GIZMO crash in 2D square test
I am trying to run GIZMO on the 2D square test but the code (master branch) crashes after a few steps. Not sure what is going on. The set-up should not have changed but there have been some minute changes to the gizmo code in the last few weeks.
Here is the output I get (added -v 1 to the run.sh):
Welcome to the cosmological hydrodynamical code
______ _________________
/ ___/ | / / _/ ___/_ __/
\__ \| | /| / // // /_ / /
___/ /| |/ |/ // // __/ / /
/____/ |__/|__/___/_/ /_/
SPH With Inter-dependent Fine-grained Tasking
Version : 0.4.0
Revision: v0.4.0-145-gf4cd515f-dirty, Branch: master
Webpage : www.swiftsim.com
Compiler: GCC, Version: 5.4.1
HDF5 library version: 1.8.16
FFTW library version: 3.x (details not available)
[00000.0] main: CPU frequency used for tick conversion: 2693725741 Hz
[00000.0] main: sizeof(struct part) is 384 bytes.
[00000.0] main: sizeof(struct xpart) is 32 bytes.
[00000.0] main: sizeof(struct gpart) is 96 bytes.
[00000.0] main: sizeof(struct task) is 64 bytes.
[00000.0] main: sizeof(struct cell) is 576 bytes.
[00000.0] main: Reading runtime parameters from file 'square.yml'
[00000.0] main: Internal unit system: U_M = 1.000000e+00 g.
[00000.0] main: Internal unit system: U_L = 1.000000e+00 cm.
[00000.0] main: Internal unit system: U_t = 1.000000e+00 s.
[00000.0] main: Internal unit system: U_I = 1.000000e+00 A.
[00000.0] main: Internal unit system: U_T = 1.000000e+00 K.
[00000.0] phys_const_print: Gravitational constant = 6.674080e-08
[00000.0] phys_const_print: Speed of light = 2.997925e+10
[00000.0] phys_const_print: Planck constant = 6.626070e-27
[00000.0] phys_const_print: Boltzmann constant = 1.380649e-16
[00000.0] phys_const_print: Thomson cross-section = 6.652459e-25
[00000.0] phys_const_print: Electron-Volt = 1.602177e-12
[00000.0] phys_const_print: Year = 3.155693e+07
[00000.0] phys_const_print: Astronomical Unit = 1.495979e+13
[00000.0] phys_const_print: Parsec = 3.085678e+18
[00000.0] phys_const_print: Solar mass = 1.988500e+33
[00000.0] main: Reading ICs from file './square.hdf5'
[00000.0] read_ic_single: IC and internal units match. No conversion needed.
[00000.0] main: Reading initial conditions took 2.919 ms.
[00000.0] main: Read 7168 gas particles and 0 gparts from the ICs.
[00000.0] space_init: max_size set to 8000000, sub_size set to 64000000, split_size set to 400
[00000.0] space_regrid: h_max is 1.929e-02 (cell_max=2.000e-02).
[00000.0] space_regrid: set cell dimensions to [ 26 26 5 ].
[00000.0] space_regrid: took 0.822 ms.
[00000.0] main: space_init took 1.391 ms.
[00000.0] main: space dimensions are [ 1.000 1.000 0.200 ].
[00000.0] main: space is periodic.
[00000.0] main: highest-level cell dimensions are [ 26 26 5 ].
[00000.0] main: 7168 parts in 3380 cells.
[00000.0] main: 0 gparts in 3380 cells.
[00000.0] main: maximum depth is 0.
[00000.0] main: map_cellcheck picked up 0 parts.
[00000.0] main: nr of cells at depth 0 is 3380.
[00000.0] engine_init: no processor affinity used
[00000.0] engine_policy: engine policies are [ steal keep numa_affinity hydro ]
[00000.0] hydro_props_print: Equation of state: Ideal gas.
[00000.0] hydro_props_print: Adiabatic index gamma: 1.666667.
[00000.0] hydro_props_print: Hydrodynamic scheme: GIZMO (Hopkins 2015) in 2D.
