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Segmentation fault with [email protected] #9

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tcarion opened this issue Jan 18, 2023 · 0 comments · Fixed by JuliaPackaging/Yggdrasil#9002
Open

Segmentation fault with [email protected] #9

tcarion opened this issue Jan 18, 2023 · 0 comments · Fixed by JuliaPackaging/Yggdrasil#9002

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@tcarion
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tcarion commented Jan 18, 2023

When updating NetCDFF_jll to v4.6.0, I get a segmentation when running Flexpart:

julia> Flexpart.run()
 Welcome to FLEXPART Version 10.4 (2019-11-12)
 FLEXPART is free software released under the GNU General Public License.
 WARNING: path not ending in /
 /home/tcarion/.julia/artifacts/8ba836dac6b721ae2792516e29d94233f3d20ecf/tests/input/deterministic                       
 fix: padded with /
 /home/tcarion/.julia/artifacts/8ba836dac6b721ae2792516e29d94233f3d20ecf/tests/input/deterministic/                      
 length(i) increased 1
              ----------------               
  INFORMATION: SUBGRIDSCALE TERRAIN EFFECT IS
  NOT PARAMETERIZED DURING THIS SIMULATION.  
              ----------------               
 ECMWF metdata detected
 Vertical levels in ECMWF data:     138    138

 Mother domain:
  Longitude range:    4.00000 to    6.00000   Grid distance:    0.20000
  Latitude range :   49.00000 to   52.20000   Grid distance:    0.20000

 Releasepoints :            1
  
 SPECIES:  24  AIRTRACER   (GAS) 
   Wet removal for gases      is turned: OFF 
   Dry deposition for gases   is turned: OFF 
   Below-cloud scavenging: OFF
   In-cloud scavenging: OFF
 Particles allocated (maxpart)  :      2000000
 Particles released (numpartmax):        10000
 Total mass released: 1.0000000E+00
 Allocating fields for global output (x,y):           10          16
 Allocating fields for nested output (x,y):            0           0

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7efe3a65d3ff in ???
#1  0x7efe3b45ded4 in nf_def_var_quantize_
        at /workspace/srcdir/netcdf-fortran-4.6.0/fortran/nf_nc4.F90:1639
#2  0x7efe3b4a5ff2 in __netcdf_MOD_nf90_def_var_manydims
        at /workspace/srcdir/netcdf-fortran-4.6.0/fortran/netcdf4_variables.F90:276
#3  0x47729a in ???
#4  0x4964c8 in ???
#5  0x403690 in ???
#6  0x7efe3a649554 in ???
#7  0x4036c0 in ???
        at ../sysdeps/x86_64/elf/start.S:113

The seg fault disappears for [email protected], but then it won't compile on [email protected]:

julia> VERSION
v"1.8.0"
julia> using Flexpart
[ Info: Precompiling Flexpart [fb362612-c2d8-4302-a9fd-a07f2890630f]
ERROR: LoadError: InitError: could not load library "/home/tcarion/.julia/artifacts/0a7f440ba143b238cc3dd0def2956d34d76755f3/lib/libnetcdf.so"
libmbedtls.so.13: cannot open shared object file: No such file or directory

So at the moment, the only way of running Flexpart is to force to use [email protected] and run it with julia v1.7

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