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Gentoo's Bugzilla – Attachment 203754 Details for
Bug 284431
sci-chemistry/gromacs-4.0.5 buffer overflow issue
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buffer overflow message
gromacs_error.txt (text/plain), 13.32 KB, created by
Yasuyuki Araki
on 2009-09-11 02:23:50 UTC
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Description:
buffer overflow message
Filename:
MIME Type:
Creator:
Yasuyuki Araki
Created:
2009-09-11 02:23:50 UTC
Size:
13.32 KB
patch
obsolete
>araki@hoata ~ $ export LANG=C >araki@hoata ~ $ grompp > :-) G R O M A C S (-: > >*** buffer overflow detected ***: grompp terminated >======= Backtrace: ========= >/lib/libc.so.6(__fortify_fail+0x37)[0x2b0b1e4688c7] >/lib/libc.so.6[0x2b0b1e4666e0] >/lib/libc.so.6[0x2b0b1e4654cd] >grompp(get_libdir+0x214)[0x4bee34] >grompp(low_libfn+0x162)[0x4bf002] >grompp(low_libopen+0x15)[0x4bf065] >grompp[0x4b69b9] >grompp(bromacs+0x1d)[0x4b6bfd] >grompp(CopyRight+0x44)[0x4b6c54] >grompp(main+0x2b7)[0x417657] >/lib/libc.so.6(__libc_start_main+0xe6)[0x2b0b1e3a0a26] >grompp[0x416809] >======= Memory map: ======== >00400000-00608000 r-xp 00000000 08:02 1083858304 /usr/bin/grompp >00807000-00808000 r-xp 00207000 08:02 1083858304 /usr/bin/grompp >00808000-0080f000 rwxp 00208000 08:02 1083858304 /usr/bin/grompp >0080f000-00841000 rwxp 00000000 00:00 0 [heap] >2b0b19f2b000-2b0b19f48000 r-xp 00000000 08:02 548029227 /lib64/ld-2.10.1.so >2b0b19f48000-2b0b19f62000 rwxp 00000000 00:00 0 >2b0b1a147000-2b0b1a148000 r-xp 0001c000 08:02 548029227 /lib64/ld-2.10.1.so >2b0b1a148000-2b0b1a149000 rwxp 0001d000 08:02 548029227 /lib64/ld-2.10.1.so >2b0b1a149000-2b0b1a29c000 r-xp 00000000 08:02 537047329 /usr/lib64/libxml2.so.2.7.3 >2b0b1a29c000-2b0b1a49b000 ---p 00153000 08:02 537047329 /usr/lib64/libxml2.so.2.7.3 >2b0b1a49b000-2b0b1a4a3000 r-xp 00152000 08:02 537047329 /usr/lib64/libxml2.so.2.7.3 >2b0b1a4a3000-2b0b1a4a5000 rwxp 0015a000 08:02 537047329 /usr/lib64/libxml2.so.2.7.3 >2b0b1a4a5000-2b0b1a4a6000 rwxp 00000000 00:00 0 >2b0b1a4a6000-2b0b1a4bb000 r-xp 00000000 08:02 1612546467 /lib64/libz.so.1.2.3 >2b0b1a4bb000-2b0b1a6ba000 ---p 00015000 08:02 1612546467 /lib64/libz.so.1.2.3 >2b0b1a6ba000-2b0b1a6bb000 r-xp 00014000 08:02 1612546467 /lib64/libz.so.1.2.3 >2b0b1a6bb000-2b0b1a6bc000 rwxp 00015000 08:02 1612546467 /lib64/libz.so.1.2.3 >2b0b1a6bc000-2b0b1a6bd000 rwxp 00000000 00:00 0 >2b0b1a6bd000-2b0b1a898000 