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Installed Stampede Specifications
1 Rack of compute hardware
The Rack containing 40 Compute Nodes, divided into 4 shelves.
Each Compute Node consists:
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File System
ZAMREN uses NFS to serve two directories, HOME and SCRATCH . The HOME directory has a 2.5 GB quota and is backed up. SCRATCH is for temporal storage and is purged periodically and hence not backed up. It has a 5TB quota.
Home
When you login,the system automatically sets you to the home directory, /home/xxxxxxxx where xxxxxxxx is replaced by your login name. Users should store important files that should be backed up in this directory up as home directory is backed up daily. This directory has a quota limit of 2.5 GB. The login node and any compute node can access this directory. Users are allowed to install applications in their home directories. However , ZAMREN will not support those applications.
Execution of jobs in the home directory is not allowed. Jobs executed from this directory will be automatically stopped.
Scratch
The directory is meant for storing temporary files and is accessible from compute nodes. Execution of jobs should be done from here.
Please note that files are not backup up in this directory and can be purged at anytime. No recovery services will be available for files once purged. Users are urged to be saving their files in their home directories.
Software
ZAMREN provides a range of third party and open source software for general use. The following packages are currently installed and supported on the cluster. Users can compile and install their own applications, however, these are not supported.
| Package Name | Brief Description | Field of Study | Link to Guides |
| GADGET | GAlaxies with Dark matter and GasintEracT - A code for collisionless and gasdynamical cosmological simulations | Astrophysics | http://astro.phy.vanderbilt.edu/~sinham/tutorials.html |
| GROMACS | GROningen MAchine for Chemical Simulations is used for simulation of Newtonian equations of motion for systems with hundreds to millions of particles. Designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded interactions | Molecular Dynamics | http://www.gromacs.org/ |
| NAMD | NAMD is a parallel, object-oriented molecular dynamics code designed for high-performance simulation of large biomolecular systems | Molecular Dynamics | http://www.ks.uiuc.edu/Research/namd/ |
| QUANTUM EXPRESSO | An integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials |
To see the list of available software on a cluster, please use the Modules command. The resulting output lists the name of the software and version number:
