BRAF HPC Resources

PARAM BioBlaze is a blade based system with peak compute power of 10.65 TF. It has 32 blade servers as compute nodes which contains total 512 computing cores of intel Xeon (sandy bridge) processor running at optimum 2.6 GHz. This cluster has 4GB per core RAM which accumulates to 2TB RAM. Compute nodes communicates with each other over 56 Gbps high speed FDR Infiniband interconnect. 20 TB of scratch storage is mounted on nodes using the same 56Gbps link so that the disk input/output is fast.

Bio Blaze
Hardware Overview
System Name PARAM BioBlaze
Operating System Redhat Enterprise Linux 6.3
Number of Nodes 32
Number of Processing Cores 512
Total Memory 2 TB
Peak Performance 10 Teraflops
Total Disk 20 TB
Interconnect Infiniband 48 port FDR
System Software/Library Overview
Compilers/Debuggers GNU, Intel Cluster Suite 2013
Batch System Open Pbs, Maui
Math Library Intel MKL

PARAM BioChrome Cluster is an advance blade server based HPC facility. The cluster has a capacity of 5 TeraFlop with 504 computing cores using 6 core Intel Xeon 2.67 GHz processor. The supercomputing environment consists of 3 Blade Chassis containing total 42 Blade servers as compute nodes. Each blade contains two 6 core processor which accumulates to 12 cores per node and a total of 504 computing cores. It has 2 Master nodes 2 Storage servers in High Available mode. Total RAM available is 2016 GB. The Storage has 20TB usable storage space configured as RAID5. High speed QDR Infiniband with 40Gb/s speed forms the main interconnection backbone network. Ethernet is also used as management network. The cluster is based on RHEL 6.0 for master nodes, compute nodes and servers. Cluster Management Utility (CMU) software from HP is used as cluster management tool. MVAPICH2 is installed for MPI communications over Infiniband and Open PBS is used as cluster level jobmanager.

Bio Chrome
Hardware Overview
System Name PARAM BioChrome
Operating System Linux ( Redhat Enterprise Linux )
Number of Nodes 42
Number of Processing Cores 504
Total Memory 2 TB
Peak Performance 5 Teraflops
Total Disk 20 TB
Interconnect 4x Infiniband 48 port QDR
System Software/Library Overview
Compilers/Debuggers GNU, Intel Cluster Suite 2013
Batch System Open Pbs, Maui
Math Library Intel MKL

Another addition to BRAF is the latest storage known as PARAM BioBank. It is a data Storage solution for the current need of BRAF facility. It is a centralized NAS facility that can be used on the high speed network. The raw storage of 540 Tera bytes configured as RAID 6 on PARAM BioBank and 386 Tera bytes of usable space accessible on a single mount point with throughput of 1.5 Giga byte per second

Bio Blaze
Hardware Overview
System Name PARAM BioBank
Operating System Isilon One FS
Total Disk 540 TB
Throughput 1.5 Gpbs

NGS Server
For NGS applications which requires high memory, BRAF facility is equipped with high memory Servers. Each has total 512 GB RAM and 32 computing cores.

CISCO UCS 450 server
CISCO UCS 450 Server

Dell PowerEdge R910
Dell PowerEdge R910

Biogene is streamlined with RCS cards having Smith-watermann algorithm for local alignment. 16 RCS cards with embedded SW are installed on 16 nodes in the cluster. Jobs showed exponential improvement in run time.
RCS Card

Results
A test run for aligning "Titin" sequence from mouse against "nr" database was done which gave the following results with reference to the time required to complete the alignment.

  • Puntime of 6days 2hrs 45min using the serial version of SW is reduced to 6hrs 13min using single RCS card saving 95.75% runtime.
  • Using 16 cards runtime is reduced to 33min saving 99.62% runtime with respect to the serial version of SW without RCS.