[gmx-users] g_membed *** glibc detected ***
Ricardo
rsoares at fcfrp.usp.br
Wed Dec 19 19:21:53 CET 2012
Dear GMX-Users,
I've been using g_membed for a while now, and recently I faced this ***
glibc detected *** error for a particular system.
Being a memory allocation issue, does anyone know something more about it?
Here's the command line:
g_membed -f system_02.tpr -p topol.top -xyinit 0.1 -xyend 1.0 -nxy 1000
-n index.ndx
- The mdp file is basically the same I always use;
- This happens when I'm trying to insert two monomers from the scratch
(using the -pieces flag) or a monomer along an already inserted (and
frozen) one;
- Inserting only one monomer in the system (in the absence of the other)
presents no problems.
Thanks,
Error:
--------------------------------------------
.
.
.
Will remove 2 POPC molecules
Will remove 122 SOL molecules
Will remove 1 NA molecules
Will remove 0 CL molecules
Back Off! I just backed up temp.top to ./#temp.top.2#
*** glibc detected *** g_membed: malloc(): memory corruption:
0x00000000021aa690 ***
======= Backtrace: =========
/lib/libc.so.6(+0x776d6)[0x7f47b99f66d6]
/lib/libc.so.6(+0x7b77f)[0x7f47b99fa77f]
/lib/libc.so.6(__libc_malloc+0x6e)[0x7f47b99fb5ae]
/lib/libc.so.6(+0x685cb)[0x7f47b99e75cb]
/home/john/gromacs455/lib/libgmx.so.6(gmx_fexist+0x15)[0x7f47ba62f185]
/home/john/gromacs455/lib/libgmx.so.6(make_backup+0x2a)[0x7f47ba62f87a]
/home/john/gromacs455/lib/libgmx.so.6(ffopen+0x24d)[0x7f47ba63017d]
/home/john/gromacs455/lib/libgmxana.so.6(top_update+0x469)[0x7f47bb4477c9]
/home/john/gromacs455/lib/libgmxana.so.6(mdrunner_membed+0x2c15)[0x7f47bb455225]
/home/john/gromacs455/lib/libgmxana.so.6(gmx_membed+0x1840)[0x7f47bb456c60]
g_membed[0x400679]
/lib/libc.so.6(__libc_start_main+0xfe)[0x7f47b999dd8e]
g_membed[0x4005a9]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:01 22416383
/home/john/gromacs455/bin/g_membed
00600000-00601000 r--p 00000000 08:01 22416383
/home/john/gromacs455/bin/g_membed
00601000-00602000 rw-p 00001000 08:01 22416383
/home/john/gromacs455/bin/g_membed
01fd2000-021cc000 rw-p 00000000 00:00 0
[heap]
7f47b0000000-7f47b0021000 rw-p 00000000 00:00 0
7f47b0021000-7f47b4000000 ---p 00000000 00:00 0
7f47b6990000-7f47b6c62000 rw-p 00000000 00:00 0
7f47b6c62000-7f47b71ca000 rw-p 00000000 00:00 0
7f47b7459000-7f47b79c1000 rw-p 00000000 00:00 0
7f47b7aea000-7f47b7dbc000 rw-p 00000000 00:00 0
7f47b7dbc000-7f47b7faf000 rw-p 00000000 00:00 0
7f47b7faf000-7f47b8874000 rw-p 00000000 00:00 0
7f47b88d7000-7f47b8ac3000 rw-p 00000000 00:00 0
7f47b8acb000-7f47b8cbe000 rw-p 00000000 00:00 0
7f47b8d2f000-7f47b8da9000 rw-p 00000000 00:00 0
7f47b8da9000-7f47b8f9c000 rw-p 00000000 00:00 0
7f47b9088000-7f47b93a5000 rw-p 00000000 00:00 0
7f47b9768000-7f47b977d000 r-xp 00000000 08:01 8912975
/lib/libgcc_s.so.1
7f47b977d000-7f47b997c000 ---p 00015000 08:01 8912975
/lib/libgcc_s.so.1
7f47b997c000-7f47b997d000 r--p 00014000 08:01 8912975
/lib/libgcc_s.so.1
7f47b997d000-7f47b997e000 rw-p 00015000 08:01 8912975
/lib/libgcc_s.so.1
7f47b997e000-7f47b997f000 rw-p 00000000 00:00 0
7f47b997f000-7f47b9af9000 r-xp 00000000 08:01 8912982
/lib/libc-2.12.1.so
7f47b9af9000-7f47b9cf9000 ---p 0017a000 08:01 8912982
/lib/libc-2.12.1.so
7f47b9cf9000-7f47b9cfd000 r--p 0017a000 08:01 8912982
/lib/libc-2.12.1.so
7f47b9cfd000-7f47b9cfe000 rw-p 0017e000 08:01 8912982
