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Software

iPython Notebook

The Harvard FAS Informatics group has a page on this topic which includes two very informative step-by-step videos for setting up an individual iPython Notebook using the Odyssey cluster. You can find it here: http://informatics.fas.harvard.edu/port-forwarding-on-odyssey-nodes.html You can also view the slide deck for previous training on this topic here. Please be aware that the video covers more than the slide deck,…

MPI for Python (mpi4py) on Odyssey

Introduction This web-page is intended to help you running MPI Python applications on the Odyssey cluster using mpi4py. To use mpi4py you need to load an appropriate Python software module. We have the Anaconda Python distribution from Continuum Analytics. In addition to mpi4py, it includes hundreds of the most popular packages for large-scale data processing and scientific computing. You can…

BEAST

BEAST2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. BEAST2 uses Markov chain Monte Carlo (MCMC) to average over tree space, and can be computationally challenging. If you are going to use BEAST and wish the best performance to reduce run times, you should make use of the BEAGLE package, which includes CPU and GPU optimizations. This…

Git and Github on Odyssey

We strongly encourage all persons writing code (C, C++, Fortran, R, etc) to make use of the version control system git. The git suite of tools is available on odyssey without having to do a module load, and is available on all login and compute nodes. Using Github, however, may be a little less straightforward. If you cloning Github repos…

Hybrid (MPI+OpenMP) Codes on Odyssey

Introduction This page will help you compile and run hybrid (MPI+OpenMP) applications on Odyssey. Currently we have both OpenMPI and Mvapich2 MPI libraries available, compuled with both Intel and GNU compiler suits. Example Code Below are simple hybrid example codes in Fortran 90 and C++. Fortran 90: !===================================================== ! Program: hybrid_test.f90 (MPI + OpenMP) ! FORTRAN 90 example - program…

R-MPI

Introduction This page is intended to help you with writing and running parallel R codes using the Rmpi package, the MPI interface for R, on the Odyssey cluster. Currently, Rmpi is available with the software module R/3.2.2-fasrc02 with both OpenMPI version 1.8.3 and Mvapich2 version 2.0 MPI libraries, compiled with both Intel version 15 and GNU version 4.8.2 compilers. In…

MPI Software on Odyssey

Introduction This web-page is intended to help you compile and run MPI applications on the Odyssey cluster. (NOTE: Instructions are based on our new Lmod module system.) The Message Passing Interface (MPI) library allows processes in your parallel application to communicate with one another by sending and receiving messages. There is no default MPI library in your environment when you…

MATLAB Figures in a Batch Mode

This web-page illustrates how to create MATLAB figures in a batch-mode (without a GUI) on the Odyssey cluster. This is especially useful if you would like to do your computations and post-processing all together in a consistent computing environment. Below is an example function which generates data, creates a figure, and saves it as a file on the cluster: %=========================================================================================…

MATLAB Parallel – PCT and DCS

Introduction This page is intended to help you with running parallel MATLAB codes on the Odyssey cluster. The latest software modules supporting parallel computing with MATLAB available on the cluster are: matlab/R2016b-fasrc01 matlab/R2016a-fasrc01 matlab/R2015b-fasrc01 matlab/R2015a-fasrc01 matlab/R2014b-fasrc01 matlab/R2014a-fasrc01 Parallel processing with MATLAB is performed with the help of two products, Parallel Computing Toolbox (PCT) and Distributed Computing Server (DCS). Parallel Computing…

Citrix

Before you can properly use Citrix from your computer, you will need to download and install the Citrix Receiver software. If you've tried to launch a Citrix session and all that happened was a .ica file was downloaded, then you need to install (or possibly reinstall) the Receiver software. You can download Citrix Receiver from https://www.citrix.com/go/receiver.html