can segfault using lammps-update-style: fast

[ExpHP]

lammps-update-style:
  fast:
    sync-positions-every: 1

was observed to segfault on some input where safe does not.

When sync-positions-every: 1, I don't think rsp2 does anything particularly special other than setting pre: no, and rsp2 uses neigh_modify delay 0 with the intent to ensure that pre: no is as safe as pre: yes. So... I'm not sure if this is an rsp2 bug or a lammps bug.

[colin-daniels]

Relevant inputs: test_sigseg.tar.gz
Command: OMP_NUM_THREADS=1 mpirun -np 4 rsp2 -c input.yaml -o test_sigseg gyroid10.vasp

Note: Does not occur when not using mpirun or with -np 1 .

Backtrace:

#0  0x00007fec5c9bed79 in LAMMPS_NS::NPairFullBinGhostOmp::build(LAMMPS_NS::NeighList*) [clone ._omp_fn.0] ()
    at /home/cc/.cargo/git/checkouts/lammps-sys-2addabf2ac48c959/6bba3ad/lammps/src/USER-OMP/npair_full_bin_ghost_omp.cpp:105
#1  0x00007fec5b7b5fa3 in GOMP_parallel (
    fn=0x7fec5c9be990 <LAMMPS_NS::NPairFullBinGhostOmp::_ZN9LAMMPS_NS20NPairFullBinGhostOmp5buildEPNS_9NeighListE._omp_fn.0(void)>, data=0x7ffe8d1234b0, num_threads=1, flags=0) at /build/gcc/src/gcc/libgomp/parallel.c:168
#2  0x00007fec5c9be900 in LAMMPS_NS::NPairFullBinGhostOmp::build (this=0x7fec5af97c00, list=0x7fec5aea8340)
    at /home/cc/.cargo/git/checkouts/lammps-sys-2addabf2ac48c959/6bba3ad/lammps/src/USER-OMP/npair_full_bin_ghost_omp.cpp:47
#3  0x00007fec5c759770 in LAMMPS_NS::Neighbor::build (this=0x7fec5af9e900, topoflag=1)
    at /home/cc/.cargo/git/checkouts/lammps-sys-2addabf2ac48c959/6bba3ad/lammps/src/neighbor.cpp:2077
#4  0x00007fec5c831617 in LAMMPS_NS::Verlet::run (this=0x7fec577f6a00, n=1)
    at /home/cc/.cargo/git/checkouts/lammps-sys-2addabf2ac48c959/6bba3ad/lammps/src/verlet.cpp:287
#5  0x00007fec5c803e46 in LAMMPS_NS::Run::command (this=this@entry=0x7ffe8d123730, narg=narg@entry=5, 
    arg=arg@entry=0x7fec5ae40ca0)
    at /home/cc/.cargo/git/checkouts/lammps-sys-2addabf2ac48c959/6bba3ad/lammps/src/run.cpp:183
#6  0x00007fec5c7120ee in LAMMPS_NS::Input::command_creator<LAMMPS_NS::Run> (lmp=<optimized out>, narg=5, 
    arg=0x7fec5ae40ca0) at /home/cc/.cargo/git/checkouts/lammps-sys-2addabf2ac48c959/6bba3ad/lammps/src/input.cpp:870
#7  0x00007fec5c71b165 in LAMMPS_NS::Input::execute_command (this=0x7fec5af7cec0)
    at /home/cc/.cargo/git/checkouts/lammps-sys-2addabf2ac48c959/6bba3ad/lammps/src/input.cpp:856
#8  0x00007fec5c71bb3c in LAMMPS_NS::Input::one (this=0x7fec5af7cec0, single=0x7fec5af40ef0 "run 1 pre no post no")
    at /home/cc/.cargo/git/checkouts/lammps-sys-2addabf2ac48c959/6bba3ad/lammps/src/input.cpp:311
#9  0x00007fec5c7292a9 in lammps_command (ptr=<optimized out>, str=<optimized out>)
    at /home/cc/.cargo/git/checkouts/lammps-sys-2addabf2ac48c959/6bba3ad/lammps/src/library.cpp:231
#10 0x000055e082926278 in <rsp2_lammps_wrap::low_level::plain::LammpsOwner as rsp2_lammps_wrap::low_level::LowLevelApi>::command::{{closure}} (cmd=0x549 <error: Cannot access memory at address 0x549>) at src/io/lammps/low_level/plain.rs:141
#11 rsp2_lammps_wrap::low_level::plain::with_temporary_c_str (s=..., f=...) at src/io/lammps/low_level/plain.rs:603
#12 <rsp2_lammps_wrap::low_level::plain::LammpsOwner as rsp2_lammps_wrap::low_level::LowLevelApi>::command (
