[gmx-users] Memory allocation - xpm2ps

[Justin A. Lemkul]

Maurício Menegatti Rigo wrote:
> Hi, 
> 
> I found the following error when I tried to run xpm2ps.
> 
> 
> *** glibc detected *** xpm2ps: realloc(): invalid pointer: 
> 0x0000000000dd0541 ***
> ======= Backtrace: =========
> /lib/libc.so.6[0x7f20a53b0dd6]
> /lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]
> xpm2ps(save_realloc+0x5e)[0x43741e]
> xpm2ps[0x42cf24]
> xpm2ps(read_xpm_entry+0x2fe)[0x42d88e]
> xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2]
> xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000]
> /lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd]
> xpm2ps[0x412949]
> ======= Memory map: ========
> 00400000-005e3000 r-xp 00000000 fc:03 7799252                           
>  /usr/local/gromacs/bin/xpm2ps
> 007e2000-007e3000 r-xp 001e2000 fc:03 7799252                           
>  /usr/local/gromacs/bin/xpm2ps
> 007e3000-007e9000 rwxp 001e3000 fc:03 7799252                           
>  /usr/local/gromacs/bin/xpm2ps
> 007e9000-007ea000 rwxp 00000000 00:00 0 
> 00dce000-00def000 rwxp 00000000 00:00 0                                 
>  [heap]
> 7f20a5124000-7f20a513a000 r-xp 00000000 fc:03 17400029                   
> /lib/libgcc_s.so.1
> 7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029                   
> /lib/libgcc_s.so.1
> 7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029                   
> /lib/libgcc_s.so.1
> 7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029                   
> /lib/libgcc_s.so.1
> 7f20a533b000-7f20a54a1000 r-xp 00000000 fc:03 17400032                   
> /lib/libc-2.10.1.so <http://libc-2.10.1.so>
> 7f20a54a1000-7f20a56a0000 ---p 00166000 fc:03 17400032                   
> /lib/libc-2.10.1.so <http://libc-2.10.1.so>
> 7f20a56a0000-7f20a56a4000 r-xp 00165000 fc:03 17400032                   
> /lib/libc-2.10.1.so <http://libc-2.10.1.so>
> 7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032                   
> /lib/libc-2.10.1.so <http://libc-2.10.1.so>
> 7f20a56a5000-7f20a56aa000 rwxp 00000000 00:00 0 
> 7f20a56aa000-7f20a56c1000 r-xp 00000000 fc:03 17400305                   
> /lib/libpthread-2.10.1.so <http://libpthread-2.10.1.so>
> 7f20a56c1000-7f20a58c0000 ---p 00017000 fc:03 17400305                   
> /lib/libpthread-2.10.1.so <http://libpthread-2.10.1.so>
> 7f20a58c0000-7f20a58c1000 r-xp 00016000 fc:03 17400305                   
> /lib/libpthread-2.10.1.so <http://libpthread-2.10.1.so>
> 7f20a58c1000-7f20a58c2000 rwxp 00017000 fc:03 17400305                   
> /lib/libpthread-2.10.1.so <http://libpthread-2.10.1.so>
> 7f20a58c2000-7f20a58c6000 rwxp 00000000 00:00 0 
> 7f20a58c6000-7f20a58c8000 r-xp 00000000 fc:03 17401201                   
> /lib/libutil-2.10.1.so <http://libutil-2.10.1.so>
> 7f20a58c8000-7f20a5ac7000 ---p 00002000 fc:03 17401201                   
> /lib/libutil-2.10.1.so <http://libutil-2.10.1.so>
> 7f20a5ac7000-7f20a5ac8000 r-xp 00001000 fc:03 17401201                   
> /lib/libutil-2.10.1.so <http://libutil-2.10.1.so>
> 7f20a5ac8000-7f20a5ac9000 rwxp 00002000 fc:03 17401201                   
> /lib/libutil-2.10.1.so <http://libutil-2.10.1.so>
> 7f20a5ac9000-7f20a5acb000 r-xp 00000000 fc:03 17400035                   
> /lib/libdl-2.10.1.so <http://libdl-2.10.1.so>
> 7f20a5acb000-7f20a5ccb000 ---p 00002000 fc:03 17400035                   
> /lib/libdl-2.10.1.so <http://libdl-2.10.1.so>
> 7f20a5ccb000-7f20a5ccc000 r-xp 00002000 fc:03 17400035                   
> /lib/libdl-2.10.1.so <http://libdl-2.10.1.so>
> 7f20a5ccc000-7f20a5ccd000 rwxp 00003000 fc:03 17400035                   
> /lib/libdl-2.10.1.so <http://libdl-2.10.1.so>
> 7f20a5ccd000-7f20a5d1b000 r-xp 00000000 fc:03 7921041                   
>  /usr/local/lib/libopen-pal.so.0.0.0
> 7f20a5d1b000-7f20a5f1b000 ---p 0004e000 fc:03 7921041                   
>  /usr/local/lib/libopen-pal.so.0.0.0
> 7f20a5f1b000-7f20a5f1c000 r-xp 0004e000 fc:03 7921041                   
>  /usr/local/lib/libopen-pal.so.0.0.0
> 7f20a5f1c000-7f20a5f1e000 rwxp 0004f000 fc:03 7921041                   
>  /usr/local/lib/libopen-pal.so.0.0.0
> 7f20a5f1e000-7f20a5f41000 rwxp 00000000 00:00 0 
> 7f20a5f41000-7f20a5f89000 r-xp 00000000 fc:03 7921099                   
>  /usr/local/lib/libopen-rte.so.0.0.0
> Aborted
> 
> 
> I note that someone already had the same problem. Could someone tell me 
> if this was fixed? 
> 

There have been several fixes to xpm2ps that are available in the development 
code.  Try the latest git version to see if you still have the same problem.

-Justin

> I'm using the gromacs version 4.5.1, in an i7 processor.
> 
> Thanks in advance,
> 
> --
> Maurício M. Rigo
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================