HPC Account and Software Setup
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1 HPC Account and Software Setup Ken-ichi Nomura MAGICS 2 nd Workshop at USC March 2, 2018
2 Wireless Network Configuration 1. USC Secure Wireless 2. eduroam 3. password: 4. USC Guest Wireless
3 Software Setup To access the USC HPC cluster, we need virtual terminal, ssh & scp client for remote login and transfer files. This slide will show you how to install Putty & FileZilla for Windows and Mac users, but you can also use any software you are familiar with. Putty FileZilla
4 Putty Setup (Windows users only) 1. Go to Putty website then click the download link. 2. After a new page opens, choose MSI( Windows Installer ) 64-bit link. 3. It will download the Putty installer executable. Double click the installer.
5 Putty Setup (Windows users only) Host Name: hpc-login3.usc.edu In Hostname (or IP address) box, type hpc-login3.usc.edu, then click Open button.
6 Putty Setup (Windows users only) You will be asked to type your username, e.g. magics35, and password. Login as: magicsxx Each of us uses one account through this workshop, so please do not lose your login information, or share with your friends.
7 How to Use Terminal (Mac users only) For Mac users, a virtual terminal called Terminal is available by default. No need to install anything. Either search it with Spotlight or go to /Applications/Utilities directory.
8 How to Use Terminal (Mac users only) Username: magicsxx Hostname: hpc-login3.usc.edu Open Terminal, then type ssh from command line. For example, $ssh You will be asked to type password. Type in your password, then press Enter key. That s it!
9 FileZilla Setup (Windows and Mac users) There are four boxes you need to type in. 1-Hostname, 2-Username, 3-Password, and 4-Port. Port is always 22. hpc-login3.usc.edu Host: hpc-login3.usc.edu Username: magicsxx
10 FileZilla Setup (Windows and Mac users) When you access a remote server first time, you will be asked to accept its host key, or not. Click OK.
11 FileZilla Setup (Windows and Mac users) Once you successfully log on the remote computer, you will see local files (red) and remote files (blue). You can drag&drop to transfer files between local and remote computers. Your Computer Remote Computer
12 Visualization & Analysis Software VMD: Visual Molecular Dynamics
13 VMD Setup Click Download VMD link on the left, then choose platform for your OS in VMD Version ( ) Platforms. Your platform is most likely LINUX_64 OpenGL, MacOS X OpenGL (32-bit Intel x86), or Windows OpenGL.
14 VMD Setup Simple registration is required to download VMD. Type username and password, then click Continue with registration or download. You will be asked a few more questions. Click the VMD license agreement button, then you will download a VMD installer with the executable.
15 Visualization & Analysis Software OVITO: Open Visualization Tool
16 OVITO Setup Click Download tab on top. Choose your OS, then click download link.
17 USC HPC Environment Setup USC HPC cluster has setup scripts (setup.sh) under /usr/usc directory to enable installed software and libraries. We are going to use Intel Fortran Compiler and OpenMPI library, Python Anaconda in the hands-on sessions. Copy dot.bashrc file to your home directory as.bashrc. $ cp ~magics35/magics/dot.bashrc ~/.bashrc Make sure you have following lines in your.bashrc file. $ cat ~/.bashrc # source /usr/usc/intel/default/setup.sh source /usr/usc/openmpi/default/setup.sh.intel source /usr/usc/python/anaconda3/setup.sh
18 Acknowledgement This work was supported as part of the Computational Materials Sciences Program funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, under Award Number DE-SC Materials software (Thermal Conductivity Plugins for LAMMPS, RXMD, QXMD, GEARS) used in this research was produced by USC MAGICS Center that is a part of the Computational Materials Sciences Program funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, under Award Number DE- SC
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