Error reading .msh

[fihu55]

Hello together,

I tried simply to load the demo.msh file as follows with Julia 1.10.2

using Gridap
using GridapGmsh

# load msh
model = GmshDiscreteModel("./demo/demo.msh")

getting this error message:

Info    : Reading './demo/demo.msh'...
Info    : 188 entities
Info    : 10257 nodes
Info    : 41006 elements
Info    : Done reading './demo/demo.msh'

Please submit a bug report with steps to reproduce this fault, and any error messages that follow (in their entirety). Thanks.
Exception: EXCEPTION_ACCESS_VIOLATION at 0x7fffa8f339e8 -- gc_try_claim_and_push at C:/workdir/src\gc.c:1834 [inlined]
gc_mark_obj8 at C:/workdir/src\gc.c:1856
in expression starting at none:0
gc_try_claim_and_push at C:/workdir/src\gc.c:1834 [inlined]
gc_mark_obj8 at C:/workdir/src\gc.c:1856
gc_mark_outrefs at C:/workdir/src\gc.c:2634 [inlined]
gc_mark_loop_serial_ at C:/workdir/src\gc.c:2690
gc_mark_loop_serial at C:/workdir/src\gc.c:2713
gc_mark_loop at C:/workdir/src\gc.c:2908 [inlined]
_jl_gc_collect at C:/workdir/src\gc.c:3241
ijl_gc_collect at C:/workdir/src\gc.c:3538
maybe_collect at C:/workdir/src\gc.c:937 [inlined]
jl_gc_pool_alloc_inner at C:/workdir/src\gc.c:1293 [inlined]
jl_gc_pool_alloc_noinline at C:/workdir/src\gc.c:1350 [inlined]
jl_gc_alloc_ at C:/workdir/src\julia_internal.h:476 [inlined]
jl_gc_alloc at C:/workdir/src\gc.c:3590
_new_array_ at C:/workdir/src\array.c:134
_new_array at C:/workdir/src\array.c:198 [inlined]
ijl_alloc_array_1d at C:/workdir/src\array.c:436
Array at .\boot.jl:477 [inlined]
Array at .\boot.jl:496 [inlined]
DomTreeNode at .\compiler/ssair\domtree.jl:207 [inlined]
compute_domtree_nodes! at .\compiler/ssair\domtree.jl:253
update_domtree! at .\compiler/ssair\domtree.jl:247 [inlined]
construct_domtree at .\compiler/ssair\domtree.jl:229
get! at .\compiler\inferencestate.jl:178 [inlined]
perform_lifting! at .\compiler/ssair\passes.jl:686
sroa_pass! at .\compiler/ssair\passes.jl:1113
run_passes at .\compiler\optimize.jl:489
run_passes at .\compiler\optimize.jl:504 [inlined]
optimize at .\compiler\optimize.jl:453 [inlined]
_typeinf at .\compiler\typeinfer.jl:272
typeinf at .\compiler\typeinfer.jl:216
typeinf_edge at .\compiler\typeinfer.jl:930
abstract_call_method at .\compiler\abstractinterpretation.jl:629
abstract_call_gf_by_type at .\compiler\abstractinterpretation.jl:95
abstract_call_known at .\compiler\abstractinterpretation.jl:2087
abstract_call at .\compiler\abstractinterpretation.jl:2169
abstract_call at .\compiler\abstractinterpretation.jl:2162
abstract_call at .\compiler\abstractinterpretation.jl:2354
abstract_eval_call at .\compiler\abstractinterpretation.jl:2370
abstract_eval_statement_expr at .\compiler\abstractinterpretation.jl:2380
abstract_eval_statement at .\compiler\abstractinterpretation.jl:2624
abstract_eval_basic_statement at .\compiler\abstractinterpretation.jl:2913
typeinf_local at .\compiler\abstractinterpretation.jl:3098
typeinf_nocycle at .\compiler\abstractinterpretation.jl:3186
_typeinf at .\compiler\typeinfer.jl:247
typeinf at .\compiler\typeinfer.jl:216
typeinf_ext at .\compiler\typeinfer.jl:1051
typeinf_ext_toplevel at .\compiler\typeinfer.jl:1082
typeinf_ext_toplevel at .\compiler\typeinfer.jl:1078
jfptr_typeinf_ext_toplevel_38986.1 at [...]\AppData\Local\Programs\Julia-1.10.2\lib\julia\sys.dll (unknown line)
_jl_invoke at C:/workdir/src\gf.c:2894 [inlined]
ijl_apply_generic at C:/workdir/src\gf.c:3076 [inlined]
jl_apply at C:/workdir/src\julia.h:1982 [inlined]
jl_type_infer at C:/workdir/src\gf.c:394
jl_generate_fptr_impl at C:/workdir/src\jitlayers.cpp:502
jl_compile_method_internal at C:/workdir/src\gf.c:2480
jl_compile_method_internal at C:/workdir/src\gf.c:2372 [inlined]
_jl_invoke at C:/workdir/src\gf.c:2886 [inlined]
ijl_apply_generic at C:/workdir/src\gf.c:3076
jl_apply at C:/workdir/src\julia.h:1982 [inlined]
jl_f__call_latest at C:/workdir/src\builtins.c:812
#invokelatest#2 at .\essentials.jl:892 [inlined]
invokelatest at .\essentials.jl:889 [inlined]
display_error at [...]\.vscode\extensions\julialang.language-julia-1.65.2\scripts\packages\VSCodeServer\src\eval.jl:375
unknown function (ip: 000001dbf27f128f)
#67 at [...]\.vscode\extensions\julialang.language-julia-1.65.2\scripts\packages\VSCodeServer\src\eval.jl:223
withpath at [...]\.vscode\extensions\julialang.language-julia-1.65.2\scripts\packages\VSCodeServer\src\repl.jl:274
#66 at [...]\.vscode\extensions\julialang.language-julia-1.65.2\scripts\packages\VSCodeServer\src\eval.jl:179
hideprompt at [...]\.vscode\extensions\julialang.language-julia-1.65.2\scripts\packages\VSCodeServer\src\repl.jl:38
#65 at [...]\.vscode\extensions\julialang.language-julia-1.65.2\scripts\packages\VSCodeServer\src\eval.jl:150
unknown function (ip: 000001dbf27ec64b)
with_logstate at .\logging.jl:515
with_logger at .\logging.jl:627 [inlined]
#64 at [...]\.vscode\extensions\julialang.language-julia-1.65.2\scripts\packages\VSCodeServer\src\eval.jl:255
unknown function (ip: 000001dbf27eae4b)
jl_apply at C:/workdir/src\julia.h:1982 [inlined]
jl_f__call_latest at C:/workdir/src\builtins.c:812
#invokelatest#2 at .\essentials.jl:892 [inlined]
invokelatest at .\essentials.jl:889
unknown function (ip: 000001dbf27e089b)
jl_apply at C:/workdir/src\julia.h:1982 [inlined]
do_apply at C:/workdir/src\builtins.c:768
#62 at [...]\.vscode\extensions\julialang.language-julia-1.65.2\scripts\packages\VSCodeServer\src\eval.jl:34
unknown function (ip: 000001dbf27c9764)
jl_apply at C:/workdir/src\julia.h:1982 [inlined]
start_task at C:/workdir/src\task.c:1238
Allocations: 10650842 (Pool: 10641834; Big: 9008); GC: 15

