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Questions and answers => General discussions (Q&As) => Topic started by: Asmita on February 28, 2013, 01:52:23 pm

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Title: dependency on GLIBC_2.14
Post by: Asmita on February 28, 2013, 01:52:23 pm
Dear Dr Xu,

  I am a Linux Debian user and have recently downloaded the latest x3dna-v2.1. when running the executables, i am getting this message :

"mutate_bases: /lib/libc.so.6: version `GLIBC_2.14' not found (required by mutate_bases)"

Now current debian distribution has 2.11 version, and there is no hope that future debian distributions will go for higher glibc versions.

Is it possible to run x3dna programs with this older version of glibc??

Thanks

Asmita
Title: Re: dependency on GLIBC_2.14
Post by: xiangjun on February 28, 2013, 02:13:07 pm
Hi Asmita,

Thanks for reporting the problem of running 3DNA v2.1 on Debian. What are your specific Debian settings? What's the output of running "uname -a"? I will look into the issue soon, and your feedback helps in solving the problem.

Xiang-Jun
Title: Re: dependency on GLIBC_2.14
Post by: Asmita on March 01, 2013, 03:00:29 am
Thanks for the response Dr Xu.

output of uname -a :

"Linux hostname 2.6.32-5-amd64 #1 SMP Fri Feb 15 15:39:52 UTC 2013 x86_64 GNU/Linux"

and of lsb_release -a :

Distributor ID: Debian
Description:    Debian GNU/Linux 6.0.7 (squeeze)
Release:        6.0.7
Codename:       squeeze

Asmita


Title: Re: dependency on GLIBC_2.14
Post by: xiangjun on March 01, 2013, 10:29:50 am
Hi Asmita,

Thanks for your feedback. Now I have access to a Debian 6 (x86_64) machine from SBGrid (http://www.sbgrid.org), and did the followings:

~ [501] lsb_release -a
No LSB modules are available.
Distributor ID:   Debian
Description:   Debian GNU/Linux 6.0.6 (squeeze)
Release:   6.0.6
Codename:   squeeze

~ [502] uname -a
Linux sbgrid-dev-vm-17 2.6.32-5-amd64 #1 SMP Sun Sep 23 10:07:46 UTC 2012 x86_64 GNU/Linux

~ [503] ldd --version
ldd (Debian EGLIBC 2.11.3-4) 2.11.3
Copyright (C) 2009 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

bin [514] ./mutate_bases
===========================================================================
NAME
        mutate_bases -- mutate bases, with backbone conformation unchanged
SYNOPSIS
        mutate_bases [OPTIONS] mutinfo pdbfile outfile
DESCRIPTION
        perform in silico base mutations of 3-dimensional nucleic acid
        structures, with two key and unique features: (1) the sugar-
        phosphate backbone conformation is untouched; (2) the base
        reference frame (position and orientation) is reserved, i.e.,
        the mutated structure shares the same base-pair/step
        parameters as the original one.
  ......
AUTHOR
        3DNA v2.1 (c) 2013 Dr. Xiang-Jun Lu (xiangjun@x3dna.org; http://x3dna.org)
===========================================================================

As shown above, the latest 3DNA v2.1 (2013feb22) is working properly on Debian 6.

Recent 3DNA v2.1 Linux 64-bit releases have been compiled on CentOS 5 (x86_64), which has "ldd (GNU libc) 2.5". Moreover, I have just verified that the latest 2013feb22  x86_64 version works on the following settings:

Unless I am missing something obvious, you must have been using a previous release of 3DNA v2.1 which was compiled on Ubuntu 12.04. Install the 2013feb22 release of 3DNA v2.1 and report back if that helps.

Does anyone else have such problem with the Linux 64 bit version of 3DNA v2.1 (2013feb22)?

Xiang-Jun
Title: Re: dependency on GLIBC_2.14
Post by: Asmita on March 01, 2013, 01:28:15 pm
This version is working perfectly.....and yes,  i was using a dec2012 version previously...

Thanks for the help Dr Xu...


Asmita

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.