Epikh Catania 2011

This is the working page and notebook of the South African exchange to Catania for the EPIKH.

Work Programme

Timothy Carr

6 September 2011

• Contributed to the SAGrid Joint Research Unit (JRU) document. It was identified that the document lacked specifics and this needed to be addressed in a more structured way.
• Started coding the ABySS? installation script for deployment to SAGrid Sites.
• Initial reading of StratusLab? .

7 September 2011

• Finished "install-abyss.sh" script with which to install ABySS? 1.2.7. The source code and dependencies are referenced in the LFC and downloaded from various SE's in South Africa. Abyss is a de novo, parallel, paired-end sequence assembler that is designed for short reads. Further information can be found here ABySS
• Submitted a grid job for the installation of ABySS? on the South African National Grid. First job went to the SAGrid VO enabled on Italian infrastructure and the job ran successfully. ABySS? has a few tricks and these are documented here
• Fixed up the /opt/exp_soft/sagrid software location at ZA-UCT-ICTS with the correct group and file system persmissions. Software deployment job for ABySS? was not able to install using the sgmsagrid002 uid
• Tagged the following grid sites with installation of ABySS? - WITS, UP, UCT, UJ, UFS, NWU
• Checked Abyss 1.2.7 installation and JDL scripts into the SAGrid SVN respository hosted at https://ops.sagrid.ac.za/repo/trunk/software_installation/ABySS/

8 September 2011

9 September 2011

12 September 2011

• Meeting with the team of the INFN - Discussion around LifeRay? and EUMED applications. INFN looking into a web based file management interface for users ( similar to dropbox ). The options are Ajax Explorer / Elfinder/ Extplorer.
• DAG jobs are proving to be a pain for a application called " Auto ". I will look into using an alternative to DAG jobs, possibly look at simple jobs and ensure standardization
• Finished Auto07p / FFTW installation and JDL scripts.
• Committed updated Auto07p / FFTW to the SVN repository hosted here and deployed application to the ZA-UCT-ICTS grid site in Cape Town, South Africa for testing. Loca

13 September 2011

• Completed documenting the application porting process. The information can be found here
• Successfully managed to submit a test Grid job of Auto07p-OMP to ZA-UCT-ICTS

14 September 2011

• Deployed Auto07p-OMP to all sites in South Africa
• Coding installation scripts and JDL scripts for the deployment of OpenFOAM2?

15 September 2011

• Compiled GCC 4.6.1 successfully under Scientific Linux 5.4. This is needed for an application called OpenFOAM? - V2, which is a monster of an application to compile. The reason for its complexity is that it requires an updated version of the compiler, gcc. The current version of the compiler which is installed with the default operating system is outdated and cannot be upgraded for reasons known to the package manager and the linux core. A compiled version of GCC will reside in user space, /opt/exp_soft, and could be referenced by other source pack applications if a requirement for the latest version is require.
• Draft version of "Compiling GCC 4.6 on SAGrid Infrastructure " has been created and will be published shortly ( NB: Make this available )

16 September 2011

• Successfully managed to compile and install OpenFOAM? 2.0 under Scientific Linux 5.4 in the user space environment at ZA-UCT-ICTS. Next, conduct the exact same procedure from within the grid application environment and deploy to /opt/exp_soft.
• Concluded the documentation for OpenFOAM? 2.0 and its can be found here
• Updated Africa5 Application Porting page

19 September 2011

• EGI Technical Forum - Lyon, France

20 September 2011

• EGI Technical Forum - Lyon, France

21 September 2011

• EGI Technical Forum - Lyon, France

22 September 2011

• EGI Technical Forum - Lyon, France

23 September 2011

• EGI Technical Forum - Lyon, France

26 September 2011

• Updated the Africa 5 Application porting for OpenFOAM? - http://wiki.sagrid.ac.za/bin/view/Training/OpenFoamDevNotesAfrica5
• Updated Auto / ABYSS Africa5 applications.

27 September 2011

• Started writing the StratusLab? report for Bruce which will reflect the feedback and direction in which the South African National Grid (SAGRID) will deploy its future infrastructure upon.
• 2 Hour session with Riccardo Rotondo about Liferay Portals/NetBEANS IDE and the JSAGA interconnect with gLite middle-ware. Thanks Riccardo