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Hardware
VIPBG is hosting a newly upgraded Beowulf cluster for Statistical analysis, GWAS analysis, Genotyping imputation, sequencing analysis and Gene Interaction, configured with a total of 248 cores, including:
| Model | # cores | # machines | Nodes / machine | CPU / node | RAM / node |
|---|---|---|---|---|---|
| Dell C610 | 192 | 4 | 4 | Dual 6-core Intel Xeon 3.6Ghz | 64 Gb |
| Dell PowerEdge R610 | 16 | 2 | 1 | Dual 4-core Intel Xeon 3.6Ghz | 32 Gb |
| HP DL135 Server | 80 | 10 | 2 | Dual 2-core AMD64 | 4 Gb |
The computation servers are configured into different function queues to process submitted jobs in order to ensure all jobs running efficiently. All of the computation servers are connected to a 100 Tb centralized network storage running parallel file system, with additional 50 Tb storage to backup the critical data.
- PBSPro 11 www.altair.com batch management system for configuring the cluster system
- Ganglia Node performance system monitoring
In addition, for modest computation, data sharing and transferring and all other functions, we have:
Locally administrated 64bit Dell PowerEdge R710 Redhat Linux server configured with 8 cores, 16 Gb RAM, 4Tb storage for users to access it remotely using ssh connection, this server has SAMBA connection enabled for users to share through windows environment for daily DNA data collection and data analysis (Sam Chen).
Locally administrated 64 bits Dell PowerEdge server running Linux centOS 5 and configured as 8 cores with 24GB RAM, 5TB network storage, users are able to access it remotely via ssh connection. This server has mySQL installed for running DNA sequencing analysis using a software progeny, it also has all additional research software installed for data analysis (Brien Riley).
PHYSIO (www.vipbg.vcu.edu)
Web server maintained locally for departmental website and information update and exchange on education, research and study events.
A local mail server running postfix cyrus IMAP service to have users send emails independently, including web calendars and email reminders for grant application deadlines.
A compilation server running Linux including older versions of compilers for users to compile code into different platforms.
All servers are physically secured, follow appropriate multilevel access control protocols, and maintain long term data security via daily and monthly backup/restore procedures. All users are connected to a TCP/IP local area network within VCU's WebVPN network or customized IP registered by specific user. Desktop resources, network storage, and email systems are protected from virus attacks via antivirus software that is automatically updated weekly. Desktop PCs and campus networks are behind appropriate firewalls. Desktops and their corresponding network resources follow appropriate multilevel access protocols; network data storage availability is assured via nightly and monthly archival procedures.