[JordiManyer]

@fihu55 I'm looking into it, but basically it's caused by the new version on the gmsh_jll artifact. A temporary fix would be to pin that package to 4.11.1.
I'll try to see what can be done to get this working also with 4.12.2, but I'm afraid I know very little about Gmsh.

EDIT:

After having a look at the changelog for Gmsh 4.12, some API calls seem be changed:

4.12.2 (January 21, 2024): small bug fixes.

4.12.1 (January 11, 2024): small bug fixes.

4.12.0 (December 21, 2023): new high-order mesh optimisation mode for periodic
meshes; new element qualities available through API; new IGES export; new volume
glyph; OCC curve loops can now be oriented based on the sign of the first curve;
better mesh node visualization; added suppport for model attributes in MSH2
files; new mesh renumbering capabilities in the API; new GAMBIT mesh reader;
replaced Geometry.OCCSafeUnbind with more flexible Geometry.OCCFastUnbind (which
can be set for boolean operations as well); added support for editing STEP
headers; small bug fixes.

* New API functions: model/getEntitiesForPhysicalName, mesh/computeRenumbering,
  mesh/getVisibility.

* Incompatible API changes: new optional argument to occ/addCircleArc,
  mesh/renumberNodes, mesh/renumberElements and view/getListData; new optional
  "interruptible" argument to gmsh.initialize() in Python

In particular, I thing we are using the renumberXXX functions. This is where the error lies.

[fihu55]

@JordiManyer thanks very much, now it works as intended.

[JordiManyer]

Hey @fihu55 , I can no longer reproduce the error.
Can you see if it's also resolved for you? Unpin the gmsh_jll artifact and try again. Hopefully it is resolved for you as well. If so, I believe it might have been caused by one of the sub-dependencies of gmsh_jll.

[fihu55]

@JordiManyer still have the same issue with gmsh_jll 4.12.2 :(

[JordiManyer]

@fihu55 Just to be sure, can you Pkg.update() and Pkg.build() and then try again?

[fihu55]

@JordiManyer now it works, thanks!