Search results

1. A guide to using OpenMP and MPI on SeaWulf

   This article will discuss how to successfully parallelize jobs using OpenMP, Message Passing Interface (MPI), and a combination of the two.

   Knowledge Base Article | Score: 12% Match

2. Using Freesurfer

   FreeSurfer is a software package for the analysis and visualization of structural and functional neuroimaging data from cross-sectional or longitudinal studies. It is developed by the Laboratory for Computational Neuroimaging at the Athinoula A. Martinos Center for Biomedical Imaging. FreeSurfer is the structural MRI analysis software of choice for the Human Connectome Project. See https://surfer.nmr.mgh.harvard.edu/fswiki for more info.

   Knowledge Base Article | Score: 11% Match

3. A guide to "embarrassingly parallel" workflows on SeaWulf

   This article will discuss how to successfully parallelize "embarrassingly parallel" workflows using multiple CPUs and multiple nodes on SeaWulf.

   Knowledge Base Article | Score: 10% Match

4. P2P VPN and Proxy Solutions

   Faculty, Researchers, Staff, Students The basic premise of these solutions is that network traffic is directed through different hosts or nodes ... of these networks are completely reliant upon the unknown network nodes your traffic ...

   Knowledge Base Article | Score: 10% Match

5. Using Darshan on SeaWulf

   Darshan is a scalable HPC I/O characterization tool designed to capture an accurate picture of application I/O behavior, including properties such as patterns of access within files, with minimum overhead. 

   Darshan was originally developed on the IBM Blue Gene series of computers deployed at the Argonne Leadership Computing Facility, but it is portable across a wide variety of platforms include the Cray XE6, Cray XC30, and Linux clusters.

   Knowledge Base Article | Score: 10% Match

6. How to use Python on Seawulf

   computing libraries. For multi-node programming in Python, mpi4py ... nodes.  Example scripts can be found here, and in our examples folder: ...

   Knowledge Base Article | Score: 10% Match

7. Using AmberMD

   Amber is a collection of software used for simulating molecules, managed by a dedicated developer community. It consists of two main parts: AmberTools23, which contains standalone packages for molecular simulations, and Amber22, an expansion that includes enhanced performance through the 'pmemd' program. This improvement makes molecular dynamics simulations significantly faster, especially when using multiple CPUs and GPUs.

   Knowledge Base Article | Score: 10% Match

8. Enrolling into the DUO Security System

   To improve our security posture, we have incorporated DUO Security as a two-factor authentication solution into all Login Nodes. Starting on April 16, 2020, you will be required to enroll in DUO using the steps found below in order to access the SeaWulf cluster.

   Knowledge Base Article | Score: 9% Match

9. How to use MatLab on Seawulf

   1--ntasks-per-node=28-p short-28core ssh-X $SLURM_NODELIST After your interactive session ...

   Knowledge Base Article | Score: 9% Match

10. How to use TensorFlow on Seawulf

    /gpfs/projects/samples/tensorflow To make sure TensorFlow can access all 8 gpus on the node, you can ...

    Knowledge Base Article | Score: 9% Match

11. Using Mathematica

    High Performance Computing Faculty, Researchers, Staff Mathematica Mathematica is currently optimized to work in a single node with multiple cores. Mathematica can be used either interactively through a GUI or as in the standard ...

    Knowledge Base Article | Score: 9% Match

12. Using R

    R is a free software environment for statistical computing and graphics. It is available as a command line application through modules on SeaWulf or as a GUI through Rstudio. 

    Knowledge Base Article | Score: 8% Match

13. Accessing SeaWulf with Open OnDemand

    users to access desktops on SeaWulf nodes in interactive sessions, instead ... account you wish to submit the job under. Number of nodes should be kept ...   Once your job allocated a node, the status on screen will update to  ...

    Knowledge Base Article | Score: 8% Match

14. Alternate Formatting of squeue

    of squeue: JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON) ...          PARTITION           NAME           USER     ST TIME    NODES NODELIST(REASON) ...

    Knowledge Base Article | Score: 8% Match

15. Using Singularity on SeaWulf

    To read more about Singularity : https://sylabs.io/guides/3.0/user-guide/

    To read more about Docker : https://www.docker.com/why-docker

    To get started with Anaconda : https://it.stonybrook.edu/help/kb/installed-software-on-seawulf

    Knowledge Base Article | Score: 7% Match

16. Getting a Project on SeaWulf

    a typical job will use, if any How many compute nodes you expect a job to use ...

    Knowledge Base Article | Score: 7% Match

17. Handling job output

    the login node in real time using a command like tail: tail-f output.txt Types ...

    Knowledge Base Article | Score: 6% Match

18. Using Globus on Seawulf

    ​Globus is a non-profit service for secure, reliable research data management.

    Knowledge Base Article | Score: 6% Match

19. Using Bioinformatics Tools (Blast, BWA, etc.)

    be launched on the login node, and Nextflow will handle submitting jobs for each ... with Nextflow: 1. ssh to a milan login node: ssh ...

    Knowledge Base Article | Score: 5% Match

20. Using Alphafold2 on SeaWulf

    Alphafold2 is a GPU-based Machine Learning method for protein structure prediction.  This article will explain how to access the software on SeaWulf and provide an example of its use.

    Knowledge Base Article | Score: 5% Match

Pages