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Running the latest version of Scipion

 

1. Add an alias the new scipion path to your ~/.bashrc.

 

2. Configure scipion (just when you run it for the first time).

 

> scipion config --update

 

 

3. Edit / check your local config file. Note that this file is in a hidden directory, and thus will not necessarily be resolved by tabbing.
> gedit ./config/scipion/scipion.conf

This should usually be in your user directory. This can ALSO be edited from the GUI. Simply type scipion (or the path to scipion if you have yet to add the path to your bashrc), and navigate to the Configuration->User tab at the top left of the project screen.

Change the SCIPION_USER_DATA to point your folder on /well
For example, SCIPION_USER_DATA = /well/strubi/<username>/ScipionUserData

 

If this project folder does not exist, it will be created.

 

4. Launch the GUI (from Belmont for CPU runs, from compG000 for GPU runs). Currently the very latest version of scipion (v1.2.2-rc) does not appear to be working on belmont due to a library dependency issue (error below). This is fine...you can always submit jobs via compg000 too!

>>>>> python /gpfs2/well/strubi/juha/apps/scipion-1.2/pyworkflow/apps/pw_manager.py
Traceback (most recent call last):
File "/gpfs2/well/strubi/juha/apps/scipion-1.2/pyworkflow/apps/pw_manager.py", line 32, in <module>
from pyworkflow.gui.project import ProjectManagerWindow
File "/gpfs2/well/strubi/juha/apps/scipion-1.2/pyworkflow/gui/__init__.py", line 27, in <module>
from gui import *
File "/gpfs2/well/strubi/juha/apps/scipion-1.2/pyworkflow/gui/gui.py", line 29, in <module>
import Tkinter as tk
File "/gpfs2/well/strubi/juha/apps/scipion-1.2/software/lib/python2.7/lib-tk/Tkinter.py", line 39, in <module>
import _tkinter # If this fails your Python may not be configured for Tk
ImportError: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /gpfs2/well/strubi/juha/apps/scipion/software/lib/libz.so.1)

 

> scipion
(ignore the cuda warning on belmont)

Some advice using the queues:

 

 

- Relion queues behave as normally, you need to select the right number of threads/MPIs for the matching queue. You can use these queues for other things as well (xmipp, frealign etc).

 

- When running GPU jobs, log in to compG000 and ask for one more MPI than you're planning to use GPUs. Maximum is 9 MPIs which will then distribute the job on the 8 GPUs. Do not use queues there.