GROMACS is a versatile package of molecular dynamics simulation programs. It is primarily designed for biochemical molecules, but it has also been used on non-biological systems. GROMACS generally scales well on OSC platforms. Starting with version 4.6 GROMACS includes GPU acceleration.
The only access to significant resources on the HPC machines is through the batch process.
Why use a batch system?
Access to the OSC clusters is through a system of login nodes. These nodes are reserved solely for the purpose of managing your files and submitting jobs to the batch system. Acceptable activities include editing/creating files, uploading and downloading files of moderate size, and managing your batch jobs. You may also compile and link small-to-moderate size programs on the login nodes.
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.
The BLAST programs are widely used tools for searching DNA and protein databases for sequence similarity to identify homologs to a query sequence. While often referred to as just "BLAST", this can really be thought of as a set of programs: blastp, blastn, blastx, tblastn, and tblastx.
There are two ways to connect to our systems. The traditional way will require you to install some software locally on your machine, including an SSH client, SFTP client, and optionally an X Windows server. The alternative is to use our zero-client web portal, OnDemand.
ANSYS offers a comprehensive software suite that spans the entire range of physics, providing access to virtually any field of engineering simulation that a design process requires. Supports are provided by ANSYS, Inc.
The Assisted Model Building with Energy Refinement (AMBER) package contains many molecular simulation programs targeted at biomolecular systems. A wide variety of modelling techniques are available. It generally scales well on modest numbers of processors, and the GPU enabled CUDA programs are very efficient.
HyperWorks is a high-performance, comprehensive toolbox of CAE software for engineering design and simulation.
The batch scheduler is configured with a number of scheduling policies to keep in mind. The policies attempt to balance the competing objectives of reasonable queue wait times and efficient system utilization. The details of these policies differ slightly on each system. Exceptions to the limits can be made under certain circumstances; contact email@example.com for details.
Several commands allow you to check job status, monitor execution, collect performance statistics or even delete your job, if necessary.
Status of queued jobs
There are many possible reasons for a long queue wait — read on to learn how to check job status and for more about how job scheduling works.
squeue command to check the status of your jobs, including whether your job is queued or running and information about requested resources. If the job is running, you can view elapsed time and resources used.