<div>Hi, </div><div><br></div><div>I copy the file gmx_xpm2ps from the repository to my gromacs folder /usl/local/gromacs/src/tools (i.e. I substitute the old file by the new one). After that, I run xpm2ps and the problem persisted. </div>
<div><br></div><div>Any ideas? </div><div><br></div><div>PS: I run the same job in another i7, but with gromacs version 4.0.7 installed, and everything occured well. </div><br><br><div class="gmail_quote">2010/10/15 Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
<br>
Maurício Menegatti Rigo wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hi,<br>
<br><div class="im">
Thank you for your answer. Unfortunately, I can't fix my problem. <br></div>
I dont know if I'm doing this right, but first I type the line "/git clone git://<a href="http://git.gromacs.org/gromacs.git" target="_blank">git.gromacs.org/gromacs.git</a> <<a href="http://git.gromacs.org/gromacs.git" target="_blank">http://git.gromacs.org/gromacs.git</a>>/" in the command line. After all the outputs, I tried to run xpm2ps again, but occured the same error. <br>
</blockquote>
<br>
Simply downloading the source code won't fix the problem. You have to install (and then use) the resulting binaries.<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
<br>
2010/10/15 Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>><div><div></div><div class="h5">
<br>
<br>
<br>
<br>
Maurício Menegatti Rigo wrote:<br>
<br>
Hi,<br>
I found the following error when I tried to run xpm2ps.<br>
<br>
<br>
*** glibc detected *** xpm2ps: realloc(): invalid pointer:<br>
0x0000000000dd0541 ***<br>
======= Backtrace: =========<br>
/lib/libc.so.6[0x7f20a53b0dd6]<br>
/lib/libc.so.6(realloc+0x2e1)[0x7f20a53b67e1]<br>
xpm2ps(save_realloc+0x5e)[0x43741e]<br>
xpm2ps[0x42cf24]<br>
xpm2ps(read_xpm_entry+0x2fe)[0x42d88e]<br>
xpm2ps(read_xpm_matrix+0xb2)[0x42eaf2]<br>
xpm2ps(gmx_xpm2ps+0x7a0)[0x41d000]<br>
/lib/libc.so.6(__libc_start_main+0xfd)[0x7f20a5359abd]<br>
xpm2ps[0x412949]<br>
======= Memory map: ========<br>
00400000-005e3000 r-xp 00000000 fc:03 7799252 /usr/local/gromacs/bin/xpm2ps<br>
007e2000-007e3000 r-xp 001e2000 fc:03 7799252 /usr/local/gromacs/bin/xpm2ps<br>
007e3000-007e9000 rwxp 001e3000 fc:03 7799252 /usr/local/gromacs/bin/xpm2ps<br>
007e9000-007ea000 rwxp 00000000 00:00 0 00dce000-00def000 rwxp<br>
00000000 00:00 0 [heap]<br>
7f20a5124000-7f20a513a000 r-xp 00000000 fc:03 17400029 /lib/libgcc_s.so.1<br>
7f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029 /lib/libgcc_s.so.1<br>
7f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029 /lib/libgcc_s.so.1<br>
7f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029 /lib/libgcc_s.so.1<br>
7f20a533b000-7f20a54a1000 r-xp 00000000 fc:03 17400032 /lib/<a href="http://libc-2.10.1.so" target="_blank">libc-2.10.1.so</a> <<a href="http://libc-2.10.1.so" target="_blank">http://libc-2.10.1.so</a>><br>
<<a href="http://libc-2.10.1.so" target="_blank">http://libc-2.10.1.so</a>><br>
7f20a54a1000-7f20a56a0000 ---p 00166000 fc:03 17400032 /lib/<a href="http://libc-2.10.1.so" target="_blank">libc-2.10.1.so</a> <<a href="http://libc-2.10.1.so" target="_blank">http://libc-2.10.1.so</a>><br>
