Biomedical Informatics Hardware

Cluster Computers

  • Cluster computers in the C2B2 environment are built using either the ROCKS distribution of Linux or BCS (basic clustering scripts). Jobs are submitted using the Sun Grid Engine batch system. GNU C, C++, Java and Fortran compilers are available. MPI programming environments are supported (MPICH, MPICH2, LAM, OpenMPI). The clusters have access to several file servers, including commercial Isilon® and BlueArc® network attached storage (NAS).
  • C2B2 also houses and maintains clusters belonging to individual C2B2 Faculty members.
NameModelClock Speed>NodesCPU Cores CPU Type Memory/NodeOSStorageComments
atlas Dell PowerEdge 1750 3.06 GHz 48 96 Intel Xenon dual core 2GB Red Hat Enterprise Linux 3 72GB local disk per node SCSI
bisr Dell dual core Xenon Pro 2.66 GHz 1 2 Intel Xenon dual core 36GB Windows Vista 700GB
cronus Western Scientific 2.0 GHz 28 56 Intel Xenon dual core 2GB Red Hat Linux 7.3 18 GB local disk per node Additional storage: 2.5 TB RAID-5 14 disk array
gaia Dell PowerEdge 1955 Blade Cluster 3.0 GHz 100 blades 400 Intel Xeon dual core 8 or 16 GB ROCKS 4.2 Linux (Red Hat Enterprise 4) 73 GB local disk per node Each blade has two sockets, each socket holds a dual-core CPU chip. 1333 MHz FSB.
titan HP BL2x220 BladeSystem c7000 3.0 GHz 464 blades 3712 Intel Xeon quad core 16 or 32 GB Fedora Core 10 120 GB local disk per node 10 GbE core switch with 1 GbE to nodes. Top500 Listing

Large Memory SMP (Symmetric MultiProcessing)

  • In this architecture, all memory is shared between the individual processors. With 8 CPUs and 32 GB of shared memory, the SunFire V880 machine "adsolaris" is our largest and most flexible general purpose computer. It is especially suitable for jobs requiring large amounts of memory in a single process, or jobs optimized to run in a multi-CPU, shared memory environment. It also hosts two legacy applications: the Paracel GenomeAssembler and the Paracel TranscriptAssembler packages. The machine "adsoltest" is intended for development and testing.
NameModelClock Speed>CPU NumberCPU Type Memory OSStorage
adsolaris SunFire V880 750 MHz 8 64 bit UltraSparc III Solaris 9 Fast IO to built in SCSI 6X73 GB for scratch
adsoltest SunFire V880 750 MHz 2 64 bit UltraSparc III 4 GB sShared Memory Solaris 9 Fast IO to built in SCSI 2X73 GB for scratch

File Servers

  • The facility has several file servers. The BlueArc is an Enterprise class server providing very high speed access. Through the use of storage pool technology, additional hard drives can be transparently added and allocated to existing or new filesystems as needed.
NameMakeCapacity>TypeClock Speed CPU Cores CPU TypeMemoryOSConnectivity
adtera custom 3 x 1.6 TB RAID-5 IDE 2.4 GHz 2 Intel Xeon Dual Core 3 GB RH Enterprise Linux 3 1 Gbit/sec eTDernet
apollo BlueArc 15TB NAS N/A N/A FPGA N/A Silicon Server 4.1 Gbit/sec eTDernet
fsnode custom 1TB RAID-5 SCSI 1.0 GHz 1 Intel Pentium III 2 GB RH Application Server 2.1 1 Gbit/sec eTDernet
fsnode1 custom 1TB RAID-5 SCSI 1.0 GHz 1 Intel Pentium III 2 GB RH Application Server 2.1 1 Gbit/sec eTDernet
ifs Isilon 120TB Clustered NAS N/A N/A N/A N/A Isilon/FreeBSD 14X1 GbE Infiniband 10 Gbps backend)
Ihn LefTDand Networks 7.2TB iSCSI SAN N/A N/A N/A N/A LHM/Linux 4X1 GbE

Database Servers

NameMakeRDMSClock SpeedCPU Cores CPU Type MemoryOSOSConnectivity
adora custom Oracle 9i 2.4 GHz 2 Intel Xeon Dual Core 4 GB WIndows Server 2003 1.6 TB, 3 x 73 GB System disk (RAID-5) 1 Gbit / sec private, 1 Gbit / sec to NAS
adsql custom MySQL 1.26 GHz 1 Intel Pentium III 2GB Red Hat Enterprise 3 4.5 GB 100 Mbit/sec, 1 Gbit/sec to NAS

Utility Servers

  • adgate (login gateway servers) - Two servers in a fail-over configuration provide a single login point for access to all other machines.
NameRoleClock SpeedCPU CoresCPU Type Memory OSStorageConnectivity
adcomp Utility 2.4 GHz 2 Intel Xeon Dual Core 4 GB Red Hat Enterprise 3 40 GB 100 Mbit/sec, 1 Gbit/sec to NAS
adcomptest Utility 2.4 GHz 2 Intel Xeon Dual Core 4 GB Red Hat Enterprise 5 40 GB 100 Mbit/sec, 1 Gbit/sec to NAS
addwnld Downloads 1.25 GHz 2 Intel Xeon Dual Core 4 GB Red Hat Enterprise 4 4.5 GB 100 Mbit/sec, 1 Gbit/sec to NAS
adgate1 Login Gateway 2.4 GHz 2 Intel Xeon Dual Core 2 GB Red Hat Enterprise 3 30 GB 100 Mbit/sec, 1 Gbit/sec to NAS
adgate2 Login Gateway 2.4 GHz 2 Intel Xeon Dual Core 2 GB Red Hat Enterprise 3 30 GB 100 Mbit/sec, 1 Gbit/sec to NAS
adparacel Utility 1.25 GHz 2 Intel Xeon Dual Core 1 GB Red Hat Application Server 2.1 18 GB 100 Mbit/sec, 1 Gbit/sec to NAS
adweb1 Webserver-Websites 400 MHz 4 Intel Pentium III 4 GB Red Hat Enterprise 3 70 GB 100 Mbit/sec, 1 Gbit/sec to NAS
adweb2 Webserver-Websites 400 MHz 4 Intel Pentium III 4 GB Red Hat Enterprise 3 70 GB 100 Mbit/sec, 1 Gbit/sec to NAS
backupserv Backups 2.4 GHz 2 Intel Xeon Dual Core 4 GB Windows Server 2003 1 TB 1 Gbit/sec

Additional Special Purpose Machines

  • A Scalar 1000 tape robot holds 256 tapes for backups.