I want to show how to write script in VMD to stream line your visulization. VMD is a visualization software developed in UIUC. The default setting of VMD, compared to other softwares like VESTA, Atomeye, Avogadro, is quite 1990s. But it has a huge potential. After you know it well, you can easily fake it as any other visualization software :P
VMD is a fancy machine that every tiny part can be tuned. The best feature is definitely scripting interface. Most of the time I work with a huge batch of simulation with the same materials, usually the same...
A scratch folder usually refers to a folder that is fast for reading and writing. If you use a supercomputer, like those in XSEDE or NERSC, you will find out that the SCRATCH folder are the best place to run your simulation (though it is not suggested to store the data there). There may be multiple reseaons that the scratch folder is faster than normal disk. In our own in-house cluster, Fractal, the scratch folder is fast, simply because it is local and large.
Fractal has one main node and multiple compute nodes, where most of the data are stored at four hard disks at the main node...
Two node in Fractal, compute-0-0 and compute-0-4, was down because a wrong distro installation and was removed by the command
. However, after we moved Fractal to MGHPCC and change the main node IP address. This compute node cannot receive any DHCP installation offer from the main node. We used the standard command to install a new node, since the nodes were deleted from the Rock's list already. insert-ethers; and the node to boot from PXE network. But after waiting for 10-15 mins, the communication...
Module is a convinient way to manage shell environment variables and aliases. And it is simple enough for linux novice users to use the right software/compiler that they want. As far as I know, there are two module software, lmod and environmental module using tcl language.
Our cluster OS came with Environmental Module 3.2.10.
1. Customize module path (only needed for adding a new parent folder for modulefiles)
the Module software searches in a environment variable, MODULEPATH, for available modulefiles. The first step is to add a...
Fractal is getting more and more troublesome recently... It has a hug lap for ssh and also su . It took me a while to debug. In the end, my labmate, Aravind, found the culprit -- log file explosion. Here's some symptons observed and the final solution offered by Aravind. :)
1. use "vvv" mode for ssh to show error information.
$ssh -vvv email@example.com
OpenSSH_7.2p2, LibreSSL 2.4.1
debug1: Reading configuration data /etc/ssh/ssh_config
debug1: /etc/ssh/ssh_config line 20: Applying options for...
The cluster was shutdown remotely since the AC in 4-033 needs to be fixed.Two days later, however, we found that the shutdown process was hanged. All the node was off except the main node. The screen showed: