error 134; ARB crashes when opening any database. *** buffer overflow detected ***: arb_ntree terminated

[guest]

Hi.

Can anyone help me with this issue? I cannot open ANY database anymore…

After the program crashed when I filtered sequences by the 'keep sequences that are marked' function, ARB will not open any of my databases (including unchanged public SILVA databases) anymore.

I am using ARB version 6.0.2 on an 16-core machine (Intel Xeon® CPU ES-2697 v3 @ 2.60 GHz x 16), with 500 GB memory and Ubuntu 12.04 LTS (16-bit) OS.

I always get the following error message (see comment below).

Can you help me resolve this issue?

Thank you!!!

[westram]

Using ARBHOME='/usr/arb'
Using properties from /home/user/.arb_prop
Please wait while the program ARB is starting .....
Waiting for '/home/user/.arb_tmp/sockets/arb_launcher.8144'..
[arb_launcher[0]: Starting 'arb_ntree'..]
Using properties from '/home/user/.arb_prop/ntree.arb'
Using properties from '/usr/arb/lib/arb_default/status.arb'
Font size 10 not found, using larger 12 point
Font size 11 not found, using larger 12 point
Font size 14 not found, using smaller 12 point
Warning: Cannot convert string "8x13bold" to type FontStruct
Warning: Cannot convert string "9x15bold" to type FontStruct
*** buffer overflow detected ***: arb_ntree terminated
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(__fortify_fail+0x37)[0x7f9bbac70db7]
/lib/x86_64-linux-gnu/libc.so.6(+0x10bcb0)[0x7f9bbac6fcb0]
/lib/x86_64-linux-gnu/libc.so.6(+0x10b119)[0x7f9bbac6f119]
/lib/x86_64-linux-gnu/libc.so.6(_IO_default_xsputn+0xdd)[0x7f9bbabdf00d]
/lib/x86_64-linux-gnu/libc.so.6(_IO_vfprintf+0x25a8)[0x7f9bbabaeb18]
/lib/x86_64-linux-gnu/libc.so.6(__vsprintf_chk+0x94)[0x7f9bbac6f1b4]
/lib/x86_64-linux-gnu/libc.so.6(__sprintf_chk+0x7d)[0x7f9bbac6f0fd]
arb_ntree(_Z32NT_insert_color_collapse_submenuP20AW_window_menu_modesP10AWT_canv                                                                                        as+0xa3)[0x587213]
arb_ntree[0x4654de]
arb_ntree(_Z21nt_create_main_windowP7AW_root+0x436)[0x46cdd6]
arb_ntree[0x470798]
arb_ntree[0x4709d0]
arb_ntree[0x470a7b]
/usr/arb/lib/libWINDOW.so(_ZN5AW_cb13run_callbacksEv+0xbf)[0x7f9bbbe82dcf]
/usr/arb/lib/libWINDOW.so(_Z18AW_server_callbackP10_WidgetRecPvS1_+0xa8)[0x7f9bb                                                                                        bea1768]
/usr/lib/x86_64-linux-gnu/libXt.so.6(XtCallCallbackList+0x130)[0x7f9bbb74b140]
/usr/lib/x86_64-linux-gnu/libXm.so.4(+0xdb517)[0x7f9bbba78517]
/usr/lib/x86_64-linux-gnu/libXt.so.6(+0x4928d)[0x7f9bbb78028d]
/usr/lib/x86_64-linux-gnu/libXt.so.6(_XtTranslateEvent+0x32b)[0x7f9bbb7810db]
/usr/lib/x86_64-linux-gnu/libXt.so.6(XtDispatchEventToWidget+0x443)[0x7f9bbb7592                                                                                        a3]
/usr/lib/x86_64-linux-gnu/libXt.so.6(+0x229e6)[0x7f9bbb7599e6]
/usr/lib/x86_64-linux-gnu/libXt.so.6(XtDispatchEvent+0xb4)[0x7f9bbb759aa4]
/usr/lib/x86_64-linux-gnu/libXt.so.6(XtAppMainLoop+0x4b)[0x7f9bbb759f4b]
arb_ntree(_Z8ARB_mainiPPc+0x189d)[0x472f8d]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7f9bbab857ed]
arb_ntree[0x449255]
======= Memory map: ========
00400000-005e5000 r-xp 00000000 08:03 13246252                           /usr/ar                                                                                        b/bin/arb_ntree
[...]
ARB: Loading 'ntree.arb'
ARB: Loading '/home/user/.arb_prop/ntree.arb' done

ARB: ARB: Loading '/home/user/ARB_databases/SSURef_SILVA_2015_user_2.arb'
ARB: ARB: no FastLoad File '/home/user/ARB_databases/SSURef_SILVA_2015_user_                                                                                        2.ARM' found => loading entire DB
ARB: ARB: Loading '/home/user/ARB_databases/SSURef_SILVA_2015_user_2.arb' do                                                                                        ne

/usr/arb/bin/arb_launcher: line 25:  8218 Aborted                 $CMD
[arb_launcher[0]: 'arb_ntree' has terminated with error 134]
[arb_launcher[0]: All launched processes terminated]

Session log has been stored in /home/user/.arb_prop/logs/session.20181106_12                                                                                        1350.8154.tgz
    and is also accessible via /home/user/ARB_last_session.tgz

ARB crashed :-(
To report this goto http://bugs.arb-home.de/wiki/BugReport
Please include the session log mentioned above

[westram]

Replying to guest:

Can anyone help me with this issue? I cannot open ANY database anymore… After the program crashed when I filtered sequences by the 'keep sequences that are marked' function, ARB will not open any of my databases (including unchanged public SILVA databases) anymore.

Does that mean arb did run w/o problems before?

I am using ARB version 6.0.2 on an 16-core machine (Intel Xeon® CPU ES-2697 v3 @ 2.60 GHz x 16), with 500 GB memory and Ubuntu 12.04 LTS (16-bit) OS.

Could you please attach the session log requested (at the end of the console output). For more privacy you may also send it via mail to devel@…

Ralf

[westram]

Assumed to be caused by broken properties.

[westram]

The problem described above was caused by a truncated arb property file.
Added followup-ticket #800 to provide better error-handling for the future.

Howto test + fix:

The properties are stored in the directory

    ~/.arb_prop/

To disable them for your account, you could rename them, e.g. from a
console/terminal window using the commands

    cd ~
    mv .arb_prop .arb_prop.20181106.broken

If arb works w/o problems after the 2nd command, the reason was inside
that directory.  Another (less likely) cause might be the directory
.arb_tmp (use same method).

If renaming does not fix the problem, you may revert the namechange
using
    cd ~
    mv .arb_prop.20181106.broken .arb_prop

If renaming does save the problem and you have a backup of the property
files - say from yesterday or last week - you may want to restore that
backup.

Main properties (for arb main program) are stored in
    ~/.arb_prop/ntree.arb
those of the arb sequence editor in
    ~/.arb_prop/edit4.arb
...
The main suspect for the crash is ~/.arb_prop/ntree.arb, so simply
renaming that file might as well work as a fix. The advantage would be,
that the saved user properties for the rest of arb remain intact.