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Indigo: a cheminformatics toolkit. Bingo: RDBMS data cartridge for Oracle, MS SQL Server, and PostgreSQL
https://lifescience.opensource.epam.com/indigo
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SIGABRT on freelibrary mono->indigo calls #8

Open dimitry42 opened 10 years ago

dimitry42 commented 10 years ago

Hello everyone,

We are getting this error after upgrade to indigo 1.1.11, Platform is Linux 64 running indigo via mono .net wrapper:

Stacktrace:

at <0xffffffff> at (wrapper managed-to-native) com.ggasoftware.indigo.LibraryLoader/LinuxLoader.dlclose (intptr) <0xffffffff> at com.ggasoftware.indigo.LibraryLoader.FreeLibrary (intptr) <0x0007f> at com.ggasoftware.indigo.IndigoDllLoader.Finalize () <0x000c7> at (wrapper runtime-invoke) object.runtime_invoke_virtual_voidthis (object,intptr,intptr,intptr) <0xffffffff>

Native stacktrace:

/opt/mono/bin/mono() [0x4942c6]
/lib64/libpthread.so.0(+0xf500) [0x7fceafec4500]
/lib64/libc.so.6(gsignal+0x35) [0x7fceafb548a5]
/lib64/libc.so.6(abort+0x175) [0x7fceafb56085]
/lib64/libc.so.6(+0x707b7) [0x7fceafb927b7]
/lib64/libc.so.6(+0x760e6) [0x7fceafb980e6]
/lib64/libc.so.6(+0x78c13) [0x7fceafb9ac13]
/tmp/GGA_indigo/indigo-dotnet/1.1.4933.3712/Linux/x64/libindigo.so(+0xb7dc1) [0x7fce9f213dc1]
/tmp/GGA_indigo/indigo-dotnet/1.1.4933.3712/Linux/x64/libindigo.so(+0xb8ed7) [0x7fce9f214ed7]
/tmp/GGA_indigo/indigo-dotnet/1.1.4933.3712/Linux/x64/libindigo.so(+0xb9321) [0x7fce9f215321]
/lib64/libc.so.6(__cxa_finalize+0x9d) [0x7fceafb5813d]
/tmp/GGA_indigo/indigo-dotnet/1.1.4933.3712/Linux/x64/libindigo.so(+0x88ce3) [0x7fce9f1e4ce3]

Debug info from gdb:

Got a SIGABRT while executing native code. This usually indicates a fatal error in the mono runtime or one of the native libraries

used by your application.

mkviatkovskii commented 10 years ago

Hello Dimitry,

Could you please give me an example of code that produce the error and versions of Linux and Mono you use? How often does the error occur? We test indigo-dotnet with Mono 2.10 on Debian Testing x64 and it works fine.

dimitry42 commented 10 years ago

Hi Mickail,

Unfortunately I do not have code that reproduces this problem at this time. Linux version is CentOS 6.3, mono version:

mono --version Mono JIT compiler version 2.11.4 ((no/417ec78 Wed Feb 6 18:24:06 EST 2013) Copyright (C) 2002-2012 Novell, Inc, Xamarin Inc and Contributors. www.mono-project.com TLS: __thread SIGSEGV: altstack Notifications: epoll Architecture: amd64 Disabled: none Misc: softdebug LLVM: supported, not enabled. GC: Included Boehm (with typed GC and Parallel Mark)

mkviatkovskii commented 10 years ago

Hello Dimitry,

I have tested Indigo 1.1.11 with same version of Mono on CentOS 6.4 and everything seems to work fine. Could you please provide a simple example of calling Indigo methods which cause the error? Does the application fail every time or not? Does the error occur at the end of executing application?

karapetk commented 10 years ago

Just wanted to add that with everything the same (code and run-time condition) this doesn't happen with 1.1.10 of Indigo. Only with 1.1.11

dimitry42 commented 10 years ago

Mikhail,

I was going to try and localize this, unfortunately next couple of week are going to be busy, don't think I will be able to get to this part soon. I was hopping that you might have some ideas about what kind of changes could have introduced this bug.

mkviatkovskii commented 10 years ago

Dimitry, sorry for the long delay. I sent the release with debug information version of Indigo to your e-mail. It can give us additional information about the problem in native part of Indigo. Could you please reproduce the error using it and print the output here?

ggasoftware commented 10 years ago

Hello Dmirty, We've just released Indigo 1.1.12. Could you check this version? Mikhail