[gmx-users] topolbuild error

Zahra Ghanbari zahraghanbari10 at gmail.com
Thu Feb 19 14:29:36 CET 2015


hi
I installed topolbuild version 1.3. I used following command line:
./topolbuild -dir /home/supermicro/topolbuild1_3/dat/gromacs -ff oplsaa -n
OXL -r OXL -meas -rename -move
I encountered with following error:
*** Error in `./topolbuild': free(): invalid next size (fast):
0x0000000001b752a0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x80996)[0x7f9fa8024996]
./topolbuild[0x40701c]
./topolbuild[0x40b01e]
./topolbuild[0x403226]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf5)[0x7f9fa7fc5de5]
./topolbuild[0x401059]
======= Memory map: ========
00400000-0042c000 r-xp 00000000 08:01 25430000
/home/supermicro/topolbuild1_3/src/topolbuild
0062b000-0062c000 r--p 0002b000 08:01 25430000
/home/supermicro/topolbuild1_3/src/topolbuild
0062c000-0062d000 rw-p 0002c000 08:01 25430000
/home/supermicro/topolbuild1_3/src/topolbuild
0062d000-0062e000 rw-p 00000000 00:00 0
01b74000-01b95000 rw-p 00000000 00:00 0
[heap]
7f9fa7d8e000-7f9fa7da3000 r-xp 00000000 08:01 58458205
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f9fa7da3000-7f9fa7fa2000 ---p 00015000 08:01 58458205
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f9fa7fa2000-7f9fa7fa3000 r--p 00014000 08:01 58458205
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f9fa7fa3000-7f9fa7fa4000 rw-p 00015000 08:01 58458205
/lib/x86_64-linux-gnu/libgcc_s.so.1
7f9fa7fa4000-7f9fa8161000 r-xp 00000000 08:01 58461967
/lib/x86_64-linux-gnu/libc-2.17.so
7f9fa8161000-7f9fa8361000 ---p 001bd000 08:01 58461967
/lib/x86_64-linux-gnu/libc-2.17.so
7f9fa8361000-7f9fa8365000 r--p 001bd000 08:01 58461967
/lib/x86_64-linux-gnu/libc-2.17.so
7f9fa8365000-7f9fa8367000 rw-p 001c1000 08:01 58461967
/lib/x86_64-linux-gnu/libc-2.17.so
7f9fa8367000-7f9fa836c000 rw-p 00000000 00:00 0
7f9fa836c000-7f9fa846f000 r-xp 00000000 08:01 58462018
/lib/x86_64-linux-gnu/libm-2.17.so
7f9fa846f000-7f9fa866e000 ---p 00103000 08:01 58462018
/lib/x86_64-linux-gnu/libm-2.17.so
7f9fa866e000-7f9fa866f000 r--p 00102000 08:01 58462018
/lib/x86_64-linux-gnu/libm-2.17.so
7f9fa866f000-7f9fa8670000 rw-p 00103000 08:01 58462018
/lib/x86_64-linux-gnu/libm-2.17.so
7f9fa8670000-7f9fa8693000 r-xp 00000000 08:01 58461943
/lib/x86_64-linux-gnu/ld-2.17.so
7f9fa8874000-7f9fa8877000 rw-p 00000000 00:00 0
7f9fa888e000-7f9fa8892000 rw-p 00000000 00:00 0
7f9fa8892000-7f9fa8893000 r--p 00022000 08:01 58461943
/lib/x86_64-linux-gnu/ld-2.17.so
7f9fa8893000-7f9fa8895000 rw-p 00023000 08:01 58461943
/lib/x86_64-linux-gnu/ld-2.17.so
7fffd7450000-7fffd7471000 rw-p 00000000 00:00 0
[stack]
7fffd749a000-7fffd749c000 r-xp 00000000 00:00 0
[vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
[vsyscall]
Aborted (core dumped)
how to resolve this problem?
any help will highly appreciated.


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