Native Crash on Ubuntu 22.04

[Mailaender]

After some preparations

sudo apt install mono-complete
chmod +x run*.sh
chmod +x mzdbtools

it sadly crashed:

./run_thermo2mzdb.sh -i small.RAW -o small.mzdb
2022.11.30 11:33:24:000 [main      ] [INFO ] <empty>.AbstractMzDbTools._thermo2mzdb:51 - --- raw to mzDB file converter ---
2022.11.30 11:33:24:000:001 [main      ] [INFO ] <empty>.AbstractMzDbTools._thermo2mzdb:74 - Opening raw file located at: /home/matthias/Downloads/mzdbtools_0.4.3_linux_x64/small.RAW
mono_coop_cond_broadcast Cannot transition thread 0x7f42345afa00 from STATE_BLOCKING with DO_BLOCKING

=================================================================

with a not too helpful stacktrace.

mono --version
Mono JIT compiler version 6.8.0.105 (Debian 6.8.0.105+dfsg-3.2 Wed Jun 30 05:34:49 UTC 2021)
Copyright (C) 2002-2014 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com
        TLS:           __thread
        SIGSEGV:       altstack
        Notifications: epoll
        Architecture:  amd64
        Disabled:      none
        Misc:          softdebug 
        Interpreter:   yes
        LLVM:          supported, not enabled.
        Suspend:       hybrid
        GC:            sgen (concurrent by default)

[david-bouyssie]

Thank you for your issue.
I also saw a similar Mono crash on a similar setup.

I'm looking for workarounds that would not use Mono, and use dotnetcore instead, but this will take time...

In the meantime, could you please try this Dockerfile?
https://github.com/mzdb/mzdb4s/blob/master/docker/Dockerfile

I can give additional details if you need.

[david-bouyssie]

Hre you go:
https://github.com/mzdb/mzdb-specs/tree/master/example_data

[veitveit]

@david-bouyssie
Also still struggling a bit with running mzdbtools on Ubuntu machine.
I started with a clear basic Debian docker container, and then installed mono-devel (version 6.8.0.105).
run_thermo2mzdb.sh fails with the same error above.

But there is also a bit more to report. After switching off the multi-threading (at least I think that happened) with MONO_THREADS_SUSPEND=preemptive, I get more meaningful output.
error.txt
stdout.txt

Does that help?