Scipion web development setup

Laura edited this page Dec 11, 2017 · 24 revisions
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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 need write permission in $SCIPION_HOME


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

Webtools setup

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

Create web tools folders

Open a console a run these commands

mkdir ~/.config/scipion/myfirstmap
mkdir ~/.config/scipion/myresmap
mkdir ~/.config/scipion/movies

You will also need to have a host.conf file on each of those folders, let’s copy the main one from scipion.


 cp config/hosts.conf ~/.config/scipion/myfirstmap/
 cp config/hosts.conf ~/.config/scipion/myresmap/
 cp config/hosts.conf ~/.config/scipion/movies/

Create a /services folder for the movie alignment project samples and give it x permissions:

sudo mkdir /services
sudo chmod 777 /services

Install necessary packages

$SCIPION_HOME/scipion install eman2.12 resmap pytz

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.

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"}]}

Run the webserver

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

The simplest way to test your installation is to run Scipion in web-server mode:

./scipion webserver

After this you should have it running at http://localhost:8000/webtools/

(Note: the script starts the web server listening to, so it might be accessible from other computers too)

Other useful commands

To list all available Django commands,

./scipion webserver help

You can run any Django command if you type it after webserver: useful for collectstatic content.

./scipion webserver <Django command>

 — Main.JesusCuenca - 2013-07-31

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