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New Fujitsu supercomputer fails on its first week in service

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June 21, 2013

Scientists at Fujitsu just had a bad week. That's because their shiny new supercomputer crashed just a few days after having been placed in service. Formally opened to user traffic on Monday, dubbed 'Raijin', the supercomputer is a Fujitsu Primergy system with 57,472 SandyBridge cores, 160 TB of main memory, 10 PB of usable high-speed filesystem space, all connected together with Mellanox FDR interconnectors.

About 68 percent of its nodes have 32 GB of memory, 31 percent feature 64 GB, and less than two percent of the nodes get 128 GB in all.

Fujitsu says its peak performance is 1.2 Pflops, and it achieved a six-fold improvement in filesystem performance compared to its predecessor, dubbed Vayu, a Sun Constellation whose 11,936 Xeon cores could only work at 140 Tflops.

On its start up day, the NCI says Raijin became Australia's number one supercomputer and number 24 in he Top 500 supercomputer list.

And how long did it take users to max out the new system? One day, according to the NCI's Ben Evans on Twitter. "We finally released the new NCI Raijin supercomputer for general access earlier this week. It took less than one day for users to spike to full capacity", he posted.

Worse, about half of that memory and CPU consumption was down to one single job. Associate Professor Evatt Hawkes had a code running on 32,769 cores - over half the system.

Hawkes’ work uses extremly detailed, first-principles simulations to answer fundamental scientific questions relating to combustion in next generation engines and combustion of new fuels.

"NCI is supplying researchers with both the infrastructure and world class expertise required to push the boundaries of innovative research in key disciplines that are of national importance to Australia. Among these are climate and earth systems science", said NCI director, Professor Lindsay Botten.

First-week jobs to run on Raijin included-- Extreme climate simulations for the Bureau of Meteorology, Geoscience Australia and other Australian centres of excellence; Quantum chromodynamics runs for a group led by Professor Derek Leinweber of the University of Adelaide; Black hole studies for ANU's Professor Geoff Bricknell; and A Queensland University study into the self-assembly and interaction of biomolecules in a membrane.

The system's administators are now in the process of porting software from Vayu to Raijin. Its clients include the ANU, the Bureau of Meteorology, Geoscience Australia, the Australian Research Council, and six research universities.

In other IT news

After a little over a year of development work and a few preview releases, Oracle is announcing the general availability of MySQL Cluster 7.3.

This brings a number of important new features and enhancements to the open source clustering module for the MySQL database.

But the real big news in this announcement is the long-awaited inclusion of the support of foreign key constraints, which had been one of the most requested feature enhancements for the database in the past three years.

MySQL's Cluster feature differs from its more powerful cousin, Oracle Real Application Clusters (RAC), in that it uses a "shared nothing" architecture, where none of the nodes share memory or disk storage. In that implementation, its design is closer to how IBM's DB2 handles clustering than to RAC.

With MySQL Cluster 7.3, the system can now automatically enforce foreign key referential integrity between tables, regardless of whether they are located in different nodes, different partitions, or even in different data centers.

An important point to mention here is that foreign key support is also available whether the application accesses the database via SQL or via one of the various non-SQL APIs that are available, such as Java, Memcached, or HTTP/REST.

The new version's SQL layer is now based on the latest MySQL 5.6 release, which allows database admins to combine the InnoDB and MySQL Cluster storage engines side-by-side on the same MySQL 5.6 server.

MySQL Cluster 7.3 also adds another major non-SQL access method, namely JavaScript support via Node.js. This allows applications written in JavaScript to directly access MySQL Cluster data stores without translating queries to and from SQL.

However, even those users who aren't interested in the new features might want to upgrade, as version 7.3 reportedly delivers between 1.5 and 7.5 times more data throughput to cluster nodes. It does this in a manner that is completely transparent to applications, meaning system admins should see their applications' performance improve as soon as they upgrade to version 7.3.

Setting up new clusters is also easier than ever, thanks to a new auto-installer that allows IT managers and admins to graphically configure and provision a cluster within a few minutes using a browser-based interface.

The full set of changes from the previous release can be reviewed in Oracle's official release notes. MySQL Cluster is open source software released under the GPLv2 license, and Oracle also offers commercial support along with a number of proprietary add-on features in the form of its MySQL Cluster Carrier Grade Edition (CGE) product.

But there are other ways to cluster a MySQL database, including ScaleDB and Galera, the latter being a set of patches that bake clustering support into the MySQL server itself.

In particular, those who have already migrated from MySQL to the competing MariaDB fork will want to consider one of the above options, as MariaDB does not support MySQL Cluster's NDB storage engine per default.

The GPL-licensed version of MySQL Cluster 7.3 is available for download from Oracle's MySQL website as of now.

Source: Fujitsu.

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