Maurício Menegatti Rigo wrote:
Hi,
Thank you for your answer. Unfortunately, I can't fix my problem.
I dont know if I'm doing this right, but first I type the line "/git
clone git://git.gromacs.org/gromacs.git
<http://git.gromacs.org/gromacs.git>/" in the command line. After all
the outputs, I tried to run xpm2ps again, but occured the same error.
Simply downloading the source code won't fix the problem. You have to install
(and then use) the resulting binaries.
-Justin
2010/10/15 Justin A. Lemkul <[email protected] <mailto:[email protected]>>
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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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>
<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 <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Maurício Menegatti 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
========================================
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