Hello everyone,
I’ve been struggling with this error for the past week, and I can’t seem to find my way around the issue.
I am trying to adapt my input to run on GPU through the Kokkos package, but whenever I change the kspace_style to pppm instead of ewald, I instantly get a memory allocation error. I am using Dreiding parameters and currently running the stable version of LAMMPS.
My input script is as simple as it gets, straight from the LAMMPS-Interface:
log log.COF-42 append
units real
atom_style full
boundary p p p
pair_style lj/cut/coul/long 12.500
bond_style harmonic
angle_style cosine/squared
dihedral_style charmm
improper_style umbrella
kspace_style pppm 1.0e-6
special_bonds dreiding
dielectric 1.0
pair_modify tail yes mix arithmetic
box tilt large
read_data data.COF-42
#### Atom Groupings ####
group fram id 1:924
#### END Atom Groupings ####
minimize 1.0e-4 1.0e-6 1000 10000
And get the following error all the time:
LAMMPS (23 Jun 2022 - Update 1)
KOKKOS mode is enabled (src/KOKKOS/kokkos.cpp:105)
will use up to 2 GPU(s) per node
WARNING: Turning off GPU-aware MPI since it is not detected, use '-pk kokkos gpu/aware on' to override (src/KOKKOS/kokkos.cpp:293)
using 16 OpenMP thread(s) per MPI task
Reading data file ...
triclinic box = (0 0 0) to (29.9768 25.96067 28.35) with tilt (-14.9884 0 0)
1 by 1 by 2 MPI processor grid
reading atoms ...
924 atoms
scanning bonds ...
3 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
scanning impropers ...
3 = max impropers/atom
reading bonds ...
966 bonds
reading angles ...
1596 angles
reading dihedrals ...
2100 dihedrals
reading impropers ...
1008 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 1
special bond factors coul: 0 0 1
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
9 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.043 seconds
924 atoms in group fram
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
PPPM initialization ...
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
G vector (1/distance) = 0.25582581
grid = 24 32 24
stencil order = 5
estimated absolute RMS force accuracy = 0.00020091006
estimated relative force accuracy = 6.0503468e-07
using double precision FFTW3
3d grid and FFT values/proc = 343 9216
terminate called after throwing an instance of 'std::runtime_error'
terminate called after throwing an instance of 'std::runtime_error'
what(): Kokkos failed to allocate memory for label "GridComm:swap_packlist". Allocation using MemorySpace named "Cuda" failed with the following error: Allocation of size 1.718e+10 G failed, likely due to insufficient memory. (The allocation mechanism was cudaMalloc(). The Cuda allocation returned the error code ""cudaErrorMemoryAllocation".)
what(): Kokkos failed to allocate memory for label "GridComm:swap_packlist". Allocation using MemorySpace named "Cuda" failed with the following error: Allocation of size 1.718e+10 G failed, likely due to insufficient memory. (The allocation mechanism was cudaMalloc(). The Cuda allocation returned the error code ""cudaErrorMemoryAllocation".)