[00000.0] hydro_props_print: Hydrodynamic kernel: Cubic spline (M4) with 15.14 +/- 0.10 neighbours (eta=1.234800).
[00000.0] hydro_props_print: Hydrodynamic integration: CFL parameter: 0.1000.
[00000.0] hydro_props_print: Hydrodynamic integration: Max change of volume: 2.00 (max|dlog(h)/dt|=0.346574).
[00000.0] engine_init: Absolute minimal timestep size: 1.490116e-08
[00000.0] engine_init: Minimal timestep size (on time-line): 9.536743e-07
[00000.0] engine_init: Maximal timestep size (on time-line): 7.812500e-03
[00000.0] engine_compute_next_snapshot_time: Next output time set to t=9.999999e-02.
[00000.0] engine_init: runner 0 using qid=0 no cpuid.
[00000.0] main: engine_init took 0.287 ms.
[00000.0] main: Running on 7168 gas particles and 0 DM particles from t=0.000e+00 until t=4.000e+00 with 1 threads and 1 queues (dt_min=1.000e-06, dt_max=1.000e-02)...
[00000.0] engine_init_particles: Running initialisation fake time-step.
[00000.0] space_regrid: h_max is 1.023e-02 (cell_max=0.000e+00).
[00000.0] space_regrid: took 0.224 ms.
[00000.0] space_parts_sort: took 1.944 ms.
[00000.0] space_gparts_sort: took 0.040 ms.
[00000.0] space_split: took 0.348 ms.
[00000.0] space_rebuild: took 3.123 ms.
[00000.0] scheduler_reweight: took 0.640 ms.
[00000.0] engine_maketasks: took 5.484 ms (including reweight).
[00000.0] engine_marktasks: took 0.359 ms.
[00000.0] engine_print_task_counts: task counts are [ none=0 sort=676 self=2028 pair=8112 sub_self=0 sub_pair=0 init=676 ghost=676 extra_ghost=676 kick=676 kick_fixdt=0 send=0 recv=0 grav_gather_m=0 grav_fft=0 grav_mm=0 grav_up=0 grav_external=0 cooling=0 skipped=0 ]
[00000.0] engine_print_task_counts: nr_parts = 7168.
[00000.0] engine_print_task_counts: nr_gparts = 0.
[00000.0] engine_rebuild: took 9.048 ms.
[00000.0] engine_prepare: took 9.050 ms (including marktask, rebuild and reweight).
[00000.0] engine_marktasks: took 0.381 ms.
[00000.2] engine_launch: took 205.332 ms.
[00000.2] engine_init_particles: took 215.251 ms.
[00000.2] engine_dump_snapshot: writing snapshot at t=0.000000e+00.
[00000.2] write_output_single: Snapshot and internal units match. No conversion needed.
[00000.2] engine_dump_snapshot: writing particle properties took 5.852 ms.
# Step Time Time-step Updates g-Updates Wall-clock time [ms]
[00000.2] engine_collect_timestep: took 0.211 ms.
0 0.000000e+00 0.000000e+00 0 0 215.251
[00000.2] engine_print_stats: took 0.170 ms.
[00000.2] engine_drift: took 0.208 ms.
[00000.2] engine_marktasks: took 0.468 ms.
[00000.2] scheduler_reweight: took 0.984 ms.
[00000.2] engine_prepare: took 1.458 ms (including marktask, rebuild and reweight).
[00000.2] engine_print_task_counts: task counts are [ none=0 sort=0 self=2028 pair=8112 sub_self=0 sub_pair=0 init=676 ghost=676 extra_ghost=676 kick=676 kick_fixdt=0 send=0 recv=0 grav_gather_m=0 grav_fft=0 grav_mm=0 grav_up=0 grav_external=0 cooling=0 skipped=676 ]
[00000.2] engine_print_task_counts: nr_parts = 7168.
[00000.2] engine_print_task_counts: nr_gparts = 0.
[00000.5] engine_launch: took 222.157 ms.
[00000.5] engine_collect_timestep: took 0.258 ms.
