apgrid core meeting phuket 20021 asia pacific biogrid initiative a/p tan tin wee, mark de silva, lim...
TRANSCRIPT
![Page 1: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/1.jpg)
APGrid Core Meeting Phuket 2002
1
Asia Pacific BioGRID initiative
A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong –
Bioinformatics Centre, National Univ of Singapore Ong Guan Sin [email protected] –
Singapore Management UniversityRaj Buyya –
Monash UniversityRaj Godhia –
Cray Inc
![Page 2: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/2.jpg)
APGrid Core Meeting Phuket 2002
2
Background
1998 - APBioNet project created a distributed database mirror which was to evolve into the basis for a DataGrid
Progress was slow – until Oct 2001, the first BioGRID meeting was organised in Singapore by BIC-NUS and APBioNet
In Dec 2001, Cray Inc was involved inpartnering us in setting up a SuperBioGRID'02 symposium
Momentum was set and first GRID was created before Christmas 2001!
![Page 3: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/3.jpg)
APGrid Core Meeting Phuket 2002
3
BioGRID Components
OS
Globus
Globus-aware Scheduler (Nimrod-G)
Bio Applications (MBOSS, PHYLIB)
CPU
OS
Globus
Globus-aware Scheduler (Nimrod-G)
Bio Applications (MBOSS, PHYLIB)
CPU
BioGRID
Web Interface
![Page 4: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/4.jpg)
APGrid Core Meeting Phuket 2002
4
Linux cluster – 14xP-III 800MHzGRID Host (Sun GridEngine)
Linux cluster – 14xP-III 800MHzGRID Host (Sun GridEngine)
SGI 3200 IrixGRID Host
Linux – P-III 800MHzGRID Host/GIIS/MDS
CRAY SV1 – 8 x CPUsGRID Host
Sun UltraSPARC SolarisGRID Host
BioGRID Architecture
![Page 5: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/5.jpg)
APGrid Core Meeting Phuket 2002
5
Software Components
Currently Globus 1.1.3/1.1.4 is the building block to the BioGRID, on the following OS platforms:– Cray Unicos SV1– SGI IRIX 6.5– Sun Solaris 7– Linux 2.4.x (Redhat 7.2 and Slackware 8)
Various scheduling systems are studied and deployed, including Nimrod/G from Monash University, LSF and Sun GridEngine.
![Page 6: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/6.jpg)
APGrid Core Meeting Phuket 2002
6
Software Components (cont.)
Various bioinformatics and biological applications with high computation and suitable for GRID will be/are deployed: EMBOSS, EMBASSY, PHYLIB, etc.
![Page 7: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/7.jpg)
APGrid Core Meeting Phuket 2002
7
Collaboration and Projects
The BioGRID is being expanded to collaborate with GRID resources of Monash University in their VLAB project.
WE ARE LOOKING FOR COLLABORATION PARTNERS TO EXCHANGE RESOURCES.
![Page 8: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/8.jpg)
APGrid Core Meeting Phuket 2002
8
Operations and Support
We run our own CA:– Signing and issuance of both host and
user certificates.– Shorter turn-around time for
APBioGRID participants
Support email:– [email protected]: cert requests– [email protected]:
administrative requests/support
![Page 9: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/9.jpg)
APGrid Core Meeting Phuket 2002
9
In the Pipeline
Globus self-installer with customisations for APBioGRID:–Well tested installation scripts for a
defined set of OS platforms– Automate configuration steps with
BioGRID specifics– No need to deal with “Globus
nightmare” - even a biologist can do it.
![Page 10: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/10.jpg)
APGrid Core Meeting Phuket 2002
10
![Page 11: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/11.jpg)
APGrid Core Meeting Phuket 2002
11
In the Pipeline (cont.)
Regional support forum for BioGRID participants, bioinformaticians and biologists.
![Page 12: APGrid Core Meeting Phuket 20021 Asia Pacific BioGRID initiative A/P Tan Tin Wee, Mark De Silva, Lim Kuan Siong – Bioinformatics Centre, National Univ](https://reader035.vdocuments.site/reader035/viewer/2022072016/56649efa5503460f94c0d0e7/html5/thumbnails/12.jpg)
APGrid Core Meeting Phuket 2002
12
Contacts
Email: [email protected]://www.bic.nus.edu.sg/biogridHuman:– Ong Guan Sin
<[email protected]>– Assoc Prof Tan Tin Wee