r-xp 00000000 08:02 1610870495 /usr/lib64/libgsl.so.0.13.0 >2b0b1a898000-2b0b1aa97000 ---p 001db000 08:02 1610870495 /usr/lib64/libgsl.so.0.13.0 >2b0b1aa97000-2b0b1aa9a000 r-xp 001da000 08:02 1610870495 /usr/lib64/libgsl.so.0.13.0 >2b0b1aa9a000-2b0b1aaa5000 rwxp 001dd000 08:02 1610870495 /usr/lib64/libgsl.so.0.13.0 >2b0b1aaa5000-2b0b1aade000 r-xp 00000000 08:02 1610921041 /usr/lib64/libgslcblas.so.0.0.0 >2b0b1aade000-2b0b1acdd000 ---p 00039000 08:02 1610921041 /usr/lib64/libgslcblas.so.0.0.0 >2b0b1acdd000-2b0b1acde000 r-xp 00038000 08:02 1610921041 /usr/lib64/libgslcblas.so.0.0.0 >2b0b1acde000-2b0b1acdf000 rwxp 00039000 08:02 1610921041 /usr/lib64/libgslcblas.so.0.0.0 >2b0b1acdf000-2b0b1acf4000 r-xp 00000000 08:02 548029221 /lib64/libnsl-2.10.1.so >2b0b1acf4000-2b0b1aef3000 ---p 00015000 08:02 548029221 /lib64/libnsl-2.10.1.so >2b0b1aef3000-2b0b1aef4000 r-xp 00014000 08:02 548029221 /lib64/libnsl-2.10.1.so >2b0b1aef4000-2b0b1aef5000 rwxp 00015000 08:02 548029221 /lib64/libnsl-2.10.1.so >2b0b1aef5000-2b0b1aef8000 rwxp 00000000 00:00 0 >2b0b1aef8000-2b0b1b058000 r-xp 00000000 08:02 1087587436 /usr/lib64/libfftw3f.so.3.2.3 >2b0b1b058000-2b0b1b257000 ---p 00160000 08:02 1087587436 /usr/lib64/libfftw3f.so.3.2.3 >2b0b1b257000-2b0b1b263000 r-xp 0015f000 08:02 1087587436 /usr/lib64/libfftw3f.so.3.2.3 >2b0b1b263000-2b0b1b264000 rwxp 0016b000 08:02 1087587436 /usr/lib64/libfftw3f.so.3.2.3 >2b0b1b264000-2b0b1b273000 r-xp 00000000 08:02 1087587446 /usr/lib64/libdmalloc.so.5.5.2 >2b0b1b273000-2b0b1b472000 ---p 0000f000 08:02 1087587446 /usr/lib64/libdmalloc.so.5.5.2 >2b0b1b472000-2b0b1b473000 r-xp 0000e000 08:02 1087587446 /usr/lib64/libdmalloc.so.5.5.2 >2b0b1b473000-2b0b1b474000 rwxp 0000f000 08:02 1087587446 /usr/lib64/libdmalloc.so.5.5.2 >2b0b1b474000-2b0b1b557000 rwxp 00000000 00:00 0 >2b0b1b557000-2b0b1b55f000 r-xp 00000000 08:02 1081986062 /usr/lib64/libSM.so.6.0.0 >2b0b1b55f000-2b0b1b75e000 ---p 00008000 08:02 1081986062 /usr/lib64/libSM.so.6.0.0 >2b0b1b75e000-2b0b1b75f000 r-xp 00007000 08:02 1081986062 /usr/lib64/libSM.so.6.0.0 >2b0b1b75f000-2b0b1b760000 rwxp 00008000 08:02 1081986062 /usr/lib64/libSM.so.6.0.0 >2b0b1b760000-2b0b1b761000 rwxp 00000000 00:00 0 >2b0b1b761000-2b0b1b765000 r-xp 00000000 08:02 62025794 /lib64/libuuid.so.1.3.0 >2b0b1b765000-2b0b1b964000 ---p 00004000 08:02 62025794 /lib64/libuuid.so.1.3.0 >2b0b1b964000-2b0b1b965000 r-xp 00003000 08:02 62025794 /lib64/libuuid.so.1.3.0 >2b0b1b965000-2b0b1b966000 rwxp 00004000 08:02 62025794 /lib64/libuuid.so.1.3.0 >2b0b1b966000-2b0b1b97d000 r-xp 00000000 08:02 1617180393 /usr/lib64/libICE.so.6.3.0 >2b0b1b97d000-2b0b1bb7d000 ---p 00017000 08:02 1617180393 /usr/lib64/libICE.so.6.3.0 >2b0b1bb7d000-2b0b1bb7e000 r-xp 00017000 08:02 1617180393 /usr/lib64/libICE.so.6.3.0 >2b0b1bb7e000-2b0b1bb7f000 rwxp 00018000 08:02 1617180393 /usr/lib64/libICE.so.6.3.0 >2b0b1bb7f000-2b0b1bb83000 rwxp 00000000 00:00 0 >2b0b1bb83000-2b0b1bc87000 r-xp 00000000 08:02 541973441 /usr/lib64/libX11.so.6.2.0 >2b0b1bc87000-2b0b1be87000 ---p 00104000 08:02 541973441 /usr/lib64/libX11.so.6.2.0 >2b0b1be87000-2b0b1be88000 r-xp 00104000 08:02 541973441 /usr/lib64/libX11.so.6.2.0 >2b0b1be88000-2b0b1be8d000 rwxp 00105000 08:02 541973441 /usr/lib64/libX11.so.6.2.0 >2b0b1be8d000-2b0b1be8e000 rwxp 00000000 00:00 0 >2b0b1be8e000-2b0b1be8f000 r-xp 00000000 08:02 1616184446 /usr/lib64/libxcb-xlib.so.0.0.0 >2b0b1be8f000-2b0b1c08f000 ---p 00001000 08:02 1616184446 /usr/lib64/libxcb-xlib.so.0.0.0 >2b0b1c08f000-2b0b1c090000 r-xp 00001000 08:02 1616184446 /usr/lib64/libxcb-xlib.so.0.0.0 >2b0b1c090000-2b0b1c091000 rwxp 00002000 08:02 1616184446 /usr/lib64/libxcb-xlib.so.0.0.0 >2b0b1c091000-2b0b1c0ad000 r-xp 00000000 08:02 1617194033 /usr/lib64/libxcb.so.1.0.0 >2b0b1c0ad000-2b0b1c2ad000 ---p 0001c000 08:02 1617194033 /usr/lib64/libxcb.so.1.0.0 >2b0b1c2ad000-2b0b1c2ae000 r-xp 0001c000 08:02 1617194033 /usr/lib64/libxcb.so.1.0.0 >2b0b1c2ae000-2b0b1c2af000 rwxp 0001d000 08:02 1617194033 /usr/lib64/libxcb.so.1.0.0 >2b0b1c2af000-2b0b1c2b1000 r-xp 00000000 08:02 47406511 /usr/lib64/libXau.so.6.0.0 >2b0b1c2b1000-2b0b1c4b0000 ---p 00002000 08:02 47406511 /usr/lib64/libXau.so.6.0.0 >2b0b1c4b0000-2b0b1c4b1000 r-xp 00001000 08:02 47406511 /usr/lib64/libXau.so.6.0.0 >2b0b1c4b1000-2b0b1c4b2000 rwxp 00002000 08:02 47406511 /usr/lib64/libXau.so.6.0.0 >2b0b1c4b2000-2b0b1c4b3000 rwxp 00000000 00:00 0 >2b0b1c4b3000-2b0b1c4b8000 r-xp 00000000 08:02 58278854 /usr/lib64/libXdmcp.so.6.0.0 >2b0b1c4b8000-2b0b1c6b7000 ---p 00005000 08:02 58278854 /usr/lib64/libXdmcp.so.6.0.0 >2b0b1c6b7000-2b0b1c6b8000 r-xp 00004000 08:02 58278854 /usr/lib64/libXdmcp.so.6.0.0 >2b0b1c6b8000-2b0b1c6b9000 rwxp 00005000 08:02 58278854 /usr/lib64/libXdmcp.so.6.0.0 >2b0b1c6b9000-2b0b1c6bb000 r-xp 00000000 08:02 547974348 /lib64/libdl-2.10.1.so >2b0b1c6bb000-2b0b1c8bb000 ---p 00002000 08:02 547974348 /lib64/libdl-2.10.1.so >2b0b1c8bb000-2b0b1c8bc000 r-xp 00002000 08:02 547974348 /lib64/libdl-2.10.1.so >2b0b1c8bc000-2b0b1c8bd000 rwxp 00003000 08:02 547974348 /lib64/libdl-2.10.1.so >2b0b1c8bd000-2b0b1c916000 r-xp 00000000 08:02 1610843022 /usr/lib64/blas/reference/libblas.so.0.0.0 >2b0b1c916000-2b0b1cb15000 ---p 00059000 08:02 1610843022 /usr/lib64/blas/reference/libblas.so.0.0.0 >2b0b1cb15000-2b0b1cb16000 r-xp 00058000 08:02 1610843022 /usr/lib64/blas/reference/libblas.so.0.0.0 >2b0b1cb16000-2b0b1cb17000 rwxp 00059000 08:02 1610843022 /usr/lib64/blas/reference/libblas.so.0.0.0 >2b0b1cb17000-2b0b1cb18000 rwxp 00000000 00:00 0 >2b0b1cb18000-2b0b1cf9b000 r-xp 00000000 08:02 543098431 /usr/lib64/lapack/reference/liblapack.so.0.0.0 >2b0b1cf9b000-2b0b1d19a000 ---p 00483000 08:02 543098431 /usr/lib64/lapack/reference/liblapack.so.0.0.0 >2b0b1d19a000-2b0b1d19b000 r-xp 00482000 08:02 543098431 /usr/lib64/lapack/reference/liblapack.so.0.0.0 >2b0b1d19b000-2b0b1d19f000 rwxp 00483000 08:02 543098431 /usr/lib64/lapack/reference/liblapack.so.0.0.0 >2b0b1d19f000-2b0b1d2ac000 rwxp 00000000 00:00 0 >2b0b1d2ac000-2b0b1d385000 r-xp 00000000 08:02 1087093722 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.3.4/libgfortran.so.3.0.0 >2b0b1d385000-2b0b1d585000 ---p 000d9000 08:02 1087093722 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.3.4/libgfortran.so.3.0.0 >2b0b1d585000-2b0b1d586000 r-xp 000d9000 08:02 1087093722 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.3.4/libgfortran.so.3.0.0 >2b0b1d586000-2b0b1d587000 rwxp 000da000 08:02 1087093722 /usr/lib64/gcc/x86_64-pc-linux-gnu/4.3.4/libgfortran.so.3.0.0 >2b0b1d587000-2b0b1d588000 rwxp 00000000 00:00 0 >2b0b1d588000-2b0b1d60a000 r-xp 00000000 08:02 547974342 /lib64/libm-2.10.1.so >2b0b1d60a000-2b0b1d809000 ---p 00082000 08:02 547974342 /lib64/libm-2.10.1.so >2b0b1d809000-2b0b1d80a000 r-xp 00081000 08:02 547974342 /lib64/libm-2.10.1.so >2b0b1d80a000-2b0b1d80b000 rwxp 00082000 08:02 547974342 /lib64/libm-2.10.1.so >2b0b1d80b000-2b0b1d80c000 rwxp 00000000 00:00 0 >2b0b1d80c000-2b0b1d892000 r-xp 00000000 08:02 542101648 /usr/lib64/libmpi.so.0.0.0 >2b0b1d892000-2b0b1da92000 ---p 00086000 08:02 542101648 /usr/lib64/libmpi.so.0.0.0 >2b0b1da92000-2b0b1da93000 r-xp 00086000 08:02 542101648 /usr/lib64/libmpi.so.0.0.0 >2b0b1da93000-2b0b1da9c000 rwxp 00087000 08:02 542101648 /usr/lib64/libmpi.so.0.0.0 >2b0b1da9c000-2b0b1daa3000 rwxp 00000000 00:00 0 >2b0b1daa3000-2b0b1dafd000 r-xp 00000000 