[phenixbb] Phenix installation issue

Nathaniel Echols NEchols at lbl.gov
Thu Dec 3 20:50:25 PST 2009

On Dec 3, 2009, at 7:59 PM, smoniot at chemie.fu-berlin.de wrote:
> I'm trying to install phenix on my computer (Linux distribution Kubuntu 64
> bits (virtual machine but it should not be an issue)) but the installation
> failed after some minutes ...
> the last lines on the installation log file are :
> /bin/tar: ./build/intel-linux-2.6-x86_64/base/bin/wx-config : un lien
> symbolique ne peut pas être créé vers
> «/net/anaconda/scratch1/phenix/phenix-1.5-2/build/intel-linux-2.6-x86_64/base/lib/wx/config/gtk2-ansi-release-2.8»:
> Opération non permise
> It's in french but basiccaly it can't create a symbolic link to
> /net/anaconda.... not allowed.
> I don't get it since I did try both the sudo ./install command and the su
> - root.

The short answer is to use the source installer:


It takes several hours to compile everything, so if you have multiple processors enabled for the virtual machine, add "--nproc=2" (or 4, etc.) when you run the install script.

The long answer: The binary installer isn't very "clean", and there are a lot of residual symlinks like this that don't get deleted, mostly because they're difficult to track and the installation scripts are already massive (and messy).  The few links that we care about are regenerated during installation, and the rest usually don't cause problems.  What is the translation of "un lien symbolique ne peut pas être créé vers"?  (Or even better, would it be possible to reproduce the error in English, so I can Google the exact phrase?)  I use vanilla 64-bit Ubuntu (8.x and 9.x) and it hasn't had any trouble with the binary installers, but there may be some difference in your system configuration, or the default behavior of 'tar' - unfortunately, these problems are difficult to diagnose remotely.  (Please send me the rest of the installation log too - I'm not entirely sure where it's breaking.)


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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