SmallWorld Documentation for Future Developer: Difference between revisions

Revision as of 00:47, 29 January 2022

Introduction

Here is the link to Smallworld's manual

Username: ucsf@nextmovesoftware.com
Password: <Ask jjiteam@googlegroups.com>

All smallworld databases live in abacus' db3.

Smallworld frontend files are consolidated and located at /export/db3/smallworld_extract/.extract.

Execute command start_smallworld to see options on which smallworld instance to start/restart.

How to Download Smallworld

Ssh to abacus and become root. Prepare directory

 mkdir /opt/nextmove/smallworld-<version> && cd /opt/nextmove/smallworld-<version>

Download Software with this link
- Username: ucsf@nextmovesoftware.com
- Password: <Ask jjiteam@googlegroups.com>
Go to releases. Look for smallworld-java-<version>.tar.gz and copy the link address.

Download using wget

 wget --user ucsf@nextmovesoftware.com --password <Ask jjiteam@googlegroups.com> <link address>

Decompress the file
- ```
 tar -xvf <file_name>
```

How to Launch Smallworld For The First Time

Prepare Files and Directories

Ssh to abacus and become root

Open a port in the firewall

firewall-cmd --permanent --add-port=<port_number>/tcp 
firewall-cmd --reload

Go to smallworld databases directory
```
cd /export/db3/
```

Create a Smallworld directory and go to it

mkdir <smallworld_dir> && cd <smallworld_dir>

Inside that directory, create these

a symbolic link to the smallworld anon map

ln -s /export/db2/smallworld_anon_21Q4 anon

a sub-directory called maps to store databases

mkdir maps

a smallworld config file

vim smallworld.cfg

Add this block of code inside the config file

[WebApp]
DepictionUrl=./depict/svg?w=%w&h=%h&smi=%s&qry=%q&cols=%c&cmap=%m
ResolverUrl=./util/smi2mol?smi=%s
SearchTimeOut=5000
SearchAsYouDraw=true
[Score]
Name=Atom Alignment
Description=Aligns and scores each hit relative to the query atom types, differences are categorised as MAJ, MIN, HYB, SUB 
Class=com.nmsoftware.smallworld.score.SimpleAtomAlignment 
EnabledByDefault=false
MappingMode=EditMap
[Score]
Name=SMARTS Alignment
Description=Treat input as SMARTS and align and score each hit relative to the query atom expressions in the input 
Class=com.nmsoftware.smallworld.score.SmartsAtomAlignment 
EnabledByDefault=false
[Score]
Name=ECFP4
Description=Extended Connectivity Circular Fingerprint
Class=com.nmsoftware.smallworld.score.EcfpTanimoto
Radius=2
EnabledByDefault=true
[Score]
Name=Daylight
Description=Path based fingerprint
Class=com.nmsoftware.smallworld.score.DaylightTanimoto
EnabledByDefault=true

SearchTimeOut should be the only option you'll change in the future. It caps search time to lessen strain on machine.

Place any *.anon.maps you've already compiled for testing into the maps sub-directory.

Start Smallworld Instance

Go to smallworld extract directory
```
cd /export/db3/smallworld_extract
```
Create a screen
```
screen -S <screen_name>
```
Export the smallworld directory you've made
```
export SWDIR=/export/db3/<smallworld_dir>
```

Launch java

java -jar /opt/nextmove/smallworld-<version>/sw-ws-<version>.jar --httpPort=<port_number>

Install and Set Up on TomCat on CentOS 6 (such as n-9-22)

Step 1: Check the CentOS version and Java version

SmallWorld currently runs on n-9-22, which runs CentOS 6.10. You can check the version of CentOS with the following command:

   cat /etc/centos-release

Check your current version of Java with the following command:

   java -version

If you do not have the correct version, install it using yum. Follow the steps on this tutorial https://www.itzgeek.com/how-tos/linux/centos-how-tos/install-apache-tomcat-7-0-on-rhel-6-centos-6.html

Step 2: Create Tomcat Service Account

This must be done as a root user and has already been done for n-9-22.

   groupadd tomcat
   mkdir /opt/tomcat
   useradd -g tomcat -d /opt/tomcat tomcat

Step 3: Create Initialization Script to Control Apache TomCat

Download the latest version of Apache TomCat from the website https://tomcat.apache.org/download-90.cgi

   vi /etc/init.d/tomcat9

Copy the bash script from here https://www.itzgeek.com/how-tos/linux/centos-how-tos/install-apache-tomcat-7-0-on-rhel-6-centos-6.html

How to Restart the TomCat Server

   service tomcat9 restart

How to Restart the SmallWorld WebApp

You do not need to restart Tomcat every time you want to restart SmallWorld. The TomCat GUI is available at

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

   http://10.20.9.22:8080/

For more information about TomCat, consult the documentation for the version installed (9.0.17 as of June 2019)

   http://10.20.9.22:8080/docs/

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

Set Environment Variable for Anonymous Graphs for TomCat

The file to modify is

   opt/tomcat/bin/catalina.sh

Add the following command to the top of the file (below the comments at the top_

   export SWDIR=/srv/db4

Modifying the Amount of Memory Allocated to SmallWorld

The memory allocated to TomCat is found in

   /opt/tomcat/bin/catalina.sh

Add the following commands to the top of the file (below the comments at the top)

   export CATALINA_OPTS="$CATALINA_OPTS -Xms80g"
   export CATALINA_OPTS="$CATALINA_OPTS -Xmx80g"
   export CATALINA_OPTS="$CATALINA_OPTS -XX:MaxPermSize=70g"

Modifying the SmallWorld GUI

The files for the SmallWorld WebApp live in

   /opt/tomcat/webapps/sw-ws

Edit the files in

   /opt/tomcat/webapps/sw-ws/WEB-INF

To add the link to go to ZINC from the SmallWorld results page, edit the swsearch.js JavaScript file

   /opt/tomcat/webapps/sw-ws/WEB-INF/static/swsearch.js

Creating Maps on SmallWorld

See the corresponding wiki page: http://wiki.docking.org/index.php/Creating_Maps_on_SmallWorld

Running SmallWorld from the Command Line

We have been running SmallWorld on n-9-22 as www which uses csh as the default shell. There is a file in /mnt/nfs/soft/www/home/smallworld called run_sw which contains the following commands to set up the SmallWorld Command Line Interface (CLI)

Set the SWDIR environment variable so SmallWorld scripts can access the 12 TB index

   setenv SWDIR /srv/db4

Set the path to the SmallWorld C++ Executables

   set path = ($path /opt/nextmove/bin)

Alias the keyword "sw" to access the Java CLI

   alias sw 'java -jar /opt/nextmove/sw.jar'

Tips for Running SmallWorld on the Command Line

Use sw help to get information about available commands

    sw help