1 2.441406e-04 2.441406e-04 7168 0 224.780
[00000.5] engine_drift: took 1.571 ms.
[00000.5] engine_marktasks: took 0.363 ms.
[00000.5] engine_drift: took 0.295 ms.
[00000.5] space_regrid: h_max is 1.929e-02 (cell_max=0.000e+00).
[00000.5] space_regrid: took 0.243 ms.
[00000.5] space_parts_sort: took 1.931 ms.
[00000.5] space_gparts_sort: took 0.065 ms.
[00000.5] space_split: took 0.440 ms.
[00000.5] space_rebuild: took 3.472 ms.
[00000.5] scheduler_reweight: took 0.629 ms.
[00000.5] engine_maketasks: took 5.470 ms (including reweight).
[00000.5] engine_marktasks: took 0.878 ms.
[00000.5] engine_print_task_counts: task counts are [ none=0 sort=676 self=2028 pair=8112 sub_self=0 sub_pair=0 init=676 ghost=676 extra_ghost=676 kick=676 kick_fixdt=0 send=0 recv=0 grav_gather_m=0 grav_fft=0 grav_mm=0 grav_up=0 grav_external=0 cooling=0 skipped=0 ]
[00000.5] engine_print_task_counts: nr_parts = 7168.
[00000.5] engine_print_task_counts: nr_gparts = 0.
[00000.5] engine_rebuild: took 9.906 ms.
[00000.5] engine_prepare: took 10.572 ms (including marktask, rebuild and reweight).
[00000.5] engine_print_task_counts: task counts are [ none=0 sort=676 self=2028 pair=8112 sub_self=0 sub_pair=0 init=676 ghost=676 extra_ghost=676 kick=676 kick_fixdt=0 send=0 recv=0 grav_gather_m=0 grav_fft=0 grav_mm=0 grav_up=0 grav_external=0 cooling=0 skipped=0 ]
[00000.5] engine_print_task_counts: nr_parts = 7168.
[00000.5] engine_print_task_counts: nr_gparts = 0.
[00000.6] engine_launch: took 140.996 ms.
[00000.6] engine_collect_timestep: took 0.202 ms.
2 4.882812e-04 2.441406e-04 7168 0 153.523
[00000.6] engine_drift: took 1.089 ms.
[00000.6] engine_marktasks: took 0.326 ms.
[00000.6] scheduler_reweight: took 0.498 ms.
[00000.6] engine_prepare: took 0.829 ms (including marktask, rebuild and reweight).
[00000.6] engine_print_task_counts: task counts are [ none=0 sort=0 self=2028 pair=8112 sub_self=0 sub_pair=0 init=676 ghost=676 extra_ghost=676 kick=676 kick_fixdt=0 send=0 recv=0 grav_gather_m=0 grav_fft=0 grav_mm=0 grav_up=0 grav_external=0 cooling=0 skipped=676 ]
[00000.7] ././hydro/Gizmo/hydro_iact.h:runner_iact_fluxes_common():374: Negative density or pressure!
[00000.6] engine_print_task_counts: nr_parts = 7168.
[00000.6] engine_print_task_counts: nr_gparts = 0.
mindt: 0.000244141
WL: 1.70118 0.00781754 -0.0102955 0 1.37784
gradWL[0]: 0.209093 31.4283 0
gradWL[1]: -2.01066e-09 -4.38257e-07 0
gradWL[2]: 0.00111747 0.243354 0
gradWL[3]: 0 0 0
gradWL[4]: -0.60619 -99.8404 0
WL': 1.91897 -0.00661305 -0.0371737 0 0.685349
WR: 3.22967 -142.281 31.4672 0 -18.0292
gradWR[0]: 0.454376 52.4166 0
gradWR[1]: -0 0 0
gradWR[2]: 9.84828e-06 -0.000108755 0
gradWR[3]: 0 0 0
gradWR[4]: -0.00404965 0.0468906 0
WR': 2.78881 -142.295 31.4315 0 -18.0296This test-case runs perfectly with Gadget-SPH and PressureEntropy-SPH.