Scipion web development setup
Scipion web requires you to have Scipion installed in the server. For that you will need to install Scipion. After this you should have Python, Django and all the modules required to run Scipion web.
Django scripts needs to write in $SCIPION_HOME (where you saved scipion-web repository), so the user executing the scipion web-tools will need write permission to this folder.
Matplotlib also needs write permission (by default, to ~/.matplotlib)
Matplotlib also needs to deafult to Agg backend:
from scipion folder:
cp software/lib/python2.7/site-packages/matplotlib-1.3.1-py2.7-linux-x86_64.egg/matplotlib/mpl-data/matplotlibrc ~/.matplotlib/ vi ~/.matplotlib/matplotlibrc Set --> backend : agg save it
You will need to set up your machine to be able to run the web-tools, so far you will need to create some folders and add some files to those folders
Open a console a run these commands
mkdir ~/.config/scipion/myfirstmap mkdir ~/.config/scipion/myresmap mkdir ~/.config/scipion/mymovies
You will also need to have a host.conf file on each of those folders, let’s copy the main one from scipion.
From the $SCIPION_HOME:
cp config/hosts.conf ~/.config/scipion/myfirstmap/ cp config/hosts.conf ~/.config/scipion/myresmap/ cp config/hosts.conf ~/.config/scipion/mymovies/
You can additionally force how each of the protocol of the webtools should run in terms of "Thread and MPI".
Add the configuration as a "section" in $SCIPION_HOME/config/scipion.conf. An example of this configuration could look like this.
[WEB_PROTOCOLS]
XmippProtRansac = {"useQueue": 0, "numberOfThreads": 4, "numberOfMpi": 1, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
EmanProtInitModel = {"useQueue": 0, "numberOfThreads": 4, "numberOfMpi": 1, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
XmippProtReconstructSignificant = {"useQueue": 0, "numberOfThreads": 1, "numberOfMpi": 4, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
XmippProtAlignVolumeForWeb = {"useQueue": 0, "numberOfThreads": 4, "numberOfMpi": 1, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
ProtMovieAlignment = {"useQueue": 0, "numberOfThreads": 1, "numberOfMpi": 1, "queueParams" : ["gpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
XmippProtCreateMask3D = {"useQueue": 0, "numberOfThreads": 1, "numberOfMpi": 1, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
ProtResMap = {"useQueue": 0, "numberOfThreads": 1, "numberOfMpi": 1, "queueParams" : ["cpu", {"JOB_MEMORY": "8192", "JOB_TIME": "72"}]}
The simplest way to test your installation is to run Scipion in webserver mode:
./scipion webserver
After this you should have it running at http://localhost:8000/
(Note: the script starts the web server listening to 0.0.0.0, so it might be accessible from other computers too)
If it is the first time you start the server you first need to run:
./scipion webserver collectstatic
The recommended procedure is to setup a replica of the production environment on your development machine. Actually it takes little work, and you will be doing the test in the same environment as production.
To generate the database that Django will use (used when uploading a file), run
./scipion webserver syncdb