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, 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