CBS Bioinformatics Resources

High Performance Computing (HPC) installation

Name	Model	Specification	Comments
genome	Origin 300	32 500 MHZ IP35 Processors (MIPS) CPU: R14000 Processor Chip Revision: 2.4 FPU: R14010 Floating Point Chip Revision: 2.4 Main memory size: 16384 Mbytes (shared memory) Instruction cache size: 32 Kbytes Data cache size: 32 Kbytes Secondary unified instruction/data cache size: 2 Mbytes Operating system: IRIX 6.5	CBS WWW server, offering a large number of public bioinformatics prediction and computation services. System administration tasks (NIS, backup, CXFS etc.) are run here as well. The system is not available to users.
cell	Origin 300	18 500 MHZ IP35 Processors (MIPS) CPU: R14000 Processor Chip Revision: 2.4 FPU: R14010 Floating Point Chip Revision: 2.4 Main memory size: 16384 Mbytes (shared memory) Instruction cache size: 32 Kbytes Data cache size: 32 Kbytes Secondary unified instruction/data cache size: 2 Mbytes Operating system: IRIX 6.5	This server is mainly used for running large parallel memory intensive jobs. This architecture is being phazed out as a bioinformatics platform!
organism	Origin 300	32 500 MHZ IP35 Processors (MIPS) CPU: R14000 Processor Chip Revision: 2.4 FPU: R14010 Floating Point Chip Revision: 2.4 Main memory size: 32768 Mbytes (shared memory) Instruction cache size: 32 Kbytes (on chip) Data cache size: 32 Kbytes (on chip) Secondary unified instruction/data cache size: 2 Mbytes Operating system: IRIX 6.5	This server is mainly used for running large parallel memory intensive jobs. This architecture is being phazed out as a bioinformatics platform!
life	Altix 3000	64 900 MHz Itanium 2 model 0 Rev. 7 Processor (Intel) CPU: Itanium 2 model 0 Rev. 7 FPU: Itanium 2 model 0 Rev. 7 Main memory size: 181.89 Gb (shared memory) Instruction cache size: 32 Kbytes Data cache size: 32 Kbytes Secondary unified instruction/data cache size: 8 Mbytes Operating system: SuSE Linux	This server is mainly used for running large parallel and extremely memory intensive jobs. This server is binary compatible with Linux; however, the performance of many programs can be improved significantly by compiling and optimizing fusing the native Intel compilers available. PBS (Portable Batch System, professional edition) is installed here.
ibiology	Altix 3000	64 1300 MHz Itanium 2 model 1 Rev. 5 Processor (Intel) CPU: Itanium 2 model 1 Rev. 5 FPU: Itanium 2 model 1 Rev. 5 Main memory size: 192 Gb (shared memory) Instruction cache size: 32 Kbytes Data cache size: 32 Kbytes Secondary unified instruction/data cache size: 8 Mbytes Operating system: SuSE Linux	This server is mainly used for running large parallel and memory intensive jobs. This server is binary compatible with Linux; however, the performance of many programs can be improved significantly by compiling and optimizing fusing the native Intel compilers available. PBS (Portable Batch System, professional edition) is installed here.
sbiology	Altix BX2	128 1500 MHz Itanium 2 model 2 Rev. 1 Processor (Intel) CPU: Itanium 2 model 2 Rev. 1 FPU: Itanium 2 model 2 Rev. 1 Main memory size: 768 Gb (shared memory) Instruction cache size: 32 Kbytes Data cache size: 32 Kbytes Secondary unified instruction/data cache size: 8 Mbytes Operating system: SuSE Linux	This server is mainly used for running large parallel and memory intensive jobs. This server is binary compatible with Linux; however, the performance of many programs can be improved significantly by compiling and optimizing fusing the native Intel compilers available. PBS (Portable Batch System, professional edition) is installed here.
interaction	Altix 3000	32 1500 MHz Itanium 2 model 1 Rev. 5 Processor (Intel) CPU: Itanium 2 model 1 Rev. 5 FPU: Itanium 2 model 1 Rev. 5 Main memory size: 118.60 Gb (shared memory) Instruction cache size: 32 Kbytes Data cache size: 32 Kbytes Secondary unified instruction/data cache size: 8 Mbytes Operating system: SuSE Linux	This server is mainly used for interactive testing and compiling, as well as for updatine and maintenance of the available data resources (datbases and databanks). It is not supposed to be used for large batch jobs. This server is binary compatible with Linux; however, the performance of many programs can be improved significantly by compiling and optimizing fusing the native Intel compilers available. The server functions as MySQL server, and is used for web based services.
/home/databases	TP9600 RAID 5	TP9500 RAID 5 storage rack 122 x 120 Gb disks 2 x RAID 4 port 1 Gbit FC ctrl 13 Tb Connected to the servers mentioned above by two 2 Gbit fiberchannel network (Storage Area Network, SAN).	The various non-relational databases (like BLAST'able sequence data) are stored here.
/home/mysql	TP9400 RAID 5	TP9400 RAID 5 storage rack 77 x 73 Gb disks 4 x RAID 4 port 1 Gbit FC ctrl 6.5 Tb Connected directly to the mysql relational database server by two 1 Gbit fiberchannel.	The relational databases are stored here.
/home/projects	IS4000 RAID 5	IS4000 RAID 5 storage rack 300 Gb disks 4 x RAID 4 port 2 Gbit FC ctrl 50 Tb Connected to the servers mentioned above by two 2 Gbit fiberchannel network (Storage Area Network, SAN).	The user (projects) data and the databases are stored here.
/home/people	RAID 5	RAID 5 storage rack 12 x 73 Gb disks 1 x RAID 1 port 1 Gbit FC ctrl 0.5 Tb Connected to dedicated NFS server by a 1 Gbit fiberchannel.	The home directories of all users are located here.

Datawarehouse