[vision1:3276138] *** Process received signal ***
[vision1:3276139] *** Process received signal ***
[vision1:3276138] Signal: Aborted (6)
[vision1:3276138] Signal code: (-6)
[vision1:3276139] Signal: Aborted (6)
[vision1:3276139] Signal code: (-6)
[vision1:3276138] [ 0] [vision1:3276139] [ 0] /lib/x86_64-linux-gnu/libpthread.so.0(+0x143c0)[0x7f6c1b4463c0]
[vision1:3276139] [ 1] /lib/x86_64-linux-gnu/libpthread.so.0(+0x143c0)[0x7f821e1f43c0]
[vision1:3276138] [ 1] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcb)[0x7f821db7503b]
[vision1:3276138] [ 2] /lib/x86_64-linux-gnu/libc.so.6(gsignal+0xcb)[0x7f6c1adc703b]
[vision1:3276139] [ 2] /lib/x86_64-linux-gnu/libc.so.6(abort+0x12b)[0x7f6c1ada6859]
[vision1:3276139] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0x12b)[0x7f821db54859]
[vision1:3276138] [ 3] /opt/software/software/GCCcore/10.3.0/lib64/libstdc++.so.6(+0xaddcc)[0x7f6c1b1cddcc]
[vision1:3276139] [ 4] /opt/software/software/GCCcore/10.3.0/lib64/libstdc++.so.6(+0xaddcc)[0x7f821df7bdcc]
[vision1:3276138] [ 4] /opt/software/software/GCCcore/10.3.0/lib64/libstdc++.so.6(+0xb8e36)[0x7f6c1b1d8e36]
[vision1:3276139] [ 5] /opt/software/software/GCCcore/10.3.0/lib64/libstdc++.so.6(+0xb8e36)[0x7f821df86e36]
[vision1:3276138] [ 5] /opt/software/software/GCCcore/10.3.0/lib64/libstdc++.so.6(+0xb8ea1)[0x7f821df86ea1]
[vision1:3276138] [ 6] /opt/software/software/GCCcore/10.3.0/lib64/libstdc++.so.6(+0xb8ea1)[0x7f6c1b1d8ea1]
[vision1:3276139] [ 6] /opt/software/software/GCCcore/10.3.0/lib64/libstdc++.so.6(+0xb9134)[0x7f821df87134]
[vision1:3276138] [ 7] /opt/software/software/GCCcore/10.3.0/lib64/libstdc++.so.6(+0xb9134)[0x7f6c1b1d9134]
[vision1:3276139] [ 7] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos4Impl23throw_runtime_exceptionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x35)[0x7f6c1c5d3ef7]
[vision1:3276139] [ 8] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos4Impl23throw_runtime_exceptionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x35)[0x7f821f381ef7]
[vision1:3276138] [ 8] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos4Impl41safe_throw_allocation_with_header_failureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_RKNS_12Experimental26RawMemoryAllocationFailureE+0x241)[0x7f8223378cf1]
[vision1:3276138] [ 9] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos4Impl41safe_throw_allocation_with_header_failureERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_RKNS_12Experimental26RawMemoryAllocationFailureE+0x241)[0x7f6c205cacf1]
[vision1:3276139] [ 9] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos4Impl30checked_allocation_with_headerINS_9CudaSpaceEEEPNS0_22SharedAllocationHeaderERKT_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm+0x5e)[0x7f8223384d4e]
[vision1:3276138] [10] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos4Impl30checked_allocation_with_headerINS_9CudaSpaceEEEPNS0_22SharedAllocationHeaderERKT_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm+0x5e)[0x7f6c205d6d4e]
[vision1:3276139] [10] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos4Impl22SharedAllocationRecordINS_9CudaSpaceEvEC1ERKS2_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmPFvPNS1_IvvEEE+0x2c)[0x7f8223381f4c]
[vision1:3276138] [11] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos4Impl22SharedAllocationRecordINS_9CudaSpaceEvEC1ERKS2_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEmPFvPNS1_IvvEEE+0x2c)[0x7f6c205d3f4c]
[vision1:3276139] [11] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos4ViewIPPiJNS_11LayoutRightENS_4CudaEvEEC1IJNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEERKNS_4Impl12ViewCtorPropIJDpT_EEERKNSt9enable_ifIXntsrSH_11has_pointerES3_E4typeE+0x1cc)[0x7f821f827f7c]
[vision1:3276138] [12] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos4ViewIPPiJNS_11LayoutRightENS_4CudaEvEEC1IJNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEERKNS_4Impl12ViewCtorPropIJDpT_EEERKNSt9enable_ifIXntsrSH_11has_pointerES3_E4typeE+0x1cc)[0x7f6c1ca79f7c]
