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The National Center for Supercomputing Applications (NCSA) gifted the Institute for Genomic Biology (IGB) at the University of Illinois at Urbana-Champaign the supercomputer Ember. Originally funded by the National Science Foundation (NSF), it will now be used to work in genomics and transcriptomics. It will be handled by the High-Performance Biological Computing (HPCBio) group, which runs the infrastructure for bioinformatics.
The Ember supercomputer was activated in 2010 to be used in a variety of scientific research, in particular in the fields of chemistry and mechanics of solids and fluids. It consists of SGI Altix UV systems with a total of 1,536 cores, 8 terabytes of memory divided between various nodes and 170 TB of storage memory. Like more then 90% of supercomputers, it uses a version of the Linux operating system.
It may not look anything exceptional compared to the most powerful supercomputers in the world but it’s estimated that today it would still cost two million dollars. The IGB already has its biocluster, a computer system consisting of several nodes to carry out their work, but its computing power was limited. For this reason, the IGB was already using the Ember supercomputer through the NCSA supercomputer and when it was decommissioned by NCSA on October 1, 2012 giving it to the IGB made sense.
In simple terms, genomics is a branch of molecular biology based on bioinformatics that studies the genome and in particular its structure, content, function and evolution. Transcriptomics, or gene expression profiling, measures the activity of thousands of genes to create a global image of cellular function.
With the addition of the Ember supercomputer to the IGB biocluster, this type of work will be performed with much greater efficience, especially thanks to the amount of RAM of its nodes, which have 2 TB against the 24 GB of the nodes that previously formed the biocluster. The bioinformatics applications used for these studies need a lot of RAM so it’s a significant step forward.
This solution is a great way to “recycle” a supercomputer. Just a few weeks ago the story of the Encanto supercomputer showed the risk of spending many millions of dollars rashly. In the case of the Ember supercomputers instead the system has been used in an optimal way and once its original task ended it was quickly transferred to another place where it can still be useful for a long time.
