[phenixbb] Unable to install phenix 1.8.1-1168 on Scientific Linux 6.3 64 bits

[Kay Diederichs]

Davi,

This looks to me like you tried installation using e.g. the fc14 
installer (that has a glibc "too new" for SL6), and installed with the 
fc3 on top of that (SL6 works well with the fc13 or lower installer).

Since the installers write to the same directory, the fc3 installer 
finds that the files are already there and does basically nothing that 
would fix the problem, i.e. replace the binaries and libs.

So just remove the /usr/local/phenix-1.8.1-1168 directory (or its 
contents) before you try a different installer.

(Side note: maybe the installer should do that automatically, but there 
are probably reasons why it doesn't)

HTH,

Kay

On 01/29/2013 12:31 AM, phenixbb-request at phenix-online.org wrote:
> Message: 5
> Date: Fri, 25 Jan 2013 16:15:01 -0800
> From: Davi de Miranda Fonseca<davi.fonseca at ntnu.no>
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] Unable to install phenix 1.8.1-1168 on Scientific
> 	Linux	6.3 64 bits
> Message-ID:<51032005.9040800 at ntnu.no>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear all,
>
> I am unable to install phenix 1.8.1-1168 on Scientific Linux 6.3 64
> bits. Hence, I would greatly appreciate any 2 cents (or diamonds).
>
> I installed Scientific Linux 6.3 64 bits, updated everything and
> installed a couple of things that I think would be necessary. Then I
> uncompressed phenix-installer-1.8.1-1168-intel-linux-2.6-x86_64-fc3.tar
> to /tmp and tried to install, however I got some errors. Hence, I
> installed a couple more things and tried installing again.
> This time it went through most of the installation but failed during the
> configuration of phenix packages.
>
> **** Here is my shell output:
>
> [root at scientifix phenix-installer-1.8.1-1168]# ./install
>
> ==========================================================================
>                         PHENIX Installation
>
>                         version: 1.8.1
>                     release tag: 1168
>                    machine type: intel-linux-2.6-x86_64
>             source machine type: intel-linux-2.6-x86_64
>                      OS version: linux
>                      user shell: /bin/bash
>                     destination: /usr/local
> =========================================================================
>
> ==========================================================================
>                        Installing from binary bundle
> ==========================================================================
>
> bundle file:
>     bundle-1.8.1-1168-intel-linux-2.6-x86_64.tar.gz
> PHENIX installation source directory set to:
>     /tmp/phenix-installer-1.8.1-1168
> PHENIX installation target directory<PHENIX_LOC>  set to:
>     /usr/local/phenix-1.8.1-1168
> PHENIX installation build directory set to:
>     <PHENIX_LOC>  /build/intel-linux-2.6-x86_64
> PHENIX temporary build directory set to:
>     build-binary/intel-linux-2.6-x86_64/scientifix/tmp
> PHENIX installation log directory set to:
>     build-binary/intel-linux-2.6-x86_64/scientifix/log
>
> ==== warning: "/usr/local/phenix-1.8.1-1168" already exists ====
> ==== warning: cannot determine installation time-stamp, proceeding ====
>
>
> installing binary components
>
> removing existing files in
> build-binary/intel-linux-2.6-x86_64/scientifix/tmp/binary
> finding installed versions
> finding binary versions
> binary components up-to-date
> the binary package will not be installed
>
> setting environment
>
> configuring PHENIX components
>
> Error configuring: see
> /tmp/phenix-installer-1.8.1-1168/build-binary/intel-linux-2.6-x86_64/scientifix/log/binary.log
> for details
>
>
>
>
> ***** And here are the last lines of
> /tmp/phenix-installer-1.8.1-1168/build-binary/intel-linux-2.6-x86_64/scientifix/log/binary.log:
>
> ./build/intel-linux-2.6-x86_64/include/
> ./build/intel-linux-2.6-x86_64/include/phaser_defaults.params
> ./build/intel-linux-2.6-x86_64/include/phaser_nma_defaults.phil
> /usr/local/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/base/bin/python:
> /lib64/libc.so.6: version `GLIBC_2.14' not found (required by
> /usr/local/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/base/bin/python)
>
> By the way, Scientific linux 6.3 comes with glibc 2.12.
>
> It might be too naive from me, but would it be possible to copy
> libc.so.6 from glibc-2.14 somewhere and use an option during the
> installation to point to it? Any better ideas? (Like a step-wise
> description used in successful installation of phenix in Scientific
> Linux 6.3 64)
>
> Thank you for your time and help.
>
> Cheers,
> Davi
>



-- 
Kay Diederichs                http://strucbio.biologie.uni-konstanz.de
email: Kay.Diederichs at uni-konstanz.de    Tel +49 7531 88 4049 Fax 3183
Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz

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