[phenixbb] Importing project to Phenix

Emilia C. Arturo (Emily) eca38 at drexel.edu
Tue Jan 13 12:29:07 PST 2015

This mail is to update my bb post, from several days ago, about an issue I
had with importing a project into phenix.

I'd been unable to import a project into a new installation of phenix, a
project that had run well on one Mac where it was created, but not on a new
Mac where I'd imported it with phenix's import tool. Nat helped me find the
problem, and I'll tell you my solution.  While the project did seem to
import fine into phenix (i.e. no errors or warnings), I could not run
refinement on files in this project because I had renamed and reorganized
some directories that phenix had created, by default, when the project was
initially created. (I should point out that the problem was not that the
file paths were wrong; regardless of the paths, the directory architecture
needed to be just-so). unfortunately, I could not undo the reorganization
I'd done in order to have the project work in phenix (i.e. I tried to
re-create the directories based on what I saw from a new project I created
as template). The solution was to create a new project alongside the old
one, where I could still at least see all the job history of the old
project. I checked that one *could* import a project from one Mac to
another if the project's directory architecture was unadulterated; and yes,
as long as the directories are not reorganized, importing from one Mac to
another worked fine.

Lesson learned: don't fuss with the default files that phenix creates,
particularly if you'd like in the future to move the project.


On Tue, Jan 6, 2015 at 6:10 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> On Tue, Jan 6, 2015 at 3:00 PM, Emilia C. Arturo (Emily) <eca38 at drexel.edu
> > wrote:
>> I'd like to take a phenix project (on which I've been working
>> successfully on the Mac where I initially created the project) from one Mac
>> to another Mac. When I tried to use the 'Import project' tool on the new
>> computer, I got a notification that "[...] the directory must contain the
>> PHENIX project tracking data (a sub-directory named 'phenix' or '.phenix',
>> and associated files)." Unfortunately, I didn't see a sub-directory named
>> 'phenix' or '.phenix' in the folder where all my project files had been
>> created and stored, and wasn't sure what to do about it, so I proceeded
>> with the Import anyway, to see what would happen. On the new computer, the
>> project was imported seemingly successfully (e.g. the project history is
>> all there), but when I tried to Run a refinement I'd configured for this
>> project, I got an error about the missing '.phenix' file. The error is:
>> "Cannot open file for write: [...] No such file or directory:
>> [...]/.phenix/project_data/refine_22.eff'
>> Can someone help me figure out how to properly move a project from one
>> computer to another?
> It sounds like you have done at least part of the import successfully -
> otherwise you would not be able to see the job history. You would not
> normally see the ".phenix" folder in the Mac Finder even if it is present,
> because all file/folder names starting with "." are hidden.  However, if
> you copy over the entire folder - not just a selection of its contents -
> this should have been copied along with everything else.
> To figure out what is breaking I need to see exactly the error messages it
> produces, with the original directory paths explicitly stated.  Could you
> please send me these off-list?
> thanks,
> Nat
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