AddressSanitizer: stack-buffer-overflow in space_init_parts_mapper
When running the latest master, configured with
./configure --with-hydro=gadget2 \
--with-hydro-dimension=3 --with-ext-potential=none \
--with-equation-of-state=ideal-gas \
--with-adiabatic-index=5/3 \
--enable-mpi=no --enable-debug=no --enable-debugging-checks=no \
--enable-optimization=no --enable-sanitizer=yesI get the following error when trying to run ZeldovichPancake_3D (also happened for SedovBlast_3D, haven't tried any other tests):
Welcome to the cosmological hydrodynamical code
______ _________________
/ ___/ | / / _/ ___/_ __/
\__ \| | /| / // // /_ / /
___/ /| |/ |/ // // __/ / /
/____/ |__/|__/___/_/ /_/
SPH With Inter-dependent Fine-grained Tasking
Version : 0.8.1
Revision: v0.8.1-828-ge990caac, Branch: master, Date: 2019-05-14 10:47:51 +0100
Webpage : www.swiftsim.com
Config. options: '--with-hydro=gadget2 --with-riemann-solver=exact --with-hydro-dimension=3 --with-ext-potential=none --with-equation-of-state=ideal-gas --with-adiabatic-index=5/3 --enable-mpi=no --enable-debug=no --enable-debugging-checks=no --enable-optimization=no --enable-sanitizer=yes'
Compiler: GCC, Version: 7.4.0
CFLAGS : '-fsanitize=address -fno-omit-frame-pointer -pthread -Wall -Wextra -Wno-unused-parameter -Wshadow -Werror -Wstrict-prototypes'
HDF5 library version: 1.10.0
FFTW library version: 3.x (details not available)
GSL library version: 2.4
[00000.0] main: CPU frequency used for tick conversion: 2300082494 Hz
[00000.0] main: Running on: apsient
[00000.0] main: sizeof(part) is 128 bytes.
[00000.0] main: sizeof(xpart) is 64 bytes.
[00000.0] main: sizeof(spart) is 128 bytes.
[00000.0] main: sizeof(bpart) is 96 bytes.
[00000.0] main: sizeof(gpart) is 64 bytes.
[00000.0] main: sizeof(multipole) is 176 bytes.
[00000.0] main: sizeof(grav_tensor) is 144 bytes.
[00000.0] main: sizeof(task) is 64 bytes.
[00000.0] main: sizeof(cell) is 1152 bytes.
[00000.0] main: Reading runtime parameters from file 'zeldovichPancake.yml'
[00000.0] main: Internal unit system: U_M = 1.988480e+43 g.
[00000.0] main: Internal unit system: U_L = 3.085678e+24 cm.
[00000.0] main: Internal unit system: U_t = 3.085678e+19 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 = 4.300927e+01
[00000.0] phys_const_print: Speed of light = 2.997925e+05
[00000.0] phys_const_print: Planck constant = 1.079902e-99
[00000.0] phys_const_print: Boltzmann constant = 6.943236e-70
[00000.0] phys_const_print: Thomson cross-section = 6.986845e-74
[00000.0] phys_const_print: Electron-Volt = 8.057293e-66
[00000.0] phys_const_print: Year = 1.022690e-12
[00000.0] phys_const_print: Astronomical Unit = 4.848137e-12
[00000.0] phys_const_print: Parsec = 1.000000e-06
[00000.0] phys_const_print: Solar mass = 1.000000e-10
[00000.0] phys_const_print: km/s/Mpc = 1.000000e+02
[00000.7] cosmology_print: Density parameters: [O_m, O_l, O_b, O_k, O_r] = [1.000000, 0.000000, 1.000000, 0.000000, 0.000000]
[00000.7] cosmology_print: Dark energy equation of state: w_0=-1.000000 w_a=0.000000
[00000.7] cosmology_print: Hubble constant: h = 1.000000, H_0 = 1.000000e+02 U_t^(-1)
[00000.7] cosmology_print: Hubble time: 1/H0 = 1.000000e-02 U_t
[00000.7] cosmology_print: Universe age at present day: 6.666667e-03 U_t
[00000.7] cooling_print_backend: Cooling function is 'No cooling'.
[00000.7] chemistry_print_backend: Chemistry function is 'No chemistry'.
[00000.7] main: Reading ICs from file './zeldovichPancake.hdf5'
[00000.7] io_read_unit_system: Reading IC units from ICs.
[00000.7] read_ic_single: IC and internal units match. No conversion needed.
[00000.7] main: Reading initial conditions took 22.369 ms.
[00000.7] main: Read 32768 gas particles, 0 stars particles, 0 black hole particles and 32768 gparts from the ICs.
[00000.7] main: space_init took 5.991 ms.
[00000.7] potential_print_backend: External potential is 'No external potential'.
[00000.7] main: space dimensions are [ 64.000 64.000 64.000 ].
[00000.7] main: space is periodic.
[00000.7] main: highest-level cell dimensions are [ 8 8 8 ].
[00000.7] main: 32768 parts in 512 cells.
[00000.7] main: 32768 gparts in 512 cells.
