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

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, [email protected] wrote:

Message: 5 Date: Fri, 25 Jan 2013 16:15:01 -0800 From: Davi de Miranda Fonseca To: [email protected] Subject: [phenixbb] Unable to install phenix 1.8.1-1168 on Scientific Linux 6.3 64 bits Message-ID:<[email protected]> 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@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 set to: /usr/local/phenix-1.8.1-1168 PHENIX installation build directory set to: /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: [email protected] Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".