    self=0x7fec5ae40ae0, cmd=...) at src/io/lammps/low_level/plain.rs:140
#13 0x000055e08292f871 in rsp2_lammps_wrap::low_level::mpi::InputCommand::invoke_method (lammps=<optimized out>, self=...)
    at src/io/lammps/low_level/mpi.rs:196
#14 <rsp2_lammps_wrap::low_level::mpi::LammpsDispatch as rsp2_lammps_wrap::low_level::mpi_helper::DispatchMultiProcess>::dispatch (self=<optimized out>, root=<optimized out>, input=...) at src/io/lammps/low_level/mpi.rs:469
#15 0x000055e08293177b in <rsp2_lammps_wrap::low_level::mpi_helper::MpiOnDemandInner<D>>::root_dispatch (
    self=0x7fec5af42e30, arg=..., root=<optimized out>) at src/io/lammps/low_level/mpi_helper.rs:220
#16 <rsp2_lammps_wrap::low_level::mpi_helper::MpiOnDemand<D>>::invoke::{{closure}} (root=...)
    at src/io/lammps/low_level/mpi_helper.rs:157
#17 rsp2_lammps_wrap::low_level::mpi_helper::with_default_root (continuation=...)
    at src/io/lammps/low_level/mpi_helper.rs:211
#18 <rsp2_lammps_wrap::low_level::mpi_helper::MpiOnDemand<D>>::invoke (self=<optimized out>, arg=...)
    at src/io/lammps/low_level/mpi_helper.rs:157
#19 0x000055e082930b57 in <rsp2_lammps_wrap::low_level::mpi::MpiLammpsOwner as rsp2_lammps_wrap::low_level::LowLevelApi>::command (self=0x549, cmd=...) at src/io/lammps/low_level/mpi.rs:207
#20 0x000055e082758874 in <rsp2_lammps_wrap::Lammps<P>>::update_lammps_with_command (self=<optimized out>, 
    iter=<optimized out>, command=...)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/lib.rs:1072
#21 <rsp2_lammps_wrap::Lammps<P>>::update_computation (self=<optimized out>)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/lib.rs:1061
#22 0x000055e082748874 in <rsp2_lammps_wrap::Lammps<P>>::compute_value (self=<optimized out>)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/lib.rs:1258
#23 <<rsp2_tasks::potential::lammps::Builder<P>>::lammps_diff_fn::MyDiffFn<Mm> as rsp2_tasks::potential::DiffFn<Mm>>::compute (self=0x7fec54f45b00, coords=<optimized out>, meta=...) at src/tasks/potential/lammps.rs:155
#24 0x000055e0827476e5 in rsp2_tasks::potential::DiffFn::compute_value (self=0x549, coords=0x7fec5764b800, meta=...)
    at src/tasks/potential/mod.rs:273
#25 0x000055e082743be7 in <alloc::boxed::Box<(dyn rsp2_tasks::potential::DiffFn<Meta> + 'd)> as rsp2_tasks::potential::DiffFn<Meta>>::compute_value (coords=0x7fec5ae40b80, meta=..., self=<optimized out>) at src/tasks/potential/mod.rs:296
#26 rsp2_tasks::cmd::relaxation::warn_on_improvable_lattice_params (pot=..., coords=<optimized out>, meta=...)
    at src/tasks/cmd/relaxation.rs:402
#27 0x000055e08270ab0c in rsp2_tasks::cmd::relaxation::<impl rsp2_tasks::cmd::trial::TrialDir>::do_ev_loop_stuff_after_diagonalization (self=<optimized out>, settings=<optimized out>, pot=..., meta=..., iteration=..., coords=..., 
    evals=<optimized out>, evecs=<optimized out>) at src/tasks/cmd/relaxation.rs:189
#28 0x000055e08270bf5e in rsp2_tasks::cmd::relaxation::<impl rsp2_tasks::cmd::trial::TrialDir>::do_main_ev_loop (
    self=<optimized out>, settings=<optimized out>, pot=..., diagonalizer=..., original_coords=..., 
    stop_after_dynmat=<optimized out>, meta=...) at src/tasks/cmd/relaxation.rs:98
#29 rsp2_tasks::cmd::<impl rsp2_tasks::cmd::trial::TrialDir>::run_relax_with_eigenvectors (self=..., on_demand=..., 