<<a href="http://libc-2.10.1.so" target="_blank">http://libc-2.10.1.so</a>><br>
7f20a56a0000-7f20a56a4000 r-xp 00165000 fc:03 17400032 /lib/<a href="http://libc-2.10.1.so" target="_blank">libc-2.10.1.so</a> <<a href="http://libc-2.10.1.so" target="_blank">http://libc-2.10.1.so</a>><br>
<<a href="http://libc-2.10.1.so" target="_blank">http://libc-2.10.1.so</a>><br>
7f20a56a4000-7f20a56a5000 rwxp 00169000 fc:03 17400032 /lib/<a href="http://libc-2.10.1.so" target="_blank">libc-2.10.1.so</a> <<a href="http://libc-2.10.1.so" target="_blank">http://libc-2.10.1.so</a>><br>
<<a href="http://libc-2.10.1.so" target="_blank">http://libc-2.10.1.so</a>><br>
7f20a56a5000-7f20a56aa000 rwxp 00000000 00:00 0<br>
7f20a56aa000-7f20a56c1000 r-xp 00000000 fc:03 17400305 /lib/<a href="http://libpthread-2.10.1.so" target="_blank">libpthread-2.10.1.so</a> <<a href="http://libpthread-2.10.1.so" target="_blank">http://libpthread-2.10.1.so</a>><br>
<<a href="http://libpthread-2.10.1.so" target="_blank">http://libpthread-2.10.1.so</a>><br>
7f20a56c1000-7f20a58c0000 ---p 00017000 fc:03 17400305 /lib/<a href="http://libpthread-2.10.1.so" target="_blank">libpthread-2.10.1.so</a> <<a href="http://libpthread-2.10.1.so" target="_blank">http://libpthread-2.10.1.so</a>><br>
<<a href="http://libpthread-2.10.1.so" target="_blank">http://libpthread-2.10.1.so</a>><br>
7f20a58c0000-7f20a58c1000 r-xp 00016000 fc:03 17400305 /lib/<a href="http://libpthread-2.10.1.so" target="_blank">libpthread-2.10.1.so</a> <<a href="http://libpthread-2.10.1.so" target="_blank">http://libpthread-2.10.1.so</a>><br>
<<a href="http://libpthread-2.10.1.so" target="_blank">http://libpthread-2.10.1.so</a>><br>
7f20a58c1000-7f20a58c2000 rwxp 00017000 fc:03 17400305 /lib/<a href="http://libpthread-2.10.1.so" target="_blank">libpthread-2.10.1.so</a> <<a href="http://libpthread-2.10.1.so" target="_blank">http://libpthread-2.10.1.so</a>><br>
<<a href="http://libpthread-2.10.1.so" target="_blank">http://libpthread-2.10.1.so</a>><br>
7f20a58c2000-7f20a58c6000 rwxp 00000000 00:00 0<br>
7f20a58c6000-7f20a58c8000 r-xp 00000000 fc:03 17401201 /lib/<a href="http://libutil-2.10.1.so" target="_blank">libutil-2.10.1.so</a> <<a href="http://libutil-2.10.1.so" target="_blank">http://libutil-2.10.1.so</a>><br>
<<a href="http://libutil-2.10.1.so" target="_blank">http://libutil-2.10.1.so</a>><br>
7f20a58c8000-7f20a5ac7000 ---p 00002000 fc:03 17401201 /lib/<a href="http://libutil-2.10.1.so" target="_blank">libutil-2.10.1.so</a> <<a href="http://libutil-2.10.1.so" target="_blank">http://libutil-2.10.1.so</a>><br>
<<a href="http://libutil-2.10.1.so" target="_blank">http://libutil-2.10.1.so</a>><br>
7f20a5ac7000-7f20a5ac8000 r-xp 00001000 fc:03 17401201 /lib/<a href="http://libutil-2.10.1.so" target="_blank">libutil-2.10.1.so</a> <<a href="http://libutil-2.10.1.so" target="_blank">http://libutil-2.10.1.so</a>><br>
<<a href="http://libutil-2.10.1.so" target="_blank">http://libutil-2.10.1.so</a>><br>