[vision1:3276139] [12] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos11impl_resizeIJEPPiJNS_11LayoutRightENS_4CudaEvEEENSt9enable_ifIXoosrSt7is_sameINS_4ViewIT0_JDpT1_EE12array_layoutENS_10LayoutLeftEE5valuesrS6_ISC_S3_E5valueEvE4typeERSB_mmmmmmmmDpRKT_+0x161)[0x7f6c1ca7dd21]
[vision1:3276139] [13] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos11impl_resizeIJEPPiJNS_11LayoutRightENS_4CudaEvEEENSt9enable_ifIXoosrSt7is_sameINS_4ViewIT0_JDpT1_EE12array_layoutENS_10LayoutLeftEE5valuesrS6_ISC_S3_E5valueEvE4typeERSB_mmmmmmmmDpRKT_+0x161)[0x7f821f82bd21]
[vision1:3276138] [13] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos8DualViewIPPiNS_11LayoutRightENS_4CudaEvE11impl_resizeIJEEEvmmmmmmmmDpRKT_+0x5d9)[0x7f6c1ca81929]
[vision1:3276139] [14] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN6Kokkos8DualViewIPPiNS_11LayoutRightENS_4CudaEvE11impl_resizeIJEEEvmmmmmmmmDpRKT_+0x5d9)[0x7f821f82f929]
[vision1:3276138] [14] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS14GridCommKokkosIN6Kokkos4CudaEE7indicesERNS1_8DualViewIPPiNS1_11LayoutRightES2_vEEiiiiiii+0x472)[0x7f6c1d9b1f12]
[vision1:3276139] [15] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS14GridCommKokkosIN6Kokkos4CudaEE7indicesERNS1_8DualViewIPPiNS1_11LayoutRightES2_vEEiiiiiii+0x472)[0x7f822075ff12]
[vision1:3276138] [15] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS14GridCommKokkosIN6Kokkos4CudaEE13setup_regularERiS4_+0x306)[0x7f6c1d9b2326]
[vision1:3276139] [16] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS14GridCommKokkosIN6Kokkos4CudaEE13setup_regularERiS4_+0x306)[0x7f8220760326]
[vision1:3276138] [16] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS10PPPMKokkosIN6Kokkos4CudaEE8allocateEv+0x15a1)[0x7f6c1e191641]
[vision1:3276139] [17] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS10PPPMKokkosIN6Kokkos4CudaEE8allocateEv+0x15a1)[0x7f8220f3f641]
[vision1:3276138] [17] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS10PPPMKokkosIN6Kokkos4CudaEE4initEv+0x5f8)[0x7f6c1e188358]
[vision1:3276139] [18] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS10PPPMKokkosIN6Kokkos4CudaEE4initEv+0x5f8)[0x7f8220f36358]
[vision1:3276138] [18] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS5Force4initEv+0x66)[0x7f821f6332d6]
[vision1:3276138] [19] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS5Force4initEv+0x66)[0x7f6c1c8852d6]
[vision1:3276139] [19] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS6LAMMPS4initEv+0x16)[0x7f6c1c8e8096]
[vision1:3276139] [20] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS6LAMMPS4initEv+0x16)[0x7f821f696096]
[vision1:3276138] [20] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS8Minimize7commandEiPPc+0x1a6)[0x7f6c1c952026]
[vision1:3276139] [21] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS8Minimize7commandEiPPc+0x1a6)[0x7f821f700026]
[vision1:3276138] [21] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xb42)[0x7f6c1c8dddd2]
[vision1:3276139] [22] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input15execute_commandEv+0xb42)[0x7f821f68bdd2]
[vision1:3276138] [22] /opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input4fileEv+0x166)[0x7f6c1c8de2d6]
[vision1:3276139] [23] lmp[0x4013fa]
[vision1:3276139] [24] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f6c1ada80b3]
[vision1:3276139] [25] lmp[0x40160e]
[vision1:3276139] *** End of error message ***
/opt/software/software/LAMMPS/23Jun2022-foss-2021a-kokkos-CUDA-11.3.1/lib/liblammps.so.0(_ZN9LAMMPS_NS5Input4fileEv+0x166)[0x7f821f68c2d6]
[vision1:3276138] [23] lmp[0x4013fa]
[vision1:3276138] [24] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x7f821db560b3]
[vision1:3276138] [25] lmp[0x40160e]
[vision1:3276138] *** End of error message ***
Thanks in advance for the help