/lib/libc-2.12.1.so
7f47b9cfe000-7f47b9d03000 rw-p 00000000 00:00 0
7f47b9d03000-7f47b9d1b000 r-xp 00000000 08:01 8913146
/lib/libpthread-2.12.1.so
7f47b9d1b000-7f47b9f1a000 ---p 00018000 08:01 8913146
/lib/libpthread-2.12.1.so
7f47b9f1a000-7f47b9f1b000 r--p 00017000 08:01 8913146
/lib/libpthread-2.12.1.so
7f47b9f1b000-7f47b9f1c000 rw-p 00018000 08:01 8913146
/lib/libpthread-2.12.1.so
7f47b9f1c000-7f47b9f20000 rw-p 00000000 00:00 0
7f47b9f20000-7f47b9fa2000 r-xp 00000000 08:01 8913136
/lib/libm-2.12.1.so
7f47b9fa2000-7f47ba1a1000 ---p 00082000 08:01 8913136
/lib/libm-2.12.1.so
7f47ba1a1000-7f47ba1a2000 r--p 00081000 08:01 8913136
/lib/libm-2.12.1.so
7f47ba1a2000-7f47ba1a3000 rw-p 00082000 08:01 8913136
/lib/libm-2.12.1.so
7f47ba1a3000-7f47ba1ba000 r-xp 00000000 08:01 8913138
/lib/libnsl-2.12.1.so
7f47ba1ba000-7f47ba3b9000 ---p 00017000 08:01 8913138
/lib/libnsl-2.12.1.so
7f47ba3b9000-7f47ba3ba000 r--p 00016000 08:01 8913138
/lib/libnsl-2.12.1.so
7f47ba3ba000-7f47ba3bb000 rw-p 00017000 08:01 8913138
/lib/libnsl-2.12.1.so
7f47ba3bb000-7f47ba3bd000 rw-p 00000000 00:00 0
7f47ba3bd000-7f47ba3bf000 r-xp 00000000 08:01 8913135
/lib/libdl-2.12.1.so
7f47ba3bf000-7f47ba5bf000 ---p 00002000 08:01 8913135
/lib/libdl-2.12.1.so
7f47ba5bf000-7f47ba5c0000 r--p 00002000 08:01 8913135
/lib/libdl-2.12.1.so
7f47ba5c0000-7f47ba5c1000 rw-p 00003000 08:01 8913135
/lib/libdl-2.12.1.so
7f47ba5c1000-7f47ba973000 r-xp 00000000 08:01 22416273
/home/john/gromacs455/lib/libgmx.so.6.0.0
7f47ba973000-7f47bab72000 ---p 003b2000 08:01 22416273
/home/john/gromacs455/lib/libgmx.so.6.0.0
7f47bab72000-7f47bab78000 r--p 003b1000 08:01 22416273
/home/john/gromacs455/lib/libgmx.so.6.0.0
7f47bab78000-7f47bab83000 rw-p 003b7000 08:01 22416273
/home/john/gromacs455/lib/libgmx.so.6.0.0
7f47bab83000-7f47bab84000 rw-p 00000000 00:00 0
7f47bab84000-7f47bacee000 r-xp 00000000 08:01 22415922
/home/john/gromacs455/lib/libfftw3f.so.3.2.4
7f47bacee000-7f47baeee000 ---p 0016a000 08:01 22415922
/home/john/gromacs455/lib/libfftw3f.so.3.2.4
7f47baeee000-7f47baefa000 r--p 0016a000 08:01 22415922
/home/john/gromacs455/lib/libfftw3f.so.3.2.4
7f47baefa000-7f47baefb000 rw-p 00176000 08:01 22415922
/home/john/gromacs455/lib/libfftw3f.so.3.2.4
7f47baefb000-7f47bb073000 r-xp 00000000 08:01 22416279
/home/john/gromacs455/lib/libmd.so.6.0.0
7f47bb073000-7f47bb272000 ---p 00178000 08:01 22416279
/home/john/gromacs455/lib/libmd.so.6.0.0
7f47bb272000-7f47bb273000 r--p 00177000 08:01 22416279
/home/john/gromacs455/lib/libmd.so.6.0.0
7f47bb273000-7f47bb275000 rw-p 00178000 08:01 22416279
/home/john/gromacs455/lib/libmd.so.6.0.0
7f47bb275000-7f47bb4b8000 r-xp 00000000 08:01 22416300
/home/john/gromacs455/lib/libgmxana.so.6.0.0
7f47bb4b8000-7f47bb6b7000 ---p 00243000 08:01 22416300
/home/john/gromacs455/lib/libgmxana.so.6.0.0
7f47bb6b7000-7f47bb6bc000 r--p 00242000 08:01 22416300
/home/john/gromacs455/lib/libgmxana.so.6.0.0
7f47bb6bc000-7f47bb6c0000 rw-p 00247000 08:01 22416300
/home/john/gromacs455/lib/libgmxana.so.6.0.0
7f47bb6c0000-7f47bb6c1000 rw-p 00000000 00:00 0
7f47bb6c1000-7f47bb6e1000 r-xp 00000000 08:01 8912899
/lib/ld-2.12.1.so
7f47bb70d000-7f47bb74a000 rw-p 00000000 00:00 0
7f47bb74a000-7f47bb8ca000 rw-p 00000000 00:00 0
7f47bb8ca000-7f47bb8cf000 rw-p 00000000 00:00 0 Aborted
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