/kk table/omp table/rx table/rx/kk tdpd
tersoff tersoff/gpu tersoff/kk tersoff/mod tersoff/mod/c
tersoff/mod/c/omp tersoff/mod/gpu tersoff/mod/kk tersoff/mod/omp
tersoff/omp tersoff/table tersoff/table/omp tersoff/zbl
tersoff/zbl/gpu tersoff/zbl/kk tersoff/zbl/omp thole threebody/table
tip4p/cut tip4p/cut/omp tip4p/long tip4p/long/omp tip4p/long/soft
tip4p/long/soft/omp tracker tri/lj uf3
uf3/kk ufm ufm/gpu ufm/omp ufm/opt
vashishta vashishta/gpu vashishta/kk vashishta/omp vashishta/table
vashishta/table/omp wf/cut ylz yukawa
yukawa/colloid yukawa/colloid/gpu yukawa/colloid/kk
yukawa/colloid/omp yukawa/gpu yukawa/kk yukawa/omp
zbl zbl/gpu zbl/kk zbl/omp zero
* Bond styles:
bpm/rotational bpm/spring bpm/spring/plastic class2
class2/kk class2/omp fene fene/expand fene/expand/omp
fene/kk fene/nm fene/omp gaussian gromos
gromos/omp harmonic harmonic/kk harmonic/omp
harmonic/restrain harmonic/shift harmonic/shift/cut
harmonic/shift/cut/omp harmonic/shift/omp hybrid
hybrid/kk lepton lepton/omp mesocnt mm3
morse morse/omp nonlinear nonlinear/omp oxdna2/fene
oxdna/fene oxrna2/fene quartic quartic/omp rheo/shell
special table table/omp zero
* Angle styles:
amoeba charmm charmm/kk charmm/omp class2
class2/kk class2/omp class2/p6 cosine cosine/buck6d
cosine/delta cosine/delta/omp cosine/kk cosine/omp
cosine/periodic cosine/periodic/omp cosine/shift cosine/shift/exp
cosine/shift/exp/omp cosine/shift/omp cosine/squared
cosine/squared/omp cosine/squared/restricted
cosine/squared/restricted/omp cross dipole dipole/omp
fourier fourier/omp fourier/simple fourier/simple/omp
gaussian harmonic harmonic/kk harmonic/omp hybrid
hybrid/kk lepton lepton/omp mesocnt mm3
mwlc quartic quartic/omp spica sdk
spica/kk sdk/kk spica/omp sdk/omp table
table/omp zero
charmm charmm/kk charmm/omp charmmfsw charmmfsw/kk
class2 class2/kk class2/omp cosine/shift/exp
cosine/shift/exp/omp cosine/squared/restricted fourier
fourier/omp harmonic harmonic/kk harmonic/omp helix
helix/omp hybrid hybrid/kk lepton lepton/omp
multi/harmonic multi/harmonic/kk multi/harmonic/omp
nharmonic nharmonic/omp opls opls/kk opls/omp
quadratic quadratic/omp spherical table table/cut
table/omp zero
* Improper styles:
amoeba class2 class2/kk class2/omp cossq
cossq/omp cvff cvff/omp distance distharm
fourier fourier/omp harmonic harmonic/kk harmonic/omp
hybrid hybrid/kk inversion/harmonic ring
ring/omp sqdistharm umbrella umbrella/omp zero
* KSpace styles:
ewald ewald/dipole ewald/dipole/spin ewald/disp
ewald/disp/dipole ewald/electrode ewald/omp msm
msm/cg msm/cg/omp msm/dielectric msm/omp pppm
pppm/cg pppm/cg/omp pppm/dielectric pppm/dipole pppm/dipole/spin
pppm/disp pppm/disp/dielectric pppm/disp/omp pppm/disp/tip4p
pppm/disp/tip4p/omp pppm/electrode pppm/gpu pppm/kk
pppm/omp pppm/stagger pppm/tip4p pppm/tip4p/omp
* Fix styles
accelerate/cos acks2/reax acks2/reaxff acks2/reaxff/kk acks2/reax/kk
adapt adapt/fep add/heat addforce addtorque
alchemy amoeba/bitorsion amoeba/pitorsion
append/atoms atom/swap ave/atom ave/chunk ave/correlate
ave/correlate/long ave/grid ave/histo ave/histo/weight
ave/moments ave/time aveforce balance bocs
bond/break bond/create bond/create/angle bond/react
bond/swap box/relax brownian brownian/asphere
brownian/sphere charge/regulation cmap cmap/kk
colvars colvars/kk controller damping/cundall deform
deform/kk deform/pressure deposit ave/spatial
ave/spatial/sphere lb/pc lb/rigid/pc/sphere
reax/c/bonds reax/c/species dpd/energy dpd/energy/kk drag
drude drude/transform/direct drude/transform/inverse
dt/reset dt/reset/kk edpd/source efield efield/kk
efield/lepton efield/tip4p ehex electrode/conp electrode/conq
electrode/thermo electron/stopping
electron/stopping/fit enforce2d enforce2d/kk eos/cv
eos/table eos/table/rx eos/table/rx/kk evaporate external
ffl filter/corotate flow/gauss freeze freeze/kk
gcmc gjf gld gle gravity
gravity/kk gravity/omp grem halt heat
heat/flow hyper/global hyper/local imd indent