[00000.7] main: 0 sparts in 512 cells.
[00000.7] main: 0 bparts in 512 cells.
[00000.7] main: maximum depth is 0.
[00000.7] engine_config: no processor affinity used
[00000.7] engine_policy: engine policies are [ 'steal' 'keep' 'numa affinity' 'hydro' 'self gravity' 'cosmological integration' ]
[00000.7] eos_print: Equation of state: Ideal gas.
[00000.7] eos_print: Adiabatic index gamma: 1.666667.
[00000.7] hydro_props_print: Hydrodynamic scheme: Gadget-2 version of SPH (Springel 2005) in 3D.
[00000.7] hydro_props_print: Hydrodynamic kernel: Cubic spline (M4) with eta=1.234800 (48.00 neighbours).
[00000.7] hydro_props_print: Hydrodynamic relative tolerance in h: 0.00010 (+/- 0.0144 neighbours).
[00000.7] hydro_props_print: Hydrodynamic integration: CFL parameter: 0.1000.
[00000.7] hydro_props_print: Artificial viscosity parameters set to alpha: 0.800, max: 2.000, min: 0.100, length: 0.100.
[00000.7] hydro_props_print: Hydrodynamic integration: Max change of volume: 1.40 (max|dlog(h)/dt|=0.112157).
[00000.7] entropy_floor_print: Entropy floor is 'no entropy floor'.
[00000.7] gravity_props_print: Self-gravity scheme: Default (no potential)
[00000.7] gravity_props_print: Self-gravity scheme: FMM-MM with m-poles of order 4
[00000.7] gravity_props_print: Self-gravity time integration: eta=0.0250
[00000.7] gravity_props_print: Self-gravity opening angle: theta=0.3000
[00000.7] gravity_props_print: Self-gravity softening functional form: Wendland-C2
[00000.7] gravity_props_print: Self-gravity comoving softening: epsilon=0.0030 (Plummer equivalent: 0.0010)
[00000.7] gravity_props_print: Self-gravity maximal physical softening: epsilon=0.0030 (Plummer equivalent: 0.0010)
[00000.7] gravity_props_print: Self-gravity mesh side-length: N=32
[00000.7] gravity_props_print: Self-gravity mesh smoothing-scale: a_smooth=1.250000
[00000.7] gravity_props_print: Self-gravity tree cut-off ratio: r_cut_max=5.000000
[00000.7] gravity_props_print: Self-gravity truncation cut-off ratio: r_cut_min=0.100000
[00000.7] gravity_props_print: Self-gravity mesh truncation function: Gadget-like (using erfc())
[00000.7] gravity_props_print: Self-gravity tree update frequency: f=0.010000
[00000.7] engine_config: Absolute minimal timestep size: 3.202383e-17
[00000.7] engine_config: Minimal timestep size (on time-line): 5.081252e-08
[00000.7] engine_config: Maximal timestep size (on time-line): 3.330049e-03
[00000.7] engine_config: Restarts will be dumped every 6.000000 hours
[00000.7] main: engine_init took 7.758 ms.
[00000.7] main: Running on 32768 gas particles, 0 stars particles 0 black hole particles and 0 DM particles (32768 gravity particles)
[00000.7] main: from t=6.568e-06 until t=6.667e-03 with 1 ranks, 8 threads / rank and 8 task queues / rank (dt_min=1.000e-07, dt_max=4.000e-03)...
=================================================================
==29718==AddressSanitizer: while reporting a bug found another one. Ignoring.
==29718==AddressSanitizer: while reporting a bug found another one. Ignoring.
==29718==AddressSanitizer: while reporting a bug found another one. Ignoring.
==29718==AddressSanitizer: while reporting a bug found another one. Ignoring.
==29718==AddressSanitizer: while reporting a bug found another one. Ignoring.
==29718==AddressSanitizer: while reporting a bug found another one. Ignoring.
==29718==AddressSanitizer: while reporting a bug found another one. Ignoring.
