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Leginon Installation on Ubuntu

Added by Long Gui about 12 years ago

To whom it may concern,

We are trying to install leginon on Ubuntu 12.04 64-bit Desktop following the tutorial on the website "myami on Ubuntu"
The installation steps go very smoothly and nicely (which is great!) However, when I tried to test if leginon starts via inputing

"start-leginon.py"

The screen returns:

“Error: image path is not writable.”

And leginon fails to start.

While we tried to input the executable file via inputting "reduxd"

The screen returns with the same result:

"Error: image path is not writable. "

We are sure that before we run reduxd, the cache file /var/cache/redux/ has been made to be writable for all the users via inputing

"chmod 777 /var/cache/redux/"

Also we disabled the cache but the reduxd still ends in the same error.

Could you please clarify for us, what does the image path mean? Is it the redux cache path or the image file saving path?

Thanks a lot in advance!

Thanks,
Long Gui, Lee Lab, University of Washington.


Replies (3)

RE: Leginon Installation on Ubuntu - Added by Anchi Cheng about 12 years ago

Please check if your leginon.cfg sets path in [Images] module to a writable path. See Configure_leginoncfg on how to set your leginon.cfg. Also read File_Server_Setup_Considerations for more information on recommended file server structure.

reduxd cache starting problem is probably caused by a missed point in the wiki doc:

Since you've created the cache directory at /var/cache/redux/, you will need to change in your myami/redux/pipeline.py the disk_cache location as well and install redux pacakge again (See Install_Leginon_Packages.

  1. cd you_myami_download/redux
  2. edit the file pipeline.py
    Change
      disk_cache_path = '/tmp/redux'

    To
    disk_cache_path = '/var/cache/redux'

Not sure why would you get the same path-not-writable error without cache on, though. Are you running reduxd as root or as a general user? While Leginon can be run as any user, redux server need to be run as root because it uses fftw wisdom that will attempt to save the wisdom file at where it is installed. While Leginon can be run as any user, redux server need to be run as root

Anchi

RE: Leginon Installation on Ubuntu - Added by Anchi Cheng about 12 years ago

By the way, image path is where Leginon saves MRC images by session while operating the microscope.

Redux cache path is separate. It is used by redux to store intermediate images created in its image processing pipeline. Redux does need access to image path of Leginon to read them. Redux is currently only used to serve images to the web-based image viewer after an image is acquired by Leginon.

Anchi

RE: Leginon Installation on Ubuntu - Added by Long Gui about 12 years ago

Hi Anchi,

Thanks a lot for your reply! I am checked the leginon.cfg file and the default [Images] module is EMPTY. So I changed it to /data/leginon and now the leginon could start well on the Ubuntu now.

Thanks again for your nice guidance!

Long

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