Open Ruth28 opened 9 years ago
This following line:
* glibc detected * prerapsearch: free(): invalid pointer: 0x00007fff44c7b320 ***
... suggests that prerapsearch is trying to free memory (man 3 free
) that it is not allowed to free, resulting in a segmentation fault.
You need to compile with debug information enabled, e.g. -g
option to gcc
, not strip
this debug information, and rerun your command line with this debug build. This is required to find the exact location in the source code where the bug occurs.
Then you need to inspect the generated core dump, e.g. via gdb prerapsearch core.PID
and input bt
in the gdb
command line to get the full backtrace.
Hi, I'm helping Ruth out. So I recompiled prerapsearch, and ran the debugger on it. I got this back - do I need to install the extra yum debuginfo install (I tried, but had some problems re RHEL and its repository):
[damion@grl-salk bin]$ gdb prerapsearch /var/spool/abrt/ccpp-2015-07-30-12:17:55-44560/coredump GNU gdb (GDB) Red Hat Enterprise Linux (7.2-50.el6) Copyright (C) 2010 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-redhat-linux-gnu". For bug reporting instructions, please see: http://www.gnu.org/software/gdb/bugs/... Reading symbols from /usr/local/packages/rapsearch/RAPSearch2.1964bits/bin/prerapsearch...done. [New Thread 44560] Missing separate debuginfo for Try: yum --disablerepo='' --enablerepo='_-debuginfo' install /usr/lib/debug/.build-id/3b/5709b4dddefce3dd0b4bae733298285d52c602 Reading symbols from /lib64/libpthread.so.0...(no debugging symbols found)...done. [Thread debugging using libthread_db enabled] Loaded symbols for /lib64/libpthread.so.0 Reading symbols from /lib64/librt.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/librt.so.1 Reading symbols from /usr/lib64/libstdc++.so.6...(no debugging symbols found)...done. Loaded symbols for /usr/lib64/libstdc++.so.6 Reading symbols from /lib64/libm.so.6...(no debugging symbols found)...done. Loaded symbols for /lib64/libm.so.6 Reading symbols from /lib64/libgcc_s.so.1...(no debugging symbols found)...done. Loaded symbols for /lib64/libgcc_s.so.1 Reading symbols from /lib64/libc.so.6...(no debugging symbols found)...done. Loaded symbols for /lib64/libc.so.6 Reading symbols from /lib64/ld-linux-x86-64.so.2...(no debugging symbols found)...done. Loaded symbols for /lib64/ld-linux-x86-64.so.2 Core was generated by `prerapsearch -d viral.1.protein.faa -n test2'. Program terminated with signal 6, Aborted.
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.149.el6_6.5.x86_64 libgcc-4.4.7-4.el6.x86_64 libstdc++-4.4.7-4.el6.x86_64 (gdb) bt
Hi, I am trying to ru n prerapsearch on the NCBI viral dataset. I have tried prerapsearch -d viral.1.protein.faa -n test2 and prerapsearch -d viral.1.protein.faa -n test2 -s 10
And both times I get the same error message, as follows:
ow building hash file hash file saved to file test2
Any suggestions on how to prevent this from happening would be greatly appreciated.
Thanks,
Ruth