Getting started example: SLURM on Longleaf
Description: This guide will provide you with enough basic information to run straight-forward jobs on Longleaf. Please use the table of contents to access more detailed information, or email research@unc.edu with questions.   Log in to longleaf.unc.edu Log into longleaf.unc.edu using UNC credentials (UNC onyen and onyen password). ssh <onyen>@longleaf.unc.edu If you are using Linux or […]
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Research Computing Resources and Services (Boilerplate)
Description: (A downloadable PDF is here: Research_Computing_Resources_and_Services_for_Researchers_20170307) UNC-Chapel Hill recognizes that computational resources are an important part of research endeavors, and that research varies with respect to its data and processing demands, and also with respect to the need to compute, modify theories/codes, re-compute, etc..  UNC-Chapel Hill is also committed to providing a base computational resource […]
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Longleaf and Pine
Description: Longleaf is a new compute cluster designed for memory and I/O intensive, loosely coupled workloads with an emphasis on aggregate job throughput over individual job performance. In particular workloads consisting of a large quantity of jobs each requiring a single compute host are best suited to Longleaf. Pine is the purpose-built filesystem for high-throughput and […]
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Longleaf Frequently Asked Questions (FAQs)
Description: How do I get an account on Longleaf (or Killdevil)? Why are you using SLURM rather than LSF (like we are accustomed to)? What are the details of the new filesystem location(s)? Why aren’t `/netscr` nor `/lustre` present on Longleaf? What is the queue structure on Longleaf? How do I transfer data between Research Computing […]
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Getting Started with Globus Connect
Description: Below are the individual steps with example screenshots regarding the setup of your Globus login account, accessing our UNC Globus endpoint named “UNC, Research Computing, Datamover” (or uncch#unc-rc-dm).   There is an optional installation and configuration of your personal Globus Connect endpoint client. Globus addresses deficiencies in secure copy requests by automating large data transfers, by […]
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Getting Started on KillDevil
Description: Table of Contents Introduction System Information Getting an Account Logging In Directory Spaces Mass Storage Development and Application environment Applications available Software Development Tools Compiling Job Submission Transferring Files Using Tar to Archive FAQs Additional Help Introduction The KillDevil cluster is a Linux-based computing system available to researchers across the campus. With more than 9600 […]
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Gaussian: Tutorial on Converting Brookhaven Protein Data Bank (PDB) Files to Gaussian Input Files
Description: If a molecular structure is described in Brookhaven Protein Data Bank (PDB) file format, it can be converted to Gaussian input file using the NewZmat command. For example, one can obtain a PDB file for water ( water.pdb) which has the following listing: HEADER REMARK WATER MOLECULE H2O HETATM 1 H UNK 0001 0.000 0.780 […]
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Gaussian: Tutorial on Using LSF Scripts to Automate Jobs
Description: Introduction When Gaussian starts running jobs for relatively big molecules, it requires more disk space in saving some intermediate results during the course of the computation. It is always better to start up the job in scratch space to take advantage of unlimited disk space. In order to avoid moving files back and forth between […]
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Scientific Application – Schrodinger
Description: Table of Contents Overview Setting up Environment and Invoking from a Research Computing Server Installing Locally on a Windows Machine Notes Links Additional Help Overview Schrodinger is a suite of molecular modeling packages that take advantage of the latest technological advances in computational chemistry. Jaguar, the high-performance ab-initio quantum mechanics application, and MacroModel, the most […]
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Gaussian: Tutorial on Water Single Point Energy and Scripts
Description: Introduction You can use a script to create and save a Gaussian file based on restricted Hartree-Fock calculations on a 6-31G(d) basis set for water single point energy. Tutorial Steps Use your favorite editor to create a script file with the following lines and save the file as “spe_hf_6-31g-3”. Water molecule is described in the […]
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