High Performance Computing

“When I care how fast I get an answer”

Cluster user setup at work this week.

HPC has a lot of jargon and acronyms.

Intro: According to XSEDE (reference?), 31% of HPC users are in Molecular Biosciences

Concerned with number of Floating Point Operations Per Second (FLOP/s). The number the environment can provide is a concern. Delivers large amounts of processing capacity over long periods of time. Sustained vs. peak cycles – as close to 100% as possible. For example, “K” supercomputer >10PetaFLOP/s at 93%

Bioinformatics requires many task computing, completing large number of relatively short jobs. Need to effectively manage. We are task parallel vs. other applications more data parallel

Cluster: one or more networks, nodes connected. Software (MPI, open source) allows nodes to communicate, allows users to reserve resources. Log on to one node. 1 master, 4 slaves. Interconnect network.

Infiniband “fabric” with multicore parallel workstation

RDMA- Infiniband mediates interconnections

UMA- memory for all

NUMA- pools of memory

1 node has 64 (or 32?) cores

AMD vs. Intel processors, we have AMD

Cannot send data faster than latency and bandwidth of network (microseconds), want low latency.

Build RAM disk, put files directly on memory of computer, just like having solid state disk on laptop

Find code for GPU, co-processors (?)


Running faster, cache memory- order in which numbers are stored changes depending on what language you use. Efficient code will not waste space. Writing loops impacts the order in which data goes into CPU memory.

Running faster pipelines, n-stage pipeline, eliminate “if” loops with branch prediction, profile code if possible

Apparently FMA (floating multiplier add) not relevant to bioinformatics tasks?

Introduce checkpoints in code.


About Lisa Johnson

PhD candidate at UC Davis in Molecular, Cellular, and Integrative Physiology
This entry was posted in High Performance Computing. Bookmark the permalink.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s