Dear David,
Sorry .. I misunderstood. Thanks for the clarification.
Below is the info printed when running under gdb. I see all these
missing debuginfos but I am not sure if those messages have something to
do with my problems ...
Best,
Vlad
vlad.kratos:~> gdb xaLeap
GNU gdb (GDB) SUSE (7.3-41.1.2)
Copyright (C) 2011 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later
<
http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-suse-linux".
For bug reporting instructions, please see:
<
http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /usr/local/apps/amber/11-1.5/bin/xaLeap...done.
(gdb) run
Starting program: /usr/local/apps/amber/11-1.5/bin/xaLeap
Missing separate debuginfo for /lib64/ld-linux-x86-64.so.2
Try: zypper install -C
"debuginfo(build-id)=f20c99249f5a5776e1377d3bd728502e3f455a3f"
Missing separate debuginfo for /usr/lib64/libXt.so.6
Try: zypper install -C
"debuginfo(build-id)=d559db27d7609bb354600072400f25b036d9685b"
Missing separate debuginfo for /usr/lib64/libXext.so.6
Try: zypper install -C
"debuginfo(build-id)=4044aa655824cfa839cacf99d438f26eb34bdcd0"
Missing separate debuginfo for /usr/lib64/libSM.so.6
Try: zypper install -C
"debuginfo(build-id)=095cdcbe468397c2edb5cde28d20889725405cb0"
Missing separate debuginfo for /usr/lib64/libICE.so.6
Try: zypper install -C
"debuginfo(build-id)=9df2261adc6432c3bf9047d060eceb95f10d8cfd"
Missing separate debuginfo for /usr/lib64/libX11.so.6
Try: zypper install -C
"debuginfo(build-id)=6e2a3fff65b38afb37e54abcc7db50e4a0bbc4f1"
Missing separate debuginfo for /usr/lib64/libXau.so.6
Try: zypper install -C
"debuginfo(build-id)=46ceb8560aee0ebd280c1618271aa86bfc2d752a"
Missing separate debuginfo for /usr/lib64/libXdmcp.so.6
Try: zypper install -C
"debuginfo(build-id)=bbf98d41fa8f19788b8908e03beed7b09f79f198"
Missing separate debuginfo for /lib64/libm.so.6
Try: zypper install -C
"debuginfo(build-id)=8ee6418257efac9e7fbadc657c30c62e0a002d57"
Missing separate debuginfo for /lib64/libpthread.so.0
Try: zypper install -C
"debuginfo(build-id)=1f368f83b776815033caab6e389d7030bba4593e"
[Thread debugging using libthread_db enabled]
Missing separate debuginfo for /lib64/libc.so.6
Try: zypper install -C
"debuginfo(build-id)=edf27158f11a5be0dec014af4bd219d9f38add32"
Missing separate debuginfo for /lib64/libuuid.so.1
Try: zypper install -C
"debuginfo(build-id)=24ae727f9cd5fb29f81b0f965859d3cf4668bf17"
Missing separate debuginfo for /usr/lib64/libxcb.so.1
Try: zypper install -C
"debuginfo(build-id)=e3769ffa477a916dce6e9d536ad334b5b652badc"
Missing separate debuginfo for /lib64/libdl.so.2
Try: zypper install -C
"debuginfo(build-id)=8d32fdb9682242cc2ebc1d9e6d717c6eaa51714e"
Missing separate debuginfo for /usr/lib64/libXcursor.so.1
Try: zypper install -C
"debuginfo(build-id)=6559ef9b185b57bf9ff42f138e28ee06edc6318d"
Missing separate debuginfo for /usr/lib64/libXrender.so.1
Try: zypper install -C
"debuginfo(build-id)=9e32e39beece8d995519eabc05474d3ed3c9f71c"
Missing separate debuginfo for /usr/lib64/libXfixes.so.3
Try: zypper install -C
"debuginfo(build-id)=c8877d033a79996c6dd7e3e7dec988bf27940fa8"
