Master Class on HPC Applications For Life Sciences A CloudAsia2010 Satellite Workshop

Job Submission Documentation Workshop Introduction Registration Programme Workshop Faculty and Speakers Workshop Materials AMBIS Annual Lecture Venue Map Accommodation Contact Us

Using the Grid Services on UPM BIRUNI A step-by-step guide You will need a Personal certificate, followed by a Grid user account to run jobs on the GENIUS web interface. Please refer to Getting started on the Grid Quick Links: Registering for a UPM Biruni Grid user account Logging in and changing your password in the Grid server Uploading your certificate Initializing your Grid service (using the built-in Java Applet) Accessing Grid services on the Genius portal Creating and manipulating files and folders in the Grid server Troubleshooting and FAQs: I am not able to upload my certificate I am not able to initialize my Grid service automatically Contact the technical support team 1. Registering for a UPM Biruni Grid user account Download and fill in the Grid user account application form. E-mail the form to support--at--biruni.upm.my. Once your application is successful, you will be notified by e-mail 2. Logging in and changing your password in the Grid server i) From the Genius web portal: Make sure Java plugin 1.6.0 or higher is installed in your web browser. Login at https://ui.biruni.upm.my. At the left panel, go to "Security" and click on "Change OS Password" Key in your old password and new password, then click "Change". ii) From a ssh client: Ssh to ui.biruni.upm.my. Login with your assigned username and password. Key in the command password to change your password. 3. Uploading your certificate Login at https://ui.biruni.upm.my Click on the "Upload User Certificate" button on the left panel Browse and select your certificate file, then enter your import password (the password which you have used to backup your certificate) and set a new password for your private key. Click "Upload" when done. This will upload and convert your certificate automatically. 4. Initializing your Grid service Before you can start using the applications hosted on the Grid, you will have to initialize your proxy. Make sure Java plugin 1.6.0 or higher is installed in your web browser. Make sure you have exported (or backed up) your certificate as according to the instructions at http://ca.grid.sinica.edu.tw/certificate/request/certificate_management.html. With your Grid user account, login at https://ui.biruni.upm.my to access the Genius portal. Click on "Initialize Your Proxy" at the top panel, or at the left panel, go to "Security" and select "Initialize Your Proxy". A Java Applet will run automically to reinitialize your proxy in order to run the Grid services. When prompted to select your certificate format, click on "P12 or PFX". Locate your certificate file in the file browser and submit. Key in your private key password which you have specified when you exported your certificate. Once successful, you will receive a message stating that "Your proxy has been created successfully". After the proxy has expired, you will have to reinitialize again with the Java applet. 6. Accessing Grid services on the Genius portal Login at https://ui.biruni.upm.my and initialize your proxy.     You can access the bioinformatics applications by clicking on "VO services" at the left panel. 7. Creating and manipulating files and folders in the Grid server i) From the Genius web portal: At the left panel, go to "File". The listed options allow you to manipulate files and folders in the Genius web portal. ii) From a ssh client: Ssh and login to ui.biruni.upm.my. You can use standard UNIX commands to create and manipulate files and folders in the server. Troubleshooting and FAQs I am not able to upload my certificate If you are having problems uploading and converting your certificate from the website, you will have to use a SSH client such as putty or ssh secure shell client to upload and convert your certificate manually Using a ssh client (putty or ssh secure shell client etc.), connect to ui.biruni.upm.my with your Grid user name and password. Create a directory .globus in your home directory. $ mkdir .globus Transfer your certificate file (*.p12 and *.pem) to the .globus directory. (this can be done either through scp, or by going to the web portal, and clicking on file->upload a file Convert your certificate into *.pem files with the following comands: $ cd .globus $ openssl pkcs12 -in xxx.p12 -clcerts -nokeys -out usercert.pem $ openssl pkcs12 -in xxx.p12 -nocerts -out userkey.pem $ chmod 644 usercert.pem $ chmod 400 userkey.pem I am not able to intialize my Grid service automatically One common problem in using the Java applet is that the user's firewall does not allow connection to voms.grid.sinica.edu.tw (port 15015). If you experience any problem running the Java applet, you will have to initialize your proxy manually using SSH: Using a ssh client (putty or ssh secure shell client etc.), connect to ui.biruni.upm.my with your Grid user name and password. Intialize your proxy: $ voms-proxy-init --voms euasia The proxy is valid for 12 hours, to renew the proxy, repeat the command voms-proxy-init --voms euasia again