CCG Computing Resources

The CCG PhyloCluster is a 280-core Apple Xserve High Performance Computing Cluster with 8-12 GB RAM/node (232 GB total). The cluster runs on the Apple Snow Leopard server OS.

Processors - 11 of the 23 nodes have dual quad-core Intel Xeon 2.8GHz processors with 8MB L3 cache per processor. The remaining 12 nodes have dual quad-core 2.26GHz Intel Xeon 5500 series “Nehalem” processors with 8MB L3 cache per processor.

Memory - 11 nodes have 8 GB of 1066MHz DDR3 ECC memory and 12 nodes have 12 GB each for a total of 232 GB of RAM.

Storage - The Headnode has 1x3TB 7200 SATA drives with 32MB disk cache configured as RAID 5.The computing nodes each have 1TB SATA drives. All data is read and written to an NFS mounted NetApp FAS 3140 file server with more than 100TB of disk space with maximum capacity of 420TB.

Power - APC Smart-UPS RT 8000 208V - 6400 watts

OS - MacOS X Server v10.6 Snow Leopard. Managed by Sun Grid Engine 6.2

Access to the cluster is via the BioTeam iNquiry web interface, which permits submission of various analyses to the cluster through a web browser. Currently available applications include PAUP, MrBayes, RAxML, Garli, BEAST, Clustal, and MAFFT. Due to license agreements with software publishers, access to the PhyloCluster is restricted to employees of the California Academy of Sciences. If you want access and are an employee of CAS contact Brian Simison.

http://phylocluster.calacademy.org/inquiry

"ChuckD" is a dual Xeon E5-2650 (8-core/16-thread = 32 total) 64-bit server with 128 GB RAM and 8TB of RAID 0+1 storage.

The system is loaded with various genomics tools, including:

• Galaxy
• R-studio
• Stacks (RADseq)
• AllPaths LG
• Discovar denovo
• SOAPdenovo
• Bowtie2
• CLC Genomics WorkBench 9
• Geneious Pro 9
• BEAST v2.4.3
• Structure v 2.3.4
• Trinity
• Velvet/Oases
• FastX toolkit
• and many others

"TdobZ" is a quad Xeon E5-4657L v2 (12 core/24 thread=96 total) 64-bit server with 512 GB RAM and 12 TB RAID 0+1 storage.

This system is dedicate to genomic analyses and is loaded with many assembly and analysis tools, such as:

• Galaxy
• R-studio
• Stacks (RADseq)
• AllPaths LG
• Bowtie2
• Discovar denovo
• SOAPdenovo
• Bowtie2
• CLC Genomics WorkBench 9
• Geneious Pro 9
• BEAST v2.4.3
• Structure v 2.3.4
• Trinity
• Velvet/Oases
• FastX toolkit
• and many others

The CCG has ten desktop computers (5 Macs and 5 Windows) with most software available for molecular studies.

• Geneious
• Mesquite
• MacClade
• BioEdit
• MrModeltest2
• PAUP
• ​TreeView
• FigTree
• Tracer
• BEAST
• RAxML
• Sequencher
• MrBayes
• ​MAFFT
• Clustal
• ​Muscle
• Arlequin
• Genepop
• Migrate
• IMa
• BEST
• DNAsp
• SimCoal2