*** glibc detected *** /usr/local/apps/amber/11-1.5/bin/xaLeap: free():
invalid pointer: 0x00007ffff7f34010 ***
Missing separate debuginfo for /lib64/libgcc_s.so.1
Try: zypper install -C
"debuginfo(build-id)=04626951231c50274a41cb283a3a41208ac47efe"
======= Backtrace: =========
/lib64/libc.so.6(+0x74c06)[0x7ffff6663c06]
/usr/lib64/libX11.so.6(+0x2f312)[0x7ffff722b312]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4fb9bb]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x496f88]
/usr/lib64/libXt.so.6(+0x16a1f)[0x7ffff7b8ba1f]
/usr/lib64/libXt.so.6(_XtConvert+0xe6)[0x7ffff7b8c9c6]
/usr/lib64/libXt.so.6(+0x33b96)[0x7ffff7ba8b96]
/usr/lib64/libXt.so.6(_XtGetResources+0x107)[0x7ffff7ba9ae7]
/usr/lib64/libXt.so.6(+0x1d646)[0x7ffff7b92646]
/usr/lib64/libXt.so.6(_XtCreateWidget+0xeb)[0x7ffff7b92b0b]
/usr/lib64/libXt.so.6(XtCreateWidget+0xde)[0x7ffff7b92e1e]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ede51]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee4c2]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee0dd]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee471]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee4e8]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee0dd]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee471]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee4e8]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee0dd]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee471]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee4e8]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4edf54]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee426]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x4ee735]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x497670]
/lib64/libc.so.6(__libc_start_main+0xed)[0x7ffff661023d]
/usr/local/apps/amber/11-1.5/bin/xaLeap[0x407789]
======= Memory map: ========
00400000-00548000 r-xp 00000000 08:19 3555806
/usr/local/apps/amber/11-1.5/bin/xaLeap
00747000-00748000 r--p 00147000 08:19 3555806
/usr/local/apps/amber/11-1.5/bin/xaLeap
00748000-0076f000 rw-p 00148000 08:19 3555806
/usr/local/apps/amber/11-1.5/bin/xaLeap
0076f000-0088e000 rw-p 00000000 00:00 0
[heap]
7ffff5796000-7ffff57ab000 r-xp 00000000 08:16 1050997
/lib64/libgcc_s.so.1
7ffff57ab000-7ffff59aa000 ---p 00015000 08:16 1050997
/lib64/libgcc_s.so.1
7ffff59aa000-7ffff59ab000 r--p 00014000 08:16 1050997
/lib64/libgcc_s.so.1
7ffff59ab000-7ffff59ac000 rw-p 00015000 08:16 1050997
/lib64/libgcc_s.so.1
7ffff59ac000-7ffff59b1000 r-xp 00000000 08:16 1050497
/usr/lib64/libXfixes.so.3.1.0
7ffff59b1000-7ffff5bb1000 ---p 00005000 08:16 1050497
/usr/lib64/libXfixes.so.3.1.0
7ffff5bb1000-7ffff5bb2000 r--p 00005000 08:16 1050497
/usr/lib64/libXfixes.so.3.1.0
7ffff5bb2000-7ffff5bb3000 rw-p 00006000 08:16 1050497
/usr/lib64/libXfixes.so.3.1.0
7ffff5bb3000-7ffff5bbd000 r-xp 00000000 08:16 1050522
/usr/lib64/libXrender.so.1.3.0
7ffff5bbd000-7ffff5dbc000 ---p 0000a000 08:16 1050522
/usr/lib64/libXrender.so.1.3.0
7ffff5dbc000-7ffff5dbd000 r--p 00009000 08:16 1050522
