[gmx-users] topolbuild error

[Ray, Bruce D]

On Feb 19, 2015, at 9:49 AM, Zahra Ghanbari, <zahraghanbari10 at gmail.com>
wrote:

> 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.
> 

This looks like a compilation problem.  The error message is not a topolbuild
error.  From what is shown, I cannot tell from where the call to free() was made
and cannot give further help until that can be determined.


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202



-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202