Tools

Data analysis tools

Computer simulations involve the use of a set of analysis tools. Here, we share notes and ideas on programs commonly used in the CSML.

• Autocorrelation
• Generic Analyzer
• Gnuplot
• Compressed data files

Programming

• Compiler notes
• Debugging
• Programming notes

Document processing

Ideally, we prepare manuscripts in LaTeX. Occasionally, especially when collaborating with other research groups, it may be necessary to work in Microsoft Word.

• Notes on using LaTeX for manuscripts
• Notes on using Microsoft Word for manuscripts

Job submission and scheduling

• Notes on Torque
• Notes on Maui

UNIX

• Password-less login via ssh
• Short version of password-less login: (1) go to your home folder (e.g. ariadne:~/ ). (2) type "ssh-keygen" and press the enter key a few times to leave all answers blank (unless you are prompted to override the existing key in which case you should type "yes"). (3) type "ssh-copy-id XX" , where "XX" is the server name or IP address you wish to ssh into and enter the password. You can repeat this step and add multiple addresses. (4) On servers running Open-SUSE (ariadne, minotaur, hydra) you should also copy the generated key to: "cp ~/.ssh/authorized_keys ~/.ssh/authorized_keys2 ". Re-login and voilà, no more password needed. The same procedure also works on a macOS. However, ssh-copy-id needs to be installed (e.g. via brew install ssh-copy-id) and step (4) should be skipped.
• Command-line interface on Linux/UNIX

Data visualization tools

In order to communicate our research effectively, it is often useful to visualize the data from simulations. Here are a set of tools for creating/editing images and videos.

Visualizing Dump Files

• VMD
• pymol

Handling image/video files

• FFmpeg

Miscellaneous

• Dropbox
• Clonezilla