/usr/lib64/libXrender.so.1.3.0
7ffff5dbd000-7ffff5dbe000 rw-p 0000a000 08:16 1050522
/usr/lib64/libXrender.so.1.3.0
7ffff5dbe000-7ffff5dc7000 r-xp 00000000 08:16 1050500
/usr/lib64/libXcursor.so.1.0.2
7ffff5dc7000-7ffff5fc7000 ---p 00009000 08:16 1050500
/usr/lib64/libXcursor.so.1.0.2
7ffff5fc7000-7ffff5fc8000 r--p 00009000 08:16 1050500
/usr/lib64/libXcursor.so.1.0.2
7ffff5fc8000-7ffff5fc9000 rw-p 0000a000 08:16 1050500
/usr/lib64/libXcursor.so.1.0.2
7ffff5fc9000-7ffff5fcb000 r-xp 00000000 08:16 1050878
/lib64/libdl-2.14.1.so
7ffff5fcb000-7ffff61cb000 ---p 00002000 08:16 1050878
/lib64/libdl-2.14.1.so
7ffff61cb000-7ffff61cc000 r--p 00002000 08:16 1050878
/lib64/libdl-2.14.1.so
7ffff61cc000-7ffff61cd000 rw-p 00003000 08:16 1050878
/lib64/libdl-2.14.1.so
7ffff61cd000-7ffff61e9000 r-xp 00000000 08:16 1057792
/usr/lib64/libxcb.so.1.1.0
7ffff61e9000-7ffff63e8000 ---p 0001c000 08:16 1057792
/usr/lib64/libxcb.so.1.1.0
7ffff63e8000-7ffff63e9000 r--p 0001b000 08:16 1057792
/usr/lib64/libxcb.so.1.1.0
7ffff63e9000-7ffff63ea000 rw-p 0001c000 08:16 1057792
/usr/lib64/libxcb.so.1.1.0
7ffff63ea000-7ffff63ee000 r-xp 00000000 08:16 1050884
/lib64/libuuid.so.1.3.0
7ffff63ee000-7ffff65ed000 ---p 00004000 08:16 1050884
/lib64/libuuid.so.1.3.0
7ffff65ed000-7ffff65ee000 r--p 00003000 08:16 1050884
/lib64/libuuid.so.1.3.0
7ffff65ee000-7ffff65ef000 rw-p 00004000 08:16 1050884
/lib64/libuuid.so.1.3.0
7ffff65ef000-7ffff6774000 r-xp 00000000 08:16 1050999
/lib64/libc-2.14.1.so
7ffff6774000-7ffff6974000 ---p 00185000 08:16 1050999
/lib64/libc-2.14.1.so
7ffff6974000-7ffff6978000 r--p 00185000 08:16 1050999
/lib64/libc-2.14.1.so
7ffff6978000-7ffff6979000 rw-p 00189000 08:16 1050999
/lib64/libc-2.14.1.so
7ffff6979000-7ffff697e000 rw-p 00000000 00:00 0
7ffff697e000-7ffff6996000 r-xp 00000000 08:16 1050875
/lib64/libpthread-2.14.1.so
7ffff6996000-7ffff6b95000 ---p 00018000 08:16 1050875
/lib64/libpthread-2.14.1.so
7ffff6b95000-7ffff6b96000 r--p 00017000 08:16 1050875
/lib64/libpthread-2.14.1.so
7ffff6b96000-7ffff6b97000 rw-p 00018000 08:16 1050875
/lib64/libpthread-2.14.1.so
7ffff6b97000-7ffff6b9b000 rw-p 00000000 00:00 0
7ffff6b9b000-7ffff6bf1000 r-xp 00000000 08:16 1050847
/lib64/libm-2.14.1.so
7ffff6bf1000-7ffff6df0000 ---p 00056000 08:16 1050847
/lib64/libm-2.14.1.so
7ffff6df0000-7ffff6df1000 r--p 00055000 08:16 1050847
/lib64/libm-2.14.1.so
7ffff6df1000-7ffff6df2000 rw-p 00056000 08:16 1050847
/lib64/libm-2.14.1.so
7ffff6df2000-7ffff6df7000 r-xp 00000000 08:16 1050516
/usr/lib64/libXdmcp.so.6.0.0
7ffff6df7000-7ffff6ff6000 ---p 00005000 08:16 1050516
/usr/lib64/libXdmcp.so.6.0.0
7ffff6ff6000-7ffff6ff7000 r--p 00004000 08:16 1050516
/usr/lib64/libXdmcp.so.6.0.0
7ffff6ff7000-7ffff6ff8000 rw-p 00005000 08:16 1050516
/usr/lib64/libXdmcp.so.6.0.0
7ffff6ff8000-7ffff6ffa000 r-xp 00000000 08:16 1055609
/usr/lib64/libXau.so.6.0.0
7ffff6ffa000-7ffff71fa000 ---p 00002000 08:16 1055609
/usr/lib64/libXau.so.6.0.0
7ffff71fa000-7ffff71fb000 r--p 00002000 08:16 1055609
/usr/lib64/libXau.so.6.0.0
7ffff71fb000-7ffff71fc000 rw-p 00003000 08:16 1055609
/usr/lib64/libXau.so.6.0.0