    settings=0x7ffe8d125650, file_format=<optimized out>, input=<optimized out>, stop_after_dynmat=<optimized out>)
    at src/tasks/cmd/mod.rs:192
#30 0x000055e08269c119 in rsp2_tasks::entry_points::_rsp2_acgsd::{{closure}} (mpi_on_demand=..., logfile=...)
    at src/tasks/entry_points.rs:281
#31 rsp2_tasks::entry_points::wrap_main::{{closure}}::{{closure}} () at src/tasks/entry_points.rs:52
#32 rsp2_tasks::entry_points::wrap_main::{{closure}} (on_demand=...) at src/tasks/entry_points.rs:44
#33 rsp2_tasks::entry_points::wrap_main_with_lammps_on_demand::{{closure}}::{{closure}} (on_demand=...)
    at src/tasks/entry_points.rs:81
#34 rsp2_lammps_wrap::LammpsOnDemand::install::{{closure}} (on_demand=...)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/lib.rs:643
#35 <rsp2_lammps_wrap::low_level::mpi_helper::MpiOnDemand<D>>::install::{{closure}} (root=...)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/low_level/mpi_helper.rs:133
#36 rsp2_lammps_wrap::low_level::mpi_helper::with_default_root (continuation=...)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/low_level/mpi_helper.rs:211
#37 <rsp2_lammps_wrap::low_level::mpi_helper::MpiOnDemand<D>>::install (dispatch=..., func=...)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/low_level/mpi_helper.rs:130
#38 0x000055e082783019 in rsp2_lammps_wrap::LammpsOnDemand::install (continuation=...)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/lib.rs:641
#39 rsp2_tasks::entry_points::wrap_main_with_lammps_on_demand::{{closure}} () at src/tasks/entry_points.rs:81
#40 std::panicking::try::do_call (data=<optimized out>) at /checkout/src/libstd/panicking.rs:310
#41 0x000055e082aa5c5a in __rust_maybe_catch_panic () at libpanic_unwind/lib.rs:105
#42 0x000055e082691662 in std::panicking::try (f=...) at /checkout/src/libstd/panicking.rs:289
#43 std::panic::catch_unwind (f=...) at /checkout/src/libstd/panic.rs:392
#44 rsp2_lammps_wrap::low_level::mpi_helper::with_mpi_abort_on_unwind::{{closure}} (root=...)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/low_level/mpi_helper.rs:189
#45 rsp2_lammps_wrap::low_level::mpi_helper::with_default_root (continuation=...)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/low_level/mpi_helper.rs:211
#46 rsp2_lammps_wrap::low_level::mpi_helper::with_mpi_abort_on_unwind (func=...)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/low_level/mpi_helper.rs:188
#47 0x000055e08268d592 in rsp2_lammps_wrap::LammpsOnDemand::with_mpi_abort_on_unwind (func=...)
    at /run/media/cc/31b7ba32-4e18-4c56-bcc5-c904490446b5/build/rsp2-orig/src/io/lammps/lib.rs:652
#48 rsp2_tasks::entry_points::wrap_main_with_lammps_on_demand (continuation=...) at src/tasks/entry_points.rs:80
#49 0x000055e08268d4ea in rsp2_tasks::entry_points::wrap_main (version=..., main=...) at src/tasks/entry_points.rs:42
#50 0x000055e08268eb68 in rsp2_tasks::entry_points::_rsp2_acgsd (stop_after_dynmat=false, bin_name=..., 
    version=<error reading variable: Cannot access memory at address 0x4b>) at src/tasks/entry_points.rs:263
#51 0x000055e08268eb27 in rsp2_tasks::entry_points::rsp2 (bin_name=..., version=...) at src/tasks/entry_points.rs:249
#52 0x000055e082678c85 in rsp2::main () at src/binary-shims/rsp2.rs:7