Creating Maps on SmallWorld

From DISI
Revision as of 18:17, 6 May 2019 by Jyoung (talk | contribs) (→‎Run)
Jump to navigation Jump to search

Written by Jennifer Young on April 10, 2019

Install

Step 1: Create the /sw directory

SmallWorld requires a /sw directory which contains /anon and /maps The /sw directory is located on n-9-22 in

   /srv/db4

This directory contains:

The /anon directory contains 12 TB of pre-computed subgraphs

The /maps directory contains text files computed by SmallWorld that map your molecules of choice to the corresponding nodes in the anonymous graph index

Step 2: Find a location for the sw.jar file

Copy the sw.jar file to a reasonable location such as

   /opt/nextmove/sw.jar

Run

Important! Currently, we only run SmallWorld map generation on n-9-22

Step 1: Set SWDIR environment variable

Determine where the /sw directory with the /anon and /maps directory and if using csh, set the SWDIR variable using

   setenv SWDIR /srv/db4

If using bash, set the SWDIR variable using

   export SWDIR=/srv/db4

Step 2: Generate the map files

Run sw.jar to convert your smiles file into a map file.

(Optional: use the time command to see how long this takes)

(Optional: tee your results into a log file to check progress)

Here is an example where wait-ok.smi is your .smi file to map:

   (time java -jar /opt/nextmove/sw.jar map /mnt/nfs/ex9/work/smallworld/wait-ok.smi 
   -T /mnt/nfs/ex9/work/smallworld/scratch_sw 
   -o /mnt/nfs/ex9/work/smallworld/wait-ok.anon.map 
   -u /mnt/nfs/ex9/work/smallworld/wait-ok.anon.unmapped)
    |& tee /mnt/nfs/ex9/work/smallworld/wait-ok_log

For now, generate the map files in the

   /mnt/nfs/ex9/work/smallworld 

directory so they can be easily moved to the maps directory when the server is restarted

Step 3: How to Make the New Database Available. Stop the server first!

First, stop the server. You do not need to restart Tomcat every time you want to restart SmallWorld. The TomCat GUI is available at

   http://10.20.9.22:8080/

You need the tunnel to access the private network or this link will not work! Also, the admin username and password is required.

In the Manager App, in the Applications section, use the Stop and Start buttons for the sw-ws app to restart the SmallWorld server

Step 4: Move the Map File into the /maps directory

If you followed the example above, your .anon.map file should be located in

   /mnt/nfs/ex9/work/smallworld

Now, simply move the map file into the "/sw/maps" directory so it can be recognized by SmallWorld.

   mv <your-file-name>.anon.map /mnt/nfs/ex9/work/smallworld/maps

Or, simply

   mv <your-file-name>.anon.map maps


Step 5: Restart the Server

Again, go to the TomCat manager under applications and click Start once you are finished moving around the map files.