Re: [gmx-users] Memory allocation - xpm2ps

Justin A. Lemkul Fri, 15 Oct 2010 14:12:00 -0700


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 newone). 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 ofGromacs to see any effect. Further, simply replacing a file likely will notwork 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 4.0.7installed, and everything occured well.

Yes, there was a bug introduced in version 4.5. Please either install the gitversion properly, use xpm2ps included in version 4.0.7, or wait for the releaseof version 4.5.2.


-Justin


2010/10/15 Justin A. Lemkul <jalem...@vt.edu <mailto:jalem...@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 <jalem...@vt.edu
        <mailto:jalem...@vt.edu> <mailto:jalem...@vt.edu
        <mailto:jalem...@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/xpm2ps007e2000-007e3000 r-xp 001e2000 fc:03 7799252/usr/local/gromacs/bin/xpm2ps007e3000-007e9000 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.17f20a513a000-7f20a5339000 ---p 00016000 fc:03 17400029/lib/libgcc_s.so.17f20a5339000-7f20a533a000 r-xp 00015000 fc:03 17400029/lib/libgcc_s.so.17f20a533a000-7f20a533b000 rwxp 00016000 fc:03 17400029/lib/libgcc_s.so.17f20a533b000-7f20a54a1000 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.0.0.07f20a5d1b000-7f20a5f1b000 ---p 0004e000 fc:03 7921041/usr/local/lib/libopen-pal.so.0.0.07f20a5f1b000-7f20a5f1c000 r-xp 0004e000 fc:03 7921041/usr/local/lib/libopen-pal.so.0.0.07f20a5f1c000-7f20a5f1e000 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

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

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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

========================================
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Re: [gmx-users] Memory allocation - xpm2ps

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