Computer News No. 114 Mar.-Apr. 2005

Upgrade of the BIOINFO Server

    1. Hardware upgrade of the BIOINFO server system
    2. Software upgrade of the system  

1. Hardware upgrade of the BIOINFO server system

The BIOINFO server system, which supports large-scale genome and protein research, was installed in 2002 under the umbrella of the BIOSUPPORT project, a collaboration between HKU Pasteur Research Centre, HKU Computer Centre , and Centre de Ressources INFOBIOGEN, France, with funding support from the HKSAR Government Innovation and Technology Fund.  The system is available for access by users in HKU as well as other research organizations.

Since 2004, the BIOINFO server system was heavily used, especially by researchers doing statistical analysis and gene signal modeling in the bioinformatics area.  We are pleased to report that an hardware upgrade on the BIOINFO system to a SUN-Fire 6900 system, with the last contribution of funding from the BIOSUPPORT project, was completed in February 2005.  The upgraded system consists of 24 "SUN 1.2GHz UltraSPARC-IV" CPUs and 96GB of physical memory (previously 24GB).  In addition to the original 2,400 GB of raw disk storage, the system is also enhanced with new 3,500 GB (raw capacity) of SUN StorEdge 6130 disk storage and a L100 tape library with 4 LTO-2 tape drives for doing backup.  The CPU benchmark of this high performance new system is now 295 SPECint_rate2000, and 112.7 GFLOPS.  It is estimated 2.5 times faster than the system before upgrade.  Details of its hardware configuration can be viewed at http://bioinfo.hku.hk/hardware.html

2. Software upgrade of the system

The operating system (OS) is also upgraded from Solaris 8 to Solaris 9 during the hardware upgrade.  All the previously installed software packages and programs are binary compatible to execute on this upgraded system.  All the compilers and linker libraries are also compatible under new OS environment.  Therefore all the existing users programs can run without re-compilation.  As this upgrade had greatly enhanced the computational power and storage capacity of this system for running more computational intensive bioinformatics analysis, we shall migrate the GCG & Seqweb programs, now running on the HKUCC system, to the BIOINFO system soon.  Our users will be informed accordingly and we shall report in a future issue of the Computer News.  Please address all enquiries about the BIOINFO system to biosupport@bioinfo.hku.hk