EXPRESS INSTALL - The quickest way to install and run
Before you install ABCGrid, please make sure you have JRE1.5 (http://java.sun.com/javase/) or above installed. Use command "/JAVA_HOME/bin/java -version" to see current version.
You can install all the three applications into one machine to try to run them (If your machine has firewall installed, please disable it temporarily or open port 4170 and 4171 for ABCGrid). For demonstration, ABCUser is not used.
- Downloaded master-bin.zip and worker-bin.zip
- Unzip master-bin.zip and worker-bin.zip using WinZip, WinRAR (Windows) or unzip (UNIX/Linux). Suppose you have unzipped them to c:\master and c:\worker respectively.
- Open two command windows: click "start"->"run", input "cmd" to start a command window. You should create two command windows for ABCMaster and ABCWorker respectively.
- Run ABCMaster
>cd c:\master\bin
If everything is OK, a console windows appears:
>java -jar master.jar
The line: "ip=162.105.250.165, port=4170, service=ABCGrid" specified the master node's address (in my machine). The IP should be different in your machine. The IP address is required when start ABCWorker since it must be told which master to connect with.
- Run ABCWorker
Switch to the second command window.
>cd c:\worker\bin
>java -jar worker.jar -h 162.105.250.165 -v
The parameters "-h 162.105.250.165" is used to specify that the host(master)'s IP address. Change this value to your machine's IP address. The "-h xxx.xxx.xxx.xxx" is only needed when you start the ABCWorker for the first time or you changed the master's address since last launch of ABCWorker. If master's address is not changed, just type:
>java -jar worker.jar
is OK. The parameter "-v" is "verbose" mode. If everything is OK, the Worker will download and update local applications and databases. You will see a console window:
Wait until the updating process is over.The last line with "update finished" denotes that the updating process is over and the ABCWorker is ready to accept jobs. If it failed and print a message like "error to connect ftp:xxxxx", that is because the connection is not established between ABCWorker and FTP server.
In a default configuation, ABCGrid use ftp://202.38.125.2 to download NCBI BLAST executables and "pataa" database. The size of pataa database is ~50MB, hence the download process may need some minutes depends on your machine's internet connection to that FTP server. For your convenience, you should setup a local FTP server to store all databases and executables.
- OK, run a job now
Switch to the ABCMaster's console window. Input commands after the ">>>" prompter.>>>r blastall
If you see the printed help message of blastall, the NCBI BLAST is installed into your worker node successfully. Next, input:>>>r blastall -p blastp -i pdb_10.fasta -d pataa -o pdb_10.blastp -m 9
If everything is OK, you will see a messages says your job is accepted with an automated assigned integer value begins from 1. This command will do a blastp search using query sequence file pdb_10.fasta (under c:\master\user\admin\) against database pataa (under c:\worker\service\NCBI_BLAST\data\). Once finished, the output file pdb_10.blastp can be found under c:\master\user\admin\. It is the working directory of user "admin".During the computation, you can query the status of submitted job by using command "j"
>>>j
The fourth column with name "finished" shows the progress. If it was "100%", the computation is over. Check the output file.
By default, ABCGrid defined two users: "demo" and "admin". User who operates in the console window of ABCMaster is considered as "admin" automatically.
please see USER GUIDE (PDF) for common install procedures.