TemperatureDifferenceAllparams.jl: seg fault near end of loop through dicts

[ggebbie]

Intermittent segfault on TemperatureDifferenceAllparams.jl

Hypothesis: related to PyPlot

signal (11): Segmentation fault
in expression starting at /home/gebbie/projects/HistoricalIndianOcean/scripts/TemperatureDifferenceAllparams.jl:54
unknown function (ip: 0x2)
Allocations: 129685817 (Pool: 129641812; Big: 44005); GC: 66
Segmentation fault (core dumped)

[ggebbie]

signal (11): Segmentation fault
in expression starting at /home/gebbie/projects/HistoricalIndianOcean/scripts/TemperatureDifferenceAllparams.jl:54
H5F_addr_decode at /home/gebbie/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5VL__native_blob_specific at /home/gebbie/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5VL_blob_specific at /home/gebbie/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5T__vlen_disk_isnull at /home/gebbie/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5T__conv_vlen at /home/gebbie/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5T_convert at /home/gebbie/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5D_get_create_plist at /home/gebbie/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5VL__native_dataset_get at /home/gebbie/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5VL_dataset_get at /home/gebbie/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
H5Dget_create_plist at /home/gebbie/.julia/artifacts/997813d46a8a06e6e9871a2a01483f91ce954eca/lib/libhdf5.so (unknown line)
nc4_get_var_meta at /home/gebbie/.julia/artifacts/0a7f440ba143b238cc3dd0def2956d34d76755f3/lib/libnetcdf.so (unknown line)
nc4_hdf5_find_grp_var_att at /home/gebbie/.julia/artifacts/0a7f440ba143b238cc3dd0def2956d34d76755f3/lib/libnetcdf.so (unknown line)
NC4_HDF5_inq_var_all at /home/gebbie/.julia/artifacts/0a7f440ba143b238cc3dd0def2956d34d76755f3/lib/libnetcdf.so (unknown line)
nc_inq_var at /home/gebbie/.julia/artifacts/0a7f440ba143b238cc3dd0def2956d34d76755f3/lib/libnetcdf.so (unknown line)
nc_inq_varname at /home/gebbie/.julia/artifacts/0a7f440ba143b238cc3dd0def2956d34d76755f3/lib/libnetcdf.so (unknown line)
nc_inq_varname at /home/gebbie/.julia/packages/NCDatasets/XVX8L/src/netcdf_c.jl:1481
listVar at /home/gebbie/.julia/packages/NCDatasets/XVX8L/src/variable.jl:12
keys at /home/gebbie/.julia/packages/NCDatasets/XVX8L/src/dataset.jl:237 [inlined]
initboundsmap! at /home/gebbie/.julia/packages/NCDatasets/XVX8L/src/dataset.jl:80
NCDataset#1 at /home/gebbie/.julia/packages/NCDatasets/XVX8L/src/types.jl:104
NCDataset at /home/gebbie/.julia/packages/NCDatasets/XVX8L/src/types.jl:85 [inlined]
#NCDataset#12 at /home/gebbie/.julia/packages/NCDatasets/XVX8L/src/dataset.jl:206
NCDataset at /home/gebbie/.julia/packages/NCDatasets/XVX8L/src/dataset.jl:157 [inlined]
NCDataset at /home/gebbie/.julia/packages/NCDatasets/XVX8L/src/dataset.jl:157 [inlined]
read_historical_data at /home/gebbie/projects/HistoricalIndianOcean/src/HistoricalIndianOcean.jl:293
unknown function (ip: 0x7f0064bbcd99)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
basinwide_avg at /home/gebbie/projects/HistoricalIndianOcean/src/HistoricalIndianOcean.jl:215
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
top-level scope at /home/gebbie/projects/HistoricalIndianOcean/scripts/TemperatureDifferenceAllparams.jl:56
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:876
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:830
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:944
eval at ./boot.jl:373 [inlined]
include_string at ./loading.jl:1196
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
_include at ./loading.jl:1253
include at ./client.jl:451
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
do_call at /buildworker/worker/package_linux64/build/src/interpreter.c:126
eval_value at /buildworker/worker/package_linux64/build/src/interpreter.c:215
eval_stmt_value at /buildworker/worker/package_linux64/build/src/interpreter.c:166 [inlined]
eval_body at /buildworker/worker/package_linux64/build/src/interpreter.c:587
jl_interpret_toplevel_thunk at /buildworker/worker/package_linux64/build/src/interpreter.c:731
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:885
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:830
jl_toplevel_eval_flex at /buildworker/worker/package_linux64/build/src/toplevel.c:830
jl_toplevel_eval_in at /buildworker/worker/package_linux64/build/src/toplevel.c:944
eval at ./boot.jl:373 [inlined]
eval_user_input at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:150
repl_backend_loop at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:246
start_repl_backend at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:231
#run_repl#47 at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:364
run_repl at /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.7/REPL/src/REPL.jl:351
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
#930 at ./client.jl:394
jfptr_YY.930_45169.clone_1 at /opt/julia-1.7.2/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
jl_f__call_latest at /buildworker/worker/package_linux64/build/src/builtins.c:757
#invokelatest#2 at ./essentials.jl:716 [inlined]
invokelatest at ./essentials.jl:714 [inlined]
run_main_repl at ./client.jl:379
exec_options at ./client.jl:309
_start at ./client.jl:495
jfptr__start_38732.clone_1 at /opt/julia-1.7.2/lib/julia/sys.so (unknown line)
_jl_invoke at /buildworker/worker/package_linux64/build/src/gf.c:2247 [inlined]
jl_apply_generic at /buildworker/worker/package_linux64/build/src/gf.c:2429
jl_apply at /buildworker/worker/package_linux64/build/src/julia.h:1788 [inlined]
true_main at /buildworker/worker/package_linux64/build/src/jlapi.c:559
jl_repl_entrypoint at /buildworker/worker/package_linux64/build/src/jlapi.c:701
main at julia (unknown line)
unknown function (ip: 0x7f011ab7dfcf)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x400808)
Allocations: 119307503 (Pool: 119263521; Big: 43982); GC: 78

[ggebbie]

revert NetCDF to 0.11.5. Works most of the time.

[ggebbie]

https://stackoverflow.com/questions/49317927/errno-101-netcdf-hdf-error-when-opening-netcdf-file

Problem with file lock. Be sure to close NetCDF file when done.

[ggebbie]

solved in commit f3a5510