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Update Julia manifest #1204

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Update Julia manifest #1204

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@github-actions github-actions bot commented Mar 2, 2024

Update Julia dependencies to the latest version.

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visr commented Mar 2, 2024

This causes test ribasim_api to fail, only on Linux. There is no real error to go by however.

[21:20:46 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_181_181&logView=flowAware)  ============================= test session starts ==============================
[21:20:46 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_182_182&logView=flowAware)  platform linux -- Python 3.11.7, pytest-8.0.0, pluggy-1.4.0
[21:20:46 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_183_183&logView=flowAware)  rootdir: /opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim
[21:20:46 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_184_184&logView=flowAware)  plugins: anyio-4.2.0, typeguard-4.1.5, xdist-3.5.0, cov-4.1.0
[21:20:46 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_185_185&logView=flowAware)  collected 14 items
[21:20:46 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_186_186&logView=flowAware)  
[21:20:47 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_187_187&logView=flowAware)  python/ribasim_api/tests/test_bmi.py
[21:20:47 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_188_188&logView=flowAware)  Process exited with code 1
[21:20:47 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_190_190&logView=flowAware)  Process exited with code 1 (Step: Run tests (Command Line))
[21:20:47 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_191_191&logView=flowAware)  Step Run tests (Command Line) failed
[21:20:48 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_193_193&logView=flowAware)Ant JUnit report watcher
[21:20:48 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_194_194&logView=flowAware)  No reports found for paths:
[21:20:48 ](https://dpcbuild.deltares.nl/buildConfiguration/Ribasim_Linux_TestRibasimApi/3430168?expandBuildDeploymentsSection=false&hideTestsFromDependencies=false&hideProblemsFromDependencies=false&expandBuildProblemsSection=true&showLog=3430168_195_195&logView=flowAware)  /opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/report.xml

@visr visr marked this pull request as draft March 2, 2024 20:32
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There is no real error to go by however.

Seems like it just crashes.
With MODFLOW I stop pytest from capturing the output by passing the flag -s.
I was hoping that wouldn't be necessary with Ribasim, but for now we could try that.

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visr commented Mar 5, 2024

Thanks, that shows a segfault:

[7476] signal (11.1): Segmentation fault
in expression starting at none:0
initialize_env at /workspace/srcdir/gcc-13.2.0/libgomp/env.c:2062
_dl_init at /lib64/ld-linux-x86-64.so.2 (unknown line)
dl_open_worker at /lib64/ld-linux-x86-64.so.2 (unknown line)
_dl_catch_error at /lib64/ld-linux-x86-64.so.2 (unknown line)
_dl_open at /lib64/ld-linux-x86-64.so.2 (unknown line)
dlopen_doit at /lib64/libdl.so.2 (unknown line)
_dl_catch_error at /lib64/ld-linux-x86-64.so.2 (unknown line)
_dlerror_run at /lib64/libdl.so.2 (unknown line)
dlopen at /lib64/libdl.so.2 (unknown line)
ijl_load_dynamic_library at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/dlload.c:365
#dlopen#3 at ./libdl.jl:117
dlopen at ./libdl.jl:116 [inlined]
dlopen at ./libdl.jl:116 [inlined]
__init__ at /opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/utils/juliaup/julia-1.10.2+0.x64.linux.gnu/share/julia/stdlib/v1.10/CompilerSupportLibraries_jll/src/CompilerSupportLibraries_jll.jl:62
jfptr___init___126548 at /opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/build/libribasim/lib/libribasim.so (unknown line)
_jl_invoke at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:2894 [inlined]
ijl_apply_generic at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/gf.c:3076
jl_apply at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/julia.h:1982 [inlined]
jl_module_run_initializer at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/toplevel.c:76
_finish_julia_init at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/init.c:901
julia_init at /cache/build/builder-amdci5-1/julialang/julia-release-1-dot-10/src/init.c:844
ffi_call_unix64 at /opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/lib/python3.11/lib-dynload/../../libffi.so.8 (unknown line)
ffi_call_int at /opt/teamcityagent/work/ecd2b8f9b25b1609/ribasim/.pixi/envs/default/lib/python3.11/lib-dynload/../../libffi.so.8 (unknown line)
_call_function_pointer at /usr/local/src/conda/python-3.11.7/Modules/_ctypes/callproc.c:923 [inlined]

The libgomp line in question is here: https://github.com/gcc-mirror/gcc/blob/c891d8dc23e1a46ad9f3e757d09e57b500d40044/libgomp/env.c#L2062

I suspect it is related to the update of CompilerSupportLibraries_jll, which is updated from "1.0.5+1" to "1.1.0+0" as you can see in the Manifest.toml. It looks like this is a stdlib that we cannot update separately from Julia itself.

I see this has already been patched in JuliaPackaging/Yggdrasil#8205. Not sure yet if we can get this fixed CompilerSupportLibraries_jll with julia 1.10.2 or that we should wait until 1.10.3. We need CompilerSupportLibraries_jll v1.1.1.

@visr visr mentioned this pull request Mar 5, 2024
@visr visr added the on hold label Mar 5, 2024
Hofer-Julian pushed a commit that referenced this pull request Mar 5, 2024
Taken out of #1204 whilst that is on hold.

The directories changed in #1021, causing our precompile run to return
error code 1 with a "TOML not found error". That means we were not
precompiling an actual run and therefore probably need to wait a bit
longer before the start of a simulation. This fixes the directory and
adds an assertion to make sure the simulation is successful.
@visr visr closed this Mar 5, 2024
@visr visr deleted the update/julia-manifest branch March 5, 2024 22:54
visr added a commit that referenced this pull request Mar 6, 2024
I was wondering why the automated part of #1204 bumps the Julia version
in the Manifest.toml. It is because we didn't run `juliaup default
1.10.0` yet, so 1.10.2 is the default. This fixes that. There is no need
to run all of `pixi run install` for this action.

---------

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