7f20a5ac8000-7f20a5ac9000 rwxp 00002000 fc:03 17401201 /lib/<a href="http://libutil-2.10.1.so" target="_blank">libutil-2.10.1.so</a> <<a href="http://libutil-2.10.1.so" target="_blank">http://libutil-2.10.1.so</a>><br>
<<a href="http://libutil-2.10.1.so" target="_blank">http://libutil-2.10.1.so</a>><br>
7f20a5ac9000-7f20a5acb000 r-xp 00000000 fc:03 17400035 /lib/<a href="http://libdl-2.10.1.so" target="_blank">libdl-2.10.1.so</a> <<a href="http://libdl-2.10.1.so" target="_blank">http://libdl-2.10.1.so</a>><br>
<<a href="http://libdl-2.10.1.so" target="_blank">http://libdl-2.10.1.so</a>><br>
7f20a5acb000-7f20a5ccb000 ---p 00002000 fc:03 17400035 /lib/<a href="http://libdl-2.10.1.so" target="_blank">libdl-2.10.1.so</a> <<a href="http://libdl-2.10.1.so" target="_blank">http://libdl-2.10.1.so</a>><br>
<<a href="http://libdl-2.10.1.so" target="_blank">http://libdl-2.10.1.so</a>><br>
7f20a5ccb000-7f20a5ccc000 r-xp 00002000 fc:03 17400035 /lib/<a href="http://libdl-2.10.1.so" target="_blank">libdl-2.10.1.so</a> <<a href="http://libdl-2.10.1.so" target="_blank">http://libdl-2.10.1.so</a>><br>
<<a href="http://libdl-2.10.1.so" target="_blank">http://libdl-2.10.1.so</a>><br>
7f20a5ccc000-7f20a5ccd000 rwxp 00003000 fc:03 17400035 /lib/<a href="http://libdl-2.10.1.so" target="_blank">libdl-2.10.1.so</a> <<a href="http://libdl-2.10.1.so" target="_blank">http://libdl-2.10.1.so</a>><br>
<<a href="http://libdl-2.10.1.so" target="_blank">http://libdl-2.10.1.so</a>><br>
<br>
7f20a5ccd000-7f20a5d1b000 r-xp 00000000 fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0<br>
7f20a5d1b000-7f20a5f1b000 ---p 0004e000 fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0<br>
7f20a5f1b000-7f20a5f1c000 r-xp 0004e000 fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0<br>
7f20a5f1c000-7f20a5f1e000 rwxp 0004f000 fc:03 7921041 /usr/local/lib/libopen-pal.so.0.0.0<br>
7f20a5f1e000-7f20a5f41000 rwxp 00000000 00:00 0<br>
7f20a5f41000-7f20a5f89000 r-xp 00000000 fc:03 7921099 /usr/local/lib/libopen-rte.so.0.0.0<br>
Aborted<br>
<br>
<br>
I note that someone already had the same problem. Could someone<br>
tell me if this was fixed?<br>
<br>
<br>
There have been several fixes to xpm2ps that are available in the<br>
development code. Try the latest git version to see if you still<br>
have the same problem.<br>
<br>
-Justin<br>
<br>
<br>
I'm using the gromacs version 4.5.1, in an i7 processor.<br>
<br>
Thanks in advance,<br>
<br>
--<br>
Maurício M. Rigo<br>
<br>
<br>
-- ========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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<br>
<br>
-- <br>
Maurício Menegatti Rigo<br>
<br>
</div></blockquote><div><div></div><div class="h5">
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Maurício Menegatti Rigo<br>Núcleo de Bioinformática do Laboratório de Imunogenética<br>Departamento de Genética<br>Instituto de Biociências<br>Universidade Federal do Rio Grande do Sul - Campus do Vale<br>
Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M<br>CEP:91501-970 Caixa Postal 15053<br>Porto Alegre, RS, Brasil<br>Tel: +55 51 3308 9938<br>