arb crash on x86_64 with gcc 4.3

[guest]

Hi I am working on arb package for openSUSE 11.0 and program is crashing right after build.

Here is a dump.

[parts removed - see below]

Feel free to poke me on mstopka@… e-mail if any other information will be needed. BTW I used this set of patches.. see attached tarball.

[guest]

applied patches and used spec file

[guest]

Because of ugly format, I am attaching backtrace and program crash output one more time:

(gdb) bt
#0  0x00007f5a66fef5c5 in raise () from /lib64/libc.so.6
#1  0x00007f5a66ff0bb3 in abort () from /lib64/libc.so.6
#2  0x00007f5a6702d3a8 in ?? () from /lib64/libc.so.6
#3  0x00007f5a67032af8 in ?? () from /lib64/libc.so.6
#4  0x00007f5a670346e6 in free () from /lib64/libc.so.6
#5  0x00007f5a68c089ee in aw_root_init_font () from /opt/arb/lib/libAW.so
#6  0x00007f5a68c00a27 in AW_root::init () from /opt/arb/lib/libAW.so
#7  0x0000000000490048 in main ()
(gdb)  

mantisha:~/Files/prace/buildservice/home:m4r3k/arb> /opt/arb/bin/arb
Using ARBHOME='/opt/arb'
Please wait while the program ARB is starting .....
mantisha:~/Files/prace/buildservice/home:m4r3k/arb> ARB: Loading '.arb_prop/ntree.arb'
ARB: Loading '/opt/arb/lib/arb_default/ntree.arb' done

*** glibc detected *** arb_ntree: double free or corruption (!prev): 0x00000000007c8eb0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x7f3c5ca87af8]
/lib64/libc.so.6(cfree+0x76)[0x7f3c5ca896e6]
/opt/arb/lib/libAW.so(_Z17aw_root_init_fontP9_XDisplay+0x48e)[0x7f3c5e65d9ee]
/opt/arb/lib/libAW.so(_ZN7AW_root4initEPKcb+0x437)[0x7f3c5e655a27]
arb_ntree[0x490048]
/lib64/libc.so.6(__libc_start_main+0xe6)[0x7f3c5ca30436]
arb_ntree(_ZNSt8ios_base4InitD1Ev+0x69)[0x4151a9]
======= Memory map: ========
00400000-0050d000 r-xp 00000000 08:01 574930                             /opt/arb/bin/arb_ntree
0070d000-0070e000 r--p 0010d000 08:01 574930                             /opt/arb/bin/arb_ntree
0070e000-00715000 rw-p 0010e000 08:01 574930                             /opt/arb/bin/arb_ntree
00715000-007f9000 rw-p 00715000 00:00 0                                  [heap]
7f3c54000000-7f3c54021000 rw-p 7f3c54000000 00:00 0
7f3c54021000-7f3c58000000 ---p 7f3c54021000 00:00 0
7f3c5a422000-7f3c5a427000 r-xp 00000000 08:01 1051071                    /usr/lib64/libXfixes.so.3.1.0
7f3c5a427000-7f3c5a626000 ---p 00005000 08:01 1051071                    /usr/lib64/libXfixes.so.3.1.0
7f3c5a626000-7f3c5a627000 r--p 00004000 08:01 1051071                    /usr/lib64/libXfixes.so.3.1.0
7f3c5a627000-7f3c5a628000 rw-p 00005000 08:01 1051071                    /usr/lib64/libXfixes.so.3.1.0
7f3c5a628000-7f3c5a632000 r-xp 00000000 08:01 1050945                    /usr/lib64/libXcursor.so.1.0.2
7f3c5a632000-7f3c5a831000 ---p 0000a000 08:01 1050945                    /usr/lib64/libXcursor.so.1.0.2
7f3c5a831000-7f3c5a832000 r--p 00009000 08:01 1050945                    /usr/lib64/libXcursor.so.1.0.2
7f3c5a832000-7f3c5a833000 rw-p 0000a000 08:01 1050945                    /usr/lib64/libXcursor.so.1.0.2
7f3c5a833000-7f3c5a85a000 r-xp 00000000 08:01 1228894                    /lib64/libexpat.so.1.5.2
7f3c5a85a000-7f3c5aa5a000 ---p 00027000 08:01 1228894                    /lib64/libexpat.so.1.5.2
7f3c5aa5a000-7f3c5aa5c000 r--p 00027000 08:01 1228894                    /lib64/libexpat.so.1.5.2
7f3c5aa5c000-7f3c5aa5d000 rw-p 00029000 08:01 1228894                    /lib64/libexpat.so.1.5.2
7f3c5aa5d000-7f3c5aa5f000 r-xp 00000000 08:01 1228892                    /lib64/libdl-2.8.so
7f3c5aa5f000-7f3c5ac5f000 ---p 00002000 08:01 1228892                    /lib64/libdl-2.8.so
7f3c5ac5f000-7f3c5ac60000 r--p 00002000 08:01 1228892                    /lib64/libdl-2.8.so
7f3c5ac60000-7f3c5ac61000 rw-p 00003000 08:01 1228892                    /lib64/libdl-2.8.so
7f3c5ac61000-7f3c5ac7c000 r-xp 00000000 08:01 1097856                    /usr/lib64/libxcb.so.1.0.0
7f3c5ac7c000-7f3c5ae7b000 ---p 0001b000 08:01 1097856                    /usr/lib64/libxcb.so.1.0.0
7f3c5ae7b000-7f3c5ae7c000 r--p 0001a000 08:01 1097856                    /usr/lib64/libxcb.so.1.0.0
7f3c5ae7c000-7f3c5ae7d000 rw-p 0001b000 08:01 1097856                    /usr/lib64/libxcb.so.1.0.0
7f3c5ae7d000-7f3c5ae7e000 r-xp 00000000 08:01 1097891                    /usr/lib64/libxcb-xlib.so.0.0.0
7f3c5ae7e000-7f3c5b07d000 ---p 00001000 08:01 1097891                    /usr/lib64/libxcb-xlib.so.0.0.0
7f3c5b07d000-7f3c5b07e000 r--p 00000000 08:01 1097891                    /usr/lib64/libxcb-xlib.so.0.0.0
7f3c5b07e000-7f3c5b07f000 rw-p 00001000 08:01 1097891                    /usr/lib64/libxcb-xlib.so.0.0.0
7f3c5b07f000-7f3c5b096000 r-xp 00000000 08:01 1050923                    /usr/lib64/libICE.so.6.3.0
7f3c5b096000-7f3c5b296000 ---p 00017000 08:01 1050923                    /usr/lib64/libICE.so.6.3.0
7f3c5b296000-7f3c5b297000 r--p 00017000 08:01 1050923                    /usr/lib64/libICE.so.6.3.0
7f3c5b297000-7f3c5b298000 rw-p 00018000 08:01 1050923                    /usr/lib64/libICE.so.6.3.0
7f3c5b298000-7f3c5b29c000 rw-p 7f3c5b298000 00:00 0
7f3c5b29c000-7f3c5b2a4000 r-xp 00000000 08:01 1051540                    /usr/lib64/libSM.so.6.0.0
7f3c5b2a4000-7f3c5b4a3000 ---p 00008000 08:01 1051540                    /usr/lib64/libSM.so.6.0.0
7f3c5b4a300/opt/arb/bin/arb: line 140: 18522 Neúspěšně ukončen (SIGABRT)        arb_ntree $args
ARB done