==29718==ERROR: AddressSanitizer: stack-buffer-overflow on address 0x7fffdb03d8f0 at pc 0x55616d2e6ba9 bp 0x7fffdb03c0c0 sp 0x7fffdb03c0b0
READ of size 4 at 0x7fffdb03d8f0 thread T0
#0 0x55616d2e6ba8 in space_init_parts_mapper (/data/bv7/swiftsim/examples/swift+0x74ba8)
#1 0x55616d3b9f38 in threadpool_chomp (/data/bv7/swiftsim/examples/swift+0x147f38)
#2 0x55616d3ba74f in threadpool_map (/data/bv7/swiftsim/examples/swift+0x14874f)
#3 0x55616d2e71b0 in space_init_parts (/data/bv7/swiftsim/examples/swift+0x751b0)
#4 0x55616d33e262 in engine_init_particles (/data/bv7/swiftsim/examples/swift+0xcc262)
#5 0x55616d2afd60 in main (/data/bv7/swiftsim/examples/swift+0x3dd60)
#6 0x7f2f09cd9b96 in __libc_start_main (/lib/x86_64-linux-gnu/libc.so.6+0x21b96)
#7 0x55616d2a5a79 in _start (/data/bv7/swiftsim/examples/swift+0x33a79)
Address 0x7fffdb03d8f0 is located in stack of thread T0 at offset 5184 in frame
#0 0x55616d2a6172 in main (/data/bv7/swiftsim/examples/swift+0x34172)
This frame has 72 object(s):
[32, 33) 'chemistry'
[96, 97) 'cooling_func'
[160, 161) 'potential'
[224, 225) 'starform'
[288, 289) 'feedback_properties'
[352, 353) 'entropy_floor'
[416, 420) 'with_aff'
[480, 484) 'dry_run'
[544, 548) 'dump_tasks'
[608, 612) 'dump_threadpool'
[672, 676) 'nsteps'
[736, 740) 'restart'
[800, 804) 'with_cosmology'
[864, 868) 'with_external_gravity'
[928, 932) 'with_temperature'
[992, 996) 'with_cooling'
[1056, 1060) 'with_self_gravity'
[1120, 1124) 'with_hydro'
[1184, 1188) 'with_stars'
[1248, 1252) 'with_star_formation'
[1312, 1316) 'with_feedback'
[1376, 1380) 'with_black_holes'
[1440, 1444) 'with_limiter'
[1504, 1508) 'with_fp_exceptions'
[1568, 1572) 'with_drift_all'
[1632, 1636) 'with_mpole_reconstruction'
[1696, 1700) 'with_structure_finding'
[1760, 1764) 'verbose'
[1824, 1828) 'nr_threads'
[1888, 1892) 'with_verbose_timers'
[1952, 1956) 'flag_entropy_ICs'
[2016, 2020) 'restart_nfiles'
[2080, 2084) 'icount'
[2144, 2152) 'gparts'
[2208, 2216) 'parts'
[2272, 2280) 'sparts'
[2336, 2344) 'bparts'
[2400, 2408) 'output_parameters_filename'
[2464, 2472) 'cpufreqarg'
[2528, 2536) 'cpufreq'
[2592, 2600) 'buffer'
[2656, 2664) 'Ngas'
[2720, 2728) 'Ngpart'
[2784, 2792) 'Nspart'
[2848, 2856) 'Nbpart'
[2912, 2928) 'tic'
[2976, 2992) 'toc'
[3040, 3064) 'stars_properties'
[3104, 3128) 'black_holes_properties'
[3168, 3208) 'us'
[3264, 3312) 'reparttype'
[3360, 3440) 'gravity_properties'
[3488, 3568) 'argparse'
[3616, 3720) 'hydro_properties'
[3776, 3944) 'prog_const'
[4000, 4384) 'cosmo'
[4416, 4424) 'data'
[4480, 4504) 'dim'
[4544, 4576) 'N_total'
[4608, 4696) 'mesh'
[4736, 5176) 's' <== Memory access at offset 5184 overflows this variable
[5216, 6952) 'options'
[7008, 9304) 'e'
[9344, 13448) 'cmdps'
[13504, 13544) 'dumpfile'
[13600, 13800) 'restart_file'
[13856, 14056) 'ICfileName'
[14112, 14368) '__xpg_basename'
[14400, 14656) 'stfbasename'
[14688, 14944) 'restart_dir'
[14976, 15232) 'restart_name'
[15264, 15520) 'resubmit_command'
HINT: this may be a false positive if your program uses some custom stack unwind mechanism or swapcontext
(longjmp and C++ exceptions *are* supported)
SUMMARY: AddressSanitizer: stack-buffer-overflow (/data/bv7/swiftsim/examples/swift+0x74ba8) in space_init_parts_mapper
Shadow bytes around the buggy address:
0x10007b5ffac0: f2 f2 f2 f2 f2 f2 f8 f8 f8 f2 f2 f2 f2 f2 f8 f8
0x10007b5ffad0: f8 f8 f2 f2 f2 f2 00 00 00 00 00 00 00 00 00 00
0x10007b5ffae0: 00 f2 f2 f2 f2 f2 00 00 00 00 00 00 00 00 00 00
0x10007b5ffaf0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x10007b5ffb00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
=>0x10007b5ffb10: 00 00 00 00 00 00 00 00 00 00 00 00 00 f2[f2]f2
0x10007b5ffb20: f2 f2 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x10007b5ffb30: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x10007b5ffb40: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x10007b5ffb50: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
0x10007b5ffb60: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Shadow byte legend (one shadow byte represents 8 application bytes):
Addressable: 00
Partially addressable: 01 02 03 04 05 06 07
Heap left redzone: fa
Freed heap region: fd
Stack left redzone: f1
Stack mid redzone: f2
Stack right redzone: f3
Stack after return: f5
Stack use after scope: f8
Global redzone: f9
Global init order: f6
Poisoned by user: f7
Container overflow: fc
Array cookie: ac
Intra object redzone: bb
ASan internal: fe
Left alloca redzone: ca
Right alloca redzone: cb
==29718==ABORTINGThe test seems to run fine with optimisations enabled. Without the sanitizer and without optimisations it just stops at the point where the sanitizer makes it crash.