[gmx-users] Memory allocation - xpm2ps
Shi, Chuanyin
cshi at ou.edu
Wed Mar 16 23:36:46 CET 2011
Ye, I just installed the 4.5.3 and the problem is gone.
I was using the 4.5.1 before.
Chuanyin Shi
Department of Chemistry & Biochemistry
University of Oklahoma
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
Sent: Wednesday, March 16, 2011 4:20 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] Memory allocation - xpm2ps
Shi, Chuanyin wrote:
> Too bad, I am having this problem with 4.5 now.
Version 4.5 contains the bug referenced below and was only fixed as of 4.5.2, so
make sure you're using the newest version (4.5.3) when reporting problems. In
general, fixing problems in old versions is not a high priority, especially if
they may already be fixed in an official release.
> The xpm file with larger size will counter this problem while smaller ones are fine.
> Never had any problem with previous version.
>
Depending on the amount of memory available on your machine, this could be a
Gromacs problem, a hardware problem, or a combination of both. Please test the
latest version of Gromacs (4.5.3) and report back with some diagnostic
information (i.e., size of the files that do and don't work, hardware, available
memory, etc).
-Justin
>
> Chuanyin Shi
> Department of Chemistry & Biochemistry
> University of Oklahoma
>
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Friday, October 15, 2010 4:10 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] Memory allocation - xpm2ps
>
> Maurício Menegatti Rigo wrote:
>> 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?
>>
>
> As I said before, you have to actually re-compile and install the git version of
> Gromacs to see any effect. Further, simply replacing a file likely will not
> work due to a multitude of code changes that have taken place in other source files.
>
>> PS: I run the same job in another i7, but with gromacs version 4.0.7
>> installed, and everything occured well.
>>
>
> Yes, there was a bug introduced in version 4.5. Please either install the git
> version properly, use xpm2ps included in version 4.0.7, or wait for the release
> of version 4.5.2.
>
> -Justin
>
>> 2010/10/15 Justin A. Lemkul <jalemkul at vt.edu <mailto: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>
>> <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> <mailto: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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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>
>> <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> <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 <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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>>
>>
>>
>> --
>> 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
>>
>
> --
> ========================================
>
> 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
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--
========================================
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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