mantisha:~/Files/prace/buildservice/home:m4r3k/arb>   

[epruesse]

Could you compile ARB again with 'DEBUG=1' in config.makefile? That would make the output of gdb and ARB itself will much more helpful. The output of 'ldd arb_ntree' might also be interesting.

[meierh]

the release_20071207 was not ported for 64-bit compilation.

The svn 6016 compiles on OpenSuSE 10.3_64 (gcc 4.2.1). On OpenSuSE 11.1 (gcc 4.3.2) the first compile run ends with an error (message see below), a second afterwards "make all" runs through successfully.

---

/tmp/ccMOjHcY.o: In function `main': Zuk_to_gen.c:(.text+0x3bb): warning: the `gets' function is dangerous and should not be used. gcc -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -w -DNDEBUG -DDEVEL_DEVEL_JB -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -o /home/meierh/arb_SVN_DEBUG/bin/count count.c -I. -I/home/meierh/arb_SVN_DEBUG/INCLUDE -I/usr/X11R6/include -lm gcc -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -w -DNDEBUG -DDEVEL_DEVEL_JB -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -o /home/meierh/arb_SVN_DEBUG/bin/findall findall.c -I. -I/home/meierh/arb_SVN_DEBUG/INCLUDE -I/usr/X11R6/include -lm gcc -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -w -DNDEBUG -DDEVEL_DEVEL_JB -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -o /home/meierh/arb_SVN_DEBUG/bin/lsadt lsadt.c -I. -I/home/meierh/arb_SVN_DEBUG/INCLUDE -I/usr/X11R6/include -lm gcc -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -w -DNDEBUG -DDEVEL_DEVEL_JB -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -o /home/meierh/arb_SVN_DEBUG/bin/sho_helix sho_helix.c -I. -I/home/meierh/arb_SVN_DEBUG/INCLUDE -I/usr/X11R6/include -lm gcc -O4 -pipe -fmessage-length=0 -funit-at-a-time -fPIC -DARB_OPENGL -w -DNDEBUG -DDEVEL_DEVEL_JB -DARB_64 -DLINUX -rdynamic -DFAKE_VTAB_PTR=char -DIN_ARB_GDE -DIN_ARB_SUPPORT -o /home/meierh/arb_SVN_DEBUG/bin/varpos varpos.c -I. -I/home/meierh/arb_SVN_DEBUG/INCLUDE -I/usr/X11R6/include -lm make[4]: Leaving directory `/home/meierh/arb_SVN_DEBUG/GDE/SUPPORT' make[4]: Entering directory `/home/meierh/arb_SVN_DEBUG/GDE/MOLPHY' rm -f prot_tml.h ../../MAKEBIN/aisc_mkpt getseq.c seqproc.c mltree.c altree.c qltree.c sltree.c njtree.c njmtree.c prtree.c pstree.c matrixut.c mygetopt.c protml.c protproc.c dyhfjtt.c mtrev24.c tranprb.c distan.c mlklhd.c -w prot_tml.h >prot_tml.h -w: No such file or directory make[4]: * [prot_tml.h] Fehler 1 make[4]: Leaving directory `/home/meierh/arb_SVN_DEBUG/GDE/MOLPHY' make[3]: * [MOLPHY/MOLPHY.dummy] Fehler 1 make[3]: Leaving directory `/home/meierh/arb_SVN_DEBUG/GDE' make[2]: * [GDE.a] Fehler 2 make[2]: Leaving directory `/home/meierh/arb_SVN_DEBUG/GDE' make[1]: * [GDE/GDE.dummy] Fehler 1 make[1]: Leaving directory `/home/meierh/arb_SVN_DEBUG' make: * [all] Fehler 2

---

[westram]

• applied not already applied changes (see [6140])

Thank you very much for your contribution, Marek.

Did you try ARB again since then? If you plan to, you could try the ​RC of the upcoming release.