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Computing
Systems 
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The AMDeC Bioinformatics Core Facility
currently hosts the following systems:
- ROCKS 3.2 Cluster -
A Linux-based 88 CPU cluster
for general purpose and parallel computing. Contains
44 nodes; each node contains
two 2.4 GHz Intel Pentium 4 XeonCPUs plus 2 GB of
memory and a 40 GB harddisk. The operating system is Red Hat Enterprise Linux 3 in a ROCKS configuration. The nodes are interconnected
with 2 Gbit/sec low-latency Myrinet networking. GNU C, C++, and Fortran compilers are
available. MPI programming is supported.
- Paracel GeneMatcher2 - accelerates dynamic programming algorithms such as Smith-Waterman, HMMer and Genewise.
- Paracel BlastMachine - accelerates all variants of BLAST, including PSI-BLAST, PHI-BLAST and MEGABLAST.
- Sun Sparc V880 - 8 x 750
Mhz CPUs with 32 GB of RAM, operating system is Solaris 9. Hosts Paracel GenomeAssembler
and TranscriptAssembler packages, and is available
for other programs requiring large amounts of memory.
In addition, a second V880 with 2 CPUs and 4GB of
RAM serves as a testing and development platform.
- Login servers -Two servers in a fail-over configuration provide a single login point for access to all other machines. These
are RedHat Enterprise Linux 3 based platforms. Each has dual-2.4 Ghz Intel Pentium Xeon CPUs with 2 GB
of RAM.
- File servers - There are
several file servers. The largest provides 5 TB of space and runs Red Hat Enterprise Linux 3. It has dual 2.4 GHz Xeon processors with 3 GB of memory. Two smaller fileservers run Red Hat Application Server 2.1 and provide 1 TB and 0.5 TB
of RAID-5 storage respectively. Each has a 1.0 Ghz Intel Pentium
III CPU and 2 GB of RAM, and an Adaptec 3400S quad-RAID controller.
- Additional special purpose
machines
- General purpose single node Linux computer
- Dual web servers
- Paracel access server (from which to send jobs to the BlastMachine and GeneMatcher 2)
- Oracle Database server
- MySQL server
- Dedicated download machine.
- Tape Backup Robot and Backup
Server.
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