[gmx-users] Memory allocation - xpm2ps
Maurício Menegatti Rigo
mauriciomr1985 at gmail.com
Fri Oct 15 23:03:06 CEST 2010
Hi,
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.
Any ideas?
PS: I run the same job in another i7, but with gromacs version 4.0.7
installed, and everything occured well.
2010/10/15 Justin A. Lemkul <jalemkul at vt.edu>
>
>
> 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 <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>>
>>
>>
>>
>> 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
>>
>> ========================================
>> -- gmx-users mailing list gmx-users at gromacs.org
>> <mailto:gmx-users at gromacs.org>
>>
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>>
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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
>
> ========================================
> --
> gmx-users mailing list gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
--
Maurício Menegatti Rigo
Núcleo de Bioinformática do Laboratório de Imunogenética
Departamento de Genética
Instituto de Biociências
Universidade Federal do Rio Grande do Sul - Campus do Vale
Av. Bento Gonçalves, 9500 - Bairro Agronomia - Prédio 43323 M
CEP:91501-970 Caixa Postal 15053
Porto Alegre, RS, Brasil
Tel: +55 51 3308 9938
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