ipi langevin langevin/drude langevin/eff langevin/kk
langevin/spin lb/fluid lb/momentum lb/viscous lineforce
manifoldforce mdi/qm mdi/qmmm meso/move mol/swap
momentum momentum/chunk momentum/kk move msst
mvv/dpd mvv/edpd mvv/tdpd neb neb/spin
neighbor/swap nonaffine/displacement nph nph/asphere
nph/asphere/omp nph/body nph/eff nph/kk nph/omp
nph/sphere nph/sphere/omp nphug npt npt/asphere
npt/asphere/omp npt/body npt/cauchy npt/eff npt/gpu
npt/kk npt/omp npt/sphere npt/sphere/omp npt/uef
numdiff numdiff/virial nve nve/asphere nve/asphere/gpu
nve/asphere/noforce nve/awpmd nve/body nve/bpm/sphere
nve/dot nve/dotc/langevin nve/eff nve/gpu
nve/kk nve/limit nve/limit/kk nve/line
nve/manifold/rattle nve/noforce nve/omp nve/sphere
nve/sphere/kk nve/sphere/omp nve/spin nve/tri nvk
nvt nvt/asphere nvt/asphere/omp nvt/body nvt/eff
nvt/gpu nvt/kk nvt/manifold/rattle nvt/omp
nvt/sllod nvt/sllod/eff nvt/sllod/kk nvt/sllod/omp nvt/sphere
nvt/sphere/omp nvt/uef oneway orient/bcc orient/eco
orient/fcc pafi pair phonon pimd/langevin
pimd/langevin/bosonic pimd pimd/nvt pimd/nvt/bosonic
planeforce plumed poems polarize/bem/gmres
polarize/bem/icc polarize/functional pour
precession/spin press/berendsen press/langevin print propel/self
property/atom property/atom/kk python/invoke python
python/move qbmsst qeq/comb qeq/comb/omp qeq/ctip
qeq/dynamic qeq/fire qeq/point qeq/reaxff qeq/reax
qeq/reaxff/kk qeq/reax/kk qeq/reaxff/omp qeq/reax/omp qeq/rel/reaxff
qeq/shielded qeq/slater qtb qtpie/reaxff rattle
reaxff/bonds reaxff/bonds/kk reaxff/species reaxff/species/kk
recenter recenter/kk restrain rheo rheo/oxidation
rheo/pressure rheo/thermal rheo/viscosity rhok rigid
rigid/meso rigid/nph rigid/nph/omp rigid/nph/small rigid/npt
rigid/npt/omp rigid/npt/small rigid/nve rigid/nve/omp rigid/nve/small
rigid/nvt rigid/nvt/omp rigid/nvt/small rigid/omp rigid/small
rigid/small/omp rx rx/kk saed/vtk setforce
setforce/kk setforce/spin sgcmc shake shake/kk
shardlow shardlow/kk smd smd/adjust_dt
smd/integrate_tlsph smd/integrate_ulsph
smd/move_tri_surf smd/setvel smd/wall_surface
sph sph/stationary spring spring/chunk spring/rg
spring/self spring/self/kk srd store/force store/state
tdpd/source temp/berendsen temp/berendsen/kk temp/csld
temp/csvr temp/rescale temp/rescale/eff temp/rescale/kk
tfmc tgnpt/drude tgnvt/drude thermal/conductivity
ti/spring tmd ttm ttm/grid ttm/mod
tune/kspace vector viscosity viscous viscous/kk
viscous/sphere wall/body/polygon wall/body/polyhedron
wall/colloid wall/ees wall/flow wall/flow/kk wall/gran
wall/gran/kk wall/gran/region wall/harmonic wall/lepton
wall/lj1043 wall/lj126 wall/lj93 wall/lj93/kk wall/morse
wall/piston wall/reflect wall/reflect/kk wall/reflect/stochastic
wall/region wall/region/ees wall/region/kk wall/srd wall/table
widom
* Compute styles:
ackland/atom adf aggregate/atom angle angle/local
angmom/chunk ave/sphere/atom ave/sphere/atom/kk basal/atom
body/local bond bond/local born/matrix centro/atom
centroid/stress/atom chunk/atom chunk/spread/atom
cluster/atom cna/atom cnp/atom com com/chunk
composition/atom composition/atom/kk contact/atom
coord/atom coord/atom/kk count/type damage/atom mesont
dihedral dihedral/local dilatation/atom dipole dipole/chunk
dipole/tip4p dipole/tip4p/chunk displace/atom dpd
dpd/atom edpd/temp/atom efield/atom efield/wolf/atom
entropy/atom erotate/asphere erotate/rigid erotate/sphere
erotate/sphere/atom erotate/sphere/kk event/displace
fabric fep fep/ta force/tally fragment/atom
gaussian/grid/local gaussian/grid/local/kk global/atom
group/group gyration gyration/chunk gyration/shape
gyration/shape/chunk heat/flux heat/flux/tally
heat/flux/virial/tally hexorder/atom hma improper
improper/local inertia/chunk ke ke/atom ke/atom/eff
ke/eff ke/rigid mliap momentum msd
msd/chunk msd/nongauss nbond/atom omega/chunk orientorder/atom
orientorder/atom/kk pace pair pair/local
pe pe/atom pe/mol/tally pe/tally plasticity/atom
pod/atom pod/global pod/local podd/atom pressure
