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

Davi de Miranda Fonseca davi.fonseca at ntnu.no
Tue Jan 29 09:03:56 PST 2013


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 <nechols at lbl.gov>
> Date:
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> 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
> <davi.fonseca at ntnu.no> 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
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