08:02 542083902 /usr/lib64/libopen-rte.so.0.0.0 >2b0b1dafd000-2b0b1dcfd000 ---p 0005a000 08:02 542083902 /usr/lib64/libopen-rte.so.0.0.0 >2b0b1dcfd000-2b0b1dcfe000 r-xp 0005a000 08:02 542083902 /usr/lib64/libopen-rte.so.0.0.0 >2b0b1dcfe000-2b0b1dd00000 rwxp 0005b000 08:02 542083902 /usr/lib64/libopen-rte.so.0.0.0 >2b0b1dd00000-2b0b1dd01000 rwxp 00000000 00:00 0 >2b0b1dd01000-2b0b1dd3e000 r-xp 00000000 08:02 542116192 /usr/lib64/libopen-pal.so.0.0.0 >2b0b1dd3e000-2b0b1df3d000 ---p 0003d000 08:02 542116192 /usr/lib64/libopen-pal.so.0.0.0 >2b0b1df3d000-2b0b1df3e000 r-xp 0003c000 08:02 542116192 /usr/lib64/libopen-pal.so.0.0.0 >2b0b1df3e000-2b0b1df40000 rwxp 0003d000 08:02 542116192 /usr/lib64/libopen-pal.so.0.0.0 >2b0b1df40000-2b0b1df63000 rwxp 00000000 00:00 0 >2b0b1df63000-2b0b1df65000 r-xp 00000000 08:02 548029226 /lib64/libutil-2.10.1.so >2b0b1df65000-2b0b1e164000 ---p 00002000 08:02 548029226 /lib64/libutil-2.10.1.so >2b0b1e164000-2b0b1e165000 r-xp 00001000 08:02 548029226 /lib64/libutil-2.10.1.so >2b0b1e165000-2b0b1e166000 rwxp 00002000 08:02 548029226 /lib64/libutil-2.10.1.so >2b0b1e166000-2b0b1e17d000 r-xp 00000000 08:02 547974377 /lib64/libpthread-2.10.1.so >2b0b1e17d000-2b0b1e37c000 ---p 00017000 08:02 547974377 /lib64/libpthread-2.10.1.so >2b0b1e37c000-2b0b1e37d000 r-xp 00016000 08:02 547974377 /lib64/libpthread-2.10.1.so >2b0b1e37d000-2b0b1e37e000 rwxp 00017000 08:02 547974377 /lib64/libpthread-2.10.1.so >2b0b1e37e000-2b0b1e382000 rwxp 00000000 00:00 0 >2b0b1e382000-2b0b1e4d1000 r-xp 00000000 08:02 548029228 /lib64/libc-2.10.1.so >2b0b1e4d1000-2b0b1e6d1000 ---p 0014f000 08:02 548029228 /lib64/libc-2.10.1.so >2b0b1e6d1000-2b0b1e6d5000 r-xp 0014f000 08:02 548029228 /lib64/libc-2.10.1.so >2b0b1e6d5000-2b0b1e6d6000 rwxp 00153000 08:02 548029228 /lib64/libc-2.10.1.so >2b0b1e6d6000-2b0b1e6dc000 rwxp 00000000 00:00 0 >2b0b1e6dc000-2b0b1e6f2000 r-xp 00000000 08:02 67761232 /lib64/libgcc_s.so.1 >2b0b1e6f2000-2b0b1e8f1000 ---p 00016000 08:02 67761232 /lib64/libgcc_s.so.1 >2b0b1e8f1000-2b0b1e8f2000 r-xp 00015000 08:02 67761232 /lib64/libgcc_s.so.1 >2b0b1e8f2000-2b0b1e8f3000 rwxp 00016000 08:02 67761232 /lib64/libgcc_s.so.1 >2b0b1e8f3000-2b0b1e8f6000 rwxp 00000000 00:00 0 >7fffda500000-7fffda516000 rwxp 00000000 00:00 0 [stack] >7fffda576000-7fffda577000 r-xp 00000000 00:00 0 [vdso] >ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall] >Aborted
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