pressure/alchemy pressure/uef property/atom property/chunk
property/grid property/local ptm/atom rattlers/atom rdf
rheo/property/atom rigid/local saed slcsa/atom
slice smd/contact/radius smd/damage
smd/hourglass/error smd/internal/energy
smd/plastic/strain smd/plastic/strain/rate smd/rho
smd/tlsph/defgrad smd/tlsph/dt smd/tlsph/num/neighs
smd/tlsph/shape smd/tlsph/strain smd/tlsph/strain/rate
smd/tlsph/stress smd/triangle/vertices smd/ulsph/effm
smd/ulsph/num/neighs smd/ulsph/strain
smd/ulsph/strain/rate smd/ulsph/stress smd/vol
sna/atom sna/grid sna/grid/kk sna/grid/local
sna/grid/local/kk snad/atom snap snav/atom
sph/e/atom sph/rho/atom sph/t/atom spin stress/atom
stress/cartesian stress/cylinder pressure/cylinder
stress/mop stress/mop/profile stress/spherical
stress/tally tdpd/cc/atom temp temp/asphere temp/body
temp/chunk temp/com temp/cs temp/deform temp/deform/eff
temp/deform/kk temp/drude temp/eff temp/kk temp/partial
temp/profile temp/ramp temp/region temp/region/eff temp/rotate
temp/sphere temp/uef ti torque/chunk vacf
vacf/chunk vcm/chunk viscosity/cos voronoi/atom xrd
* Region styles:
block block/kk cone cylinder ellipsoid
intersect plane prism sphere sphere/kk
union
* Dump styles:
atom atom/gz atom/zstd cfg cfg/gz
cfg/uef cfg/zstd custom custom/gz custom/zstd
dcd atom/mpiio cfg/mpiio custom/mpiio xyz/mpiio
extxyz grid grid/vtk h5md image
local local/gz local/zstd molfile movie
netcdf netcdf/mpiio xtc xyz xyz/gz
xyz/zstd yaml
* Command styles
angle_write balance change_box create_atoms create_bonds
create_box delete_atoms delete_bonds box kim_init
kim_interactions kim_param kim_property kim_query
reset_ids reset_atom_ids reset_mol_ids message server
dihedral_write displace_atoms dynamical_matrix
dynamical_matrix/kk fitpod geturl group2ndx
hyper info kim mdi minimize
ndx2group neb neb/spin plugin prd
read_data read_dump read_restart region2vmd replicate
rerun run set tad temper
temper/grem temper/npt third_order third_order/kk velocity
write_coeff write_data write_dump write_restart
When you use -sf kk then you should remove all /kk suffixes in the input.
Correct, I need to update the documentation to say that -sf kk is preferred and to discourage adding /kk suffixes directly in the input, in general.
1 Like
Thanks for your answers. Now the calculation works for me, but I still see a couple of warnings:
Setting up cg/kk style minimization ...
Unit style : metal
Current step : 0
WARNING: Fix MINIMIZE/kk not compatible with sending data in Kokkos communication (src/KOKKOS/comm_kokkos.cpp:766)
WARNING: Fix with atom-based arrays not compatible with sending data in Kokkos communication, switching to classic exchange/border communication (src/KOKKOS/comm_kokkos.cpp:779)
WARNING: Fix MINIMIZE/kk not compatible with Kokkos sorting on device (src/KOKKOS/atom_kokkos.cpp:212)
WARNING: Fix with atom-based arrays not compatible with Kokkos sorting on device, switching to classic host sorting (src/KOKKOS/atom_kokkos.cpp:218)
part of input file:
min_style cg
minimize 1.0e-4 1.0e-6 1000 10000
run 0
delete_atoms group removed_atoms
Run parameters:
./lmp -k on g 1 -sf kk -pk kokkos neigh half -in input_file.lmp
Can I do anything about these warnings?
Sergii_Mamedov:
part of input file:
That part is not relevant. Why not quote the whole input?
These warnings happens when you use features in a Kokkos enabled run that have not been ported to the KOKKOS package. In KOKKOS styles, the data is kept on the GPU as much as possible and transferred to host only when needed (e.g. for output). But if you use functionality, that is not in KOKKOS, LAMMPS has to transfer all data from the GPU to the host and then back.This can cause significant slowdown depending on the specific details.
The minimize part of scripts is often just a smaller part of the total calculation, so you can probably live with it.
Yes the warnings are related to performance, not correctness, so they can safely be ignored.