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Oakley is an HP-built, Intel® Xeon® processor-based supercomputer, featuring more cores (8,328) on half as many nodes (694) as the center’s former flagship system, the IBM Opteron 1350 Glenn Cluster. The Oakley Cluster can achieve 88 teraflops, tech-speak for performing 88 trillion floating point operations per second, or, with acceleration from 128 NVIDIA® Tesla graphic processing units (GPUs), a total peak performance of just over 154 teraflops.
The Ohio Supercomputer Center's IBM Cluster 1350, named "Glenn", features AMD Opteron multi-core technologies. The system offers a peak performance of more than 54 trillion floating point operations per second and a variety of memory and processor configurations. The current Glenn Phase II components were installed and deployed in 2009, while the earlier phase of Glenn – now decommissioned – had been installed and deployed in 2007.
If you get a license error when you try to run a third-party software application, it means either the licenses are all in use or you’re not on the access list for the license. Very rarely there could be a problem with the license server. You should read the software page for the application you’re trying to use and make sure you’ve complied with all the procedures and are correctly requesting the license. Contact OSC Help with any questions.
This section summarizes two groups of batch-related commands: commands that are run on the login nodes to manage your jobs and commands that are run only inside a batch script. Only the most common options are described here.
Many of these commands are discussed in more detail elsewhere in this document. All have online manual pages (example:
man qsub) unless otherwise noted.
The batch system provides several environment variables that you may want to use in your job script. This section is a summary of the most useful of these variables. Many of them are discussed in more detail elsewhere in this document. The ones beginning with
PBS_ are described in the online manual page for
PBS directives may appear as header lines in a batch script or as options on the
qsub command line. They specify the resource requirements of your job and various other attributes. Many of the directives are discussed in more detail elsewhere in this document. The online manual page for
man qsub) describes many of them.
PBS header lines must come before any executable lines in your script. Their syntax is:
FFTW is a C subroutine library for computing the Discrete Fourier Transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. It is portable and performs well on a wide variety of platforms.
EMBOSS is "The European Molecular Biology Open Software Suite". EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole.
Within EMBOSS you will find around hundreds of programs (applications) covering areas such as:
- Sequence alignment,
- Rapid database searching with sequence patterns,
- Protein motif identification, including domain analysis,
- Nucleotide sequence pattern analysis---for example to identify CpG islands or repeats,
- Codon usage analysis for small genomes,
- Rapid identification of sequence patterns in large scale sequence sets,
- Presentation tools for publication
Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.