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

I created a virtual machine and did a brand new Scientific Linux 6.3 (64) installation. After updating its packages, I installed phenix-installer-1.8.1-1168-intel-linux-2.6-x86_64-fc3 almost without a glitch.* Following Kay's email I did a clean install of fcphenix-installer-1.8.1-1168-intel-linux-2.6-x86_64-fc12 and it also worked beautifully.* Thank you a lot Nat, Engin and Kay. Cheers, Davi * - There was the following error message: running mkfontdir Couldn't determine weight for Vera.pfa Couldn't determine weight for VeraMono.pfa rebuilding font cache Fontconfig error: Cannot load default config file fc-cache: "/usr/local/phenix-1.8.1-1168/build/intel-linux-2.6-x86_64/base/share/fonts": skipping, no such directory fc-cache: succeeded On 27/01/2013 13:54, Engin Ozkan wrote:

I just installed yesterday the latest nightly build on our Scientific Linux 6 (6.3, I believe) machine using the 64-bit FC3 installer. No problems.

Engin

Engin Özkan Garcia Lab, Stanford

-------- Original message -------- From: Nathaniel Echols Date: To: PHENIX user mailing list Subject: Re: [phenixbb] Unable to install phenix 1.8.1-1168 on Scientific Linux 6.3 64 bits

On Fri, Jan 25, 2013 at 4:15 PM, Davi de Miranda Fonseca wrote:

...

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.

The first thing to try when something like this happens is to download one of the other 64-bit installers. In most cases the fc3 build is preferred, but there are some newer distributions where an installer built on a more recent version of Fedora is preferable. I would start with fc8 and work your way up.

The second thing to try, if all of the binary installers fail, is to install from source.

...

***** 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:

...

...

/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.

To be honest I simply don't understand library versioning issues - the Fedora 3 machine we build that installer on currently has glibc 2.3, so I don't know where the GLIBC_2.14 is coming from. I think it will be significantly more work to figure out a workaround than trying the other installers, though. Unfortunately we do not actually have a Scientific Linux system here - the closest I could find was CentOS 6.2, and that works okay.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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