White Papers
11
o MPSS 3.6.1
o MLNX OFED 3.2
o OM 8.3 and DTK update
o Lab7 Bio-Builds
o Molecular dynamics simulation
Bright Cluster Manager® 7.2
Bright Cluster Manager® (BCM) for Dell EMC is a comprehensive solution for provisioning, monitoring, and managing Dell EMC
clusters
[10].
Two Dell EMC PowerEdge R430 servers are deployed as head nodes in a HA active-passive configuration by using the NSS7.0-HA
solution as shared storage . The active head node is responsible for deploying and monitoring the 24 Dell EMC PowerEdge C6320
(assuming one rack design), the Dell EMC PowerEdge R930 (if used) and the other Dell EMC PowerEdge R430 servers which act as
the login nodes. In a scenario where the active head node fails, Bright Cluster Manager® provides an option of automatically failing
over to the second head node, or a failover can also be done manually in case the active head node requires servicing. The BCM
image includes Mellanox OFED and Red Hat Enterprise Linux version (RHEL) 7.2, with which, the head nodes and compute nodes are
deployed. The Bright Cluster Manager® 7.2 can be used to perform several day-to-day tasks, a few of which are:
o Monitoring made easier with on-the-fly graphs, rack view, multiple clusters, and custom metrics
o Parallel shell to run commands on all or a subset of the nodes effortlessly
o Powerful automation: thresholds, email alerts, and actions
o Integration with key workload managers such as SLURM, PBS Pro, Moab, Maui, Torque, Grid Engine, LSF, and
OpenLava
o Simplified patching and updating OS to keep the system secure
Lab7 BioBuilds
BioBuilds is a well maintained, versioned and continuously growing collection of open-source bio-informatics tools from Lab7 [11]. They
are prebuilt and optimized for a variety of platforms and environments. BioBuilds solve the software challenges faced in the life
sciences domain.
o Imagine a newer version of a tool being released. Updating it may not be straight forward and would probably involve
updating all the dependencies the software has as well. BioBuilds include the software and its supporting dependencies
for ease of deployment.
o Using BioBuilds among all the collaborators can ensure reproducibility since everyone is running the same version of the
software.
In short, it is a turnkey application package. More information about Lab7 and BioBuilds can be found at Reference 10.
PERFORMANCE EVALUATION AND ANALYSIS
Aligner scalability
This is a base-line test in order to obtain information useful to set up fair performance tests. Burrows-Wheeler Aligner (BWA) short
sequence aligner is tested here since it is a key application in variant analysis pipelines for whole genome sequencing data.
Aligner scaling test configuration
A single PowerEdge C6320 server is used to generate baseline performance metrics and ascertain the optimum number of cores for
running BWA [12]. Two different configurations, Intel Xeon Processor E5-2680 v3 with DDR4-2133 and Intel Xeon Processor E5-2690
v4 with DDR4-2400 are tested. For Broadwell CPUs, snoop mode is set to “opportunistic snoop broadcast” while “early snoop” mode is
chosen for Haswell CPUs. The total 256 GB of memory is used for the both test cases.