SmallWorld Documentation for Future Developer: Difference between revisions

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# Launch java
# Launch java
#: <source>java -jar /opt/nextmove/smallworld-<version>/sw-ws-<version>.jar --httpPort=<port_number></source>
#: <source>java -jar /opt/nextmove/smallworld-<version>/sw-ws-<version>.jar --httpPort=<port_number></source>
==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==
==Creating Maps on SmallWorld==

Revision as of 00:48, 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

  1. Ssh to abacus and become root. Prepare directory
     mkdir /opt/nextmove/smallworld-<version> && cd /opt/nextmove/smallworld-<version>
  2. Download Software with this link
    • Username: ucsf@nextmovesoftware.com
    • Password: <Ask jjiteam@googlegroups.com>
  3. Go to releases. Look for smallworld-java-<version>.tar.gz and copy the link address.
  4. Download using wget
     wget --user ucsf@nextmovesoftware.com --password <Ask jjiteam@googlegroups.com> <link address>
  5. Decompress the file
    •  tar -xvf <file_name>

How to Launch Smallworld For The First Time

Prepare Files and Directories

  1. Ssh to abacus and become root
  2. Open a port in the firewall
    firewall-cmd --permanent --add-port=<port_number>/tcp 
    firewall-cmd --reload
  3. Go to smallworld databases directory
    cd /export/db3/
  4. Create a Smallworld directory and go to it
    mkdir <smallworld_dir> && cd <smallworld_dir>
  5. 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.
  6. Place any *.anon.maps you've already compiled for testing into the maps sub-directory.

Start Smallworld Instance

  1. Go to smallworld extract directory
    cd /export/db3/smallworld_extract
  2. Create a screen
    screen -S <screen_name>
  3. Export the smallworld directory you've made
    export SWDIR=/export/db3/<smallworld_dir>
  4. Launch java
    java -jar /opt/nextmove/smallworld-<version>/sw-ws-<version>.jar --httpPort=<port_number>

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