7ffff71fc000-7ffff7337000 r-xp 00000000 08:16 1057798
/usr/lib64/libX11.so.6.3.0
7ffff7337000-7ffff7537000 ---p 0013b000 08:16 1057798
/usr/lib64/libX11.so.6.3.0
7ffff7537000-7ffff7538000 r--p 0013b000 08:16 1057798
/usr/lib64/libX11.so.6.3.0
7ffff7538000-7ffff753d000 rw-p 0013c000 08:16 1057798
/usr/lib64/libX11.so.6.3.0
7ffff753d000-7ffff7554000 r-xp 00000000 08:16 1055633
/usr/lib64/libICE.so.6.3.0
7ffff7554000-7ffff7753000 ---p 00017000 08:16 1055633
/usr/lib64/libICE.so.6.3.0
7ffff7753000-7ffff7754000 r--p 00016000 08:16 1055633
/usr/lib64/libICE.so.6.3.0
7ffff7754000-7ffff7755000 rw-p 00017000 08:16 1055633
/usr/lib64/libICE.so.6.3.0
7ffff7755000-7ffff7759000 rw-p 00000000 00:00 0
7ffff7759000-7ffff7760000 r-xp 00000000 08:16 1055644
/usr/lib64/libSM.so.6.0.1
7ffff7760000-7ffff7960000 ---p 00007000 08:16 1055644
/usr/lib64/libSM.so.6.0.1
7ffff7960000-7ffff7961000 r--p 00007000 08:16 1055644
/usr/lib64/libSM.so.6.0.1
7ffff7961000-7ffff7962000 rw-p 00008000 08:16 1055644
/usr/lib64/libSM.so.6.0.1
7ffff7962000-7ffff7973000 r-xp 00000000 08:16 1057894
/usr/lib64/libXext.so.6.4.0
7ffff7973000-7ffff7b73000 ---p 00011000 08:16 1057894
/usr/lib64/libXext.so.6.4.0
7ffff7b73000-7ffff7b74000 r--p 00011000 08:16 1057894
/usr/lib64/libXext.so.6.4.0
7ffff7b74000-7ffff7b75000 rw-p 00012000 08:16 1057894
/usr/lib64/libXext.so.6.4.0
7ffff7b75000-7ffff7bd5000 r-xp 00000000 08:16 1055618
/usr/lib64/libXt.so.6.0.0
7ffff7bd5000-7ffff7dd5000 ---p 00060000 08:16 1055618
/usr/lib64/libXt.so.6.0.0
7ffff7dd5000-7ffff7dd6000 r--p 00060000 08:16 1055618
/usr/lib64/libXt.so.6.0.0
7ffff7dd6000-7ffff7ddb000 rw-p 00061000 08:16 1055618
/usr/lib64/libXt.so.6.0.0
7ffff7ddb000-7ffff7ddc000 rw-p 00000000 00:00 0
7ffff7ddc000-7ffff7dfc000 r-xp 00000000 08:16 1050870
/lib64/ld-2.14.1.so
7ffff7f34000-7ffff7f7c000 rw-p 00000000 00:00 0
7ffff7fc4000-7ffff7fcc000 rw-p 00000000 00:00 0
7ffff7ff9000-7ffff7ffb000 rw-p 00000000 00:00 0
7ffff7ffb000-7ffff7ffc000 r-xp 00000000 00:00 0
[vdso]
7ffff7ffc000-7ffff7ffd000 r--p 00020000 08:16 1050870
/lib64/ld-2.14.1.so
7ffff7ffd000-7ffff7ffe000 rw-p 00021000 08:16 1050870
/lib64/ld-2.14.1.so
7ffff7ffe000-7ffff7fff000 rw-p 00000000 00:00 0
7ffffffc7000-7ffffffff000 rw-p 00000000 00:00 0
[stack]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
[vsyscall]
Program received signal SIGABRT, Aborted.
0x00007ffff6623d95 in raise () from /lib64/libc.so.6
On 11/29/2011 05:38 PM, David A Case wrote:
> On Tue, Nov 29, 2011, Vlad Cojocaru wrote:
>> Thank you very much for answering.
>> I attach a log file of the recompilation of leap by using "make --debug" .
> What you need to do is to run the resulting xaLeap under a debugger, e.g.
>
> gdb $AMBERHOME/bin/xaLeap
>
> after the prompt, just type "run". You should still see an error, but with
> more detailed info about what happened.
>
> [You may need to set your XENVIRONMENT variable as indicated in
> $AMBERHOME/bin/xleap.]
>
> ...thx...dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de
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Received on Wed Nov 30 2011 - 02:00:03 PST
