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Software

Jupyter notebook server on Odyssey

This document is to help you run Jupyter server remotely on compute nodes of the cluster and connect to your computational notebook using a local browser of your workstation/laptop.  Start a job: After login to the login node on Odyssey, you will need to start a job on the cluster. While you are setting up an environment, we recommend using an interactive…

Proxy Settings

If you are on a VPN realm or server that is behind a firewall there are times when you still need to reach the outside Internet. For example, you may need to install a conda or R package. In that case, you will need to add a proxy setting to your environment.  You can issue the following commands either manually…

Singularity on Odyssey

Table of Contents: Introduction Docker vs Singularity Singularity on Odyssey Getting existing images onto Odyssey Interacting with images Singularity containers as SLURM jobs Building Singularity images References Introduction Containerization of workloads has become popular, particularly using Docker. However, Docker is not suitable for HPC applications due to security reasons. There are a couple of alternatives for HPC containers, with Singularity…

CERN ROOT software

Information on running CERN's ROOT software on the Odyssey cluster. CentOS 7 / Installing For Yourself To run the current version of ROOT, you will need to install the package yourself in your home directory using CERN's package in order to run it on the Odyssey 3 cluster. You will need to source the ROOT setup script in your installation…

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…

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/3.4.2-fasrc03 with both OpenMPI and Mvapich2 MPI libraries, compiled with both Intel version and GNU compilers. In order to use the Rmpi package, first…