ARCHIVED: Get started with NCGAS services

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Overview

Following is an outline of high performance computing, storage, and software resources available to National Center for Genome Analysis Support (NCGAS) researchers. For more, see National Center for Genome Analysis Support.

For a general introduction to the infrastructure of supercomputing systems, see these slides. If you need context for any slide, contact NCGAS.

Research supercomputers

NCGAS provides access to the following research supercomputers at Indiana University and Pittsburgh Supercomputing Center (PSC). For more about running jobs, see:

IU systems

If you have an IU username, you can create an account on any of the IU research supercomputers; for instructions, see either Create your first IU computing accounts (admitted students, faculty, staff, affiliates, and those returning to IU) or Get additional IU computing accounts.

  • ARCHIVED: Big Red 3 (bigred3.uits.iu.edu):

    Big Red 3 is a Cray XC40 supercomputer dedicated to researchers, scholars, and artists with large-scale, compute-intensive applications that can take advantage of the system's extreme processing capability and high-bandwidth network topology. Big Red 3 supports programs at the highest level of the university, including the Grand Challenges program.

  • ARCHIVED: Carbonate (carbonate.uits.iu.edu):

    Carbonate is Indiana University's large-memory computer cluster. Designed to support data-intensive computing, Carbonate is particularly well-suited for running genome assembly software, large-scale phylogenetic software, and other genome analysis applications that require large amounts of computer memory. Carbonate provides a specialized GPU partition for researchers with applications that require GPUs. Additionally, Carbonate offers a colocation service to IU researchers, research labs, departments, and schools.

  • Quartz (quartz.uits.iu.edu):

    Quartz is Indiana University's high-throughput computing cluster. Designed to deliver large amounts of processing capacity over long periods of time, Quartz provides the advanced supercomputing performance needed to run high-end, data-intensive applications that are critical to scientific discovery and innovation.

If one of the above systems is not listed among the accounts available to you, you can request an account by submitting the NCGAS contact request form:

  1. From the "Help Needed" drop-down, select Request.
  2. Enter your name, IU username, and your primary email address (for individual accounts) or a group email address (for group accounts). In your message, specify the system for which you are requesting an account.

For information about running jobs on IU research supercomputers, see Use Slurm to submit and manage jobs on IU's research computing systems

PSC systems

  • Bridges: A multi-tiered, data-intensive high performance computing system, Bridges is well-suited for high-memory (3 TB to 12 TB) jobs and "Big Data" projects.
    Hostname: bridges.psc.edu
    Regular memory
    (RM) nodes:    		 14 cores per node
    128 GB RAM per node
    Large memory
    (LM) nodes:    		 36 cores per node
    3 TB of RAM per node

    For more, see Bridges-2 User Guide.

    To request an allocation on Bridges, submit the NCGAS contact request form:

    1. From the "Help Needed" drop-down, select Request.
    2. Enter your name, IU username, and your primary email address (for individual accounts) or a group email address (for group accounts). In your message, specify that you are requesting an account on Bridges.

Research storage services

IU systems

As a member of the NCGAS research community, you have access to allocated and short-term storage capacity on UITS Research Technologies systems.

  • Home directory space: By default, IU research supercomputer users are allocated 100 GB of home directory space (with a maximum file limit of 800,000 files). When you have accounts on more than one IU research supercomputer, your 100 GB home directory allocation is shared between those accounts. When you create an account on any of IU's research supercomputers, your home directory space is created automatically within the file system at (replace username with your IU username): 
    /N/u/username

    Home directory space is intended for low-capacity, low-performance uses, such as storing documentation, configuration files, source files, and data files needed to run batch and/or interactive jobs on IU's research supercomputers. Your home directory space is not intended for storing large data sets, nor is it capable of handling data-intensive computational I/O from parallel compute jobs.

  • Scholarly Data Archive (SDA): The SDA is well suited for storing large volumes of data (that is, tens of gigabytes to several terabytes per project), and data that are accessed relatively infrequently (archival or near-line storage). The SDA backend is not designed for storing a large number of small files. Individual files should be at least 1 MB. If you need to store many small files on the SDA, use a file compression utility (such as gzip or tar) to bundle your files into a single, large archive file. To request an SDA account, see Create your first IU computing accounts (admitted students, faculty, staff, affiliates, and those returning to IU). If the SDA is not listed among the accounts available to you, you can request an account by submitting the NCGAS contact request form:
    1. From the "Help Needed" drop-down, select Request.
    2. Enter your name, IU username, and your primary email address (for individual accounts) or a group email address (for group accounts). In your message, specify that you are requesting an SDA account.

    For more about the SDA, see About the Scholarly Data Archive (SDA) at Indiana University. For guidelines on using command-line tools to securely archive and share data on the SDA, see Archiving 101 (NCGAS Blog). To store data using the IU Globus Web App, see ARCHIVED: Use the IU Globus Web App to transfer data between your accounts on IU's research computing and storage systems.

PSC systems

Several distinct file spaces are available on Bridges:

  • Home ($HOME): Your home directory on Bridges is an allocated space where you can install programs you need, and store notes and template files. Home directories are relatively small and are intended for short-term storage only. When your Bridges account is created, your home directory is located at (replace username with your PSC username): 
    /home/username
  • pylon5 ($SCRATCH): The Lustre-based pylon5 file system provides persistent storage and fast I/O access for jobs running on Bridges. Files on pylon5 are not backed up. When created, your pylon5 home directory is located at (replace groupname and username with the group associated with your account and your PSC username, respectively): 
    /pylon5/groupname/username

Software

For an updated list of software, see Software supported by NCGAS at IU.

For tutorials on installing software, see:

To request software, use the NCGAS Software Request form.

GUI resources

R

  • Rstudio.iu.edu Server: A web GUI for using R on HPC systems; available through Jetstream2 as a basic installation and with bioconductor and genomic packages pre-installed.

For tutorials, see:

  • Rtutorial: A walkthrough of R with comparisons to Unix.

Galaxy

  • Galaxy.iu.edu: A GUI front end to genomics software that NCGAS keeps updated.
  • Trinity Galaxy: A Galaxy instance specialized for the assembly of RNAseq data.

For tutorials, see:

Genepattern

  • Genepattern: A GUI to analyze microarray and