1 Short Course on Grid Computing Jornadas Chilenas de Computación 2010 INFONOR-CHILE 2010 November 15th - 19th, 2010 Antofagasta, Chile Dr. Barry Wilkinson University of North Carolina Charlotte Oct 13, 2010 © Barry Wilkinson Session 2 Using a command line to run Grid jobs

2 Remote connection to servers You will need an ssh client to make a secure shell connection. For Windows, more than one option: Putty ssh client WinSCP sftp client (also includes restricted console interface and simple text editor) Linux already has an ssh client and command.

Traditional way from a Windows system is to use PuTTY for a command line remote access. Download from above. PuTTY coit-grid01.uncc.edu or torvalds.cis.uncw.edu depending upon which server you wish to connect to Select ssh Can save entry and reload 3

WinSCP 4 Commands

5 Log onto server Use given ssh password (NOT portal password)

All files are provided for the workshop but you will need an editor such as nano below to edit the files in Task 4. Control key commands: - Control-O to save, Control-X to exit 6

Each user needs a certificate issued (signed) by a “certificate authority” (CA). A certificate authority is set up on coit- grid02.uncc.edu. Uses Globus simpleCA package. In our class assignment, students learn how to get and store their signed certificates and private key in their account (.globus directory) For Session 2, as with Session 1, we will use the myProxy server that more conveniently holds users credentials for the user. User “certificates” 7

Now need to get a proxy certificate to delegate authority. For session 2, we will obtain a proxy from the myProxy server by issuing the command: myproxy-logon -s coit-grid02.uncc.edu You will be prompted for a passphase, which will be the same as your portal password. Can check that you got a proxy with the command: grid-proxy-info which will show the proxy subject and time left. Getting a proxy 8

Task 1 Submit a simple job to the local machine Asks you to submit a job (hostname) using the –c option (to specify a binary executable and –s option to specific streaming output back to the console: globusrun-ws -submit -F localhost:8440 -s -c /bin/hostname This should simply work. You are asked to check the output. 9

Task 2 Submit a simple job to remote machine Asks you to submit job to a remote machine: globusrun-ws -submit -F torvalds.uncw.edu -s -c /bin/hostname This should simply work. You are asked to check the output. 10

Next you are asked to submit the mulch job from Session 1 but using commands and XML job description files. 11 Task 3 Submit a job with a job description document Compute area of flower bed torvaldscoit-grid01 area_ output Compute volume and cost of mulch globus-url-copy mulch_ output globus-url-copy mulch_ output area_ output

12 Provided files on coit-grid01.uncc.edu myIntegral.classJava class file for the myIntegral.java program that computes the area of the flowerbed. The instructions call for the output to be redirected to a file called area_output. myIntegral.xmlJob description file to execute myIntegral.class. myMulch.xmlJob description file to execute myMulch.class. mulch2.xmlGeneric job description file to execute myMulch.class with input and output file staging on torvalds.cis.uncw.edu, and file clean-up. myIntegral.java and myMulch.java are also provided for completeness although you do not need to use it.

13 Provided files on torvalds.cis.uncw.edu myMulch.classJava class file for myMulch.java program that computes volume and cost of mulch over flowerbed, given the area of the flowerbed in the file named as the first and only argument (area_output)

/usr/local/java/bin/java ${GLOBUS_USER_HOME} myIntegral ${GLOBUS_USER_HOME}/area_output ${GLOBUS_USER_HOME}/area_error 1 14 Java program to execute myIntegral job description file

Submit job using: globusrun-ws -submit -F localhost:8440 -f myIntegral.xml 15 Submit a job with a job description document

Transfer the output to torvalds Use globus-url-copy command: globus-url-copy file:///nfs-home/ /area_output gsiftp://torvalds.cis.uncw.edu/home/grid/ / Note first URL is source and second is destination. Use your ssh username in command 16 Note three /// to indicate localhost

17 myMulch job description /usr/local/java/bin/java ${GLOBUS_USER_HOME} myMulch area_output ${GLOBUS_USER_HOME}/mulch_output ${GLOBUS_USER_HOME}/mulch_error 1 Java program to execute

Next step is run second program, myMulch.java, from coit-grid01 but to run on remote machine torvalds.cis.uncw.edu Command: globusrun-ws -submit -F torvalds.uncw.edu -f myMulch.xml 18 Submit a job to run on a different computer

19 Task 4 File staging Modify job description file to include moving area file to torvalds and moving result back automatically rather than use globus-url-copy, and also add file clean-up

20 /usr/local/java/bin/java ${GLOBUS_USER_HOME} myMulch area_output ${GLOBUS_USER_HOME}/mulch_output ${GLOBUS_USER_HOME}/mulch_error 1 gsiftp://coit-grid01.uncc.edu:2811/nfs- home/ /area_output file:///home/grid/ /. File staging job description file

21 file:///home/grid/ /mulch_output gsiftp://coit-grid01.uncc.edu:2811/nfs- home/ / file:///home/grid/ /area_output file:///home/grid/ /mulch_output file:///home/grid/ /mulch_error File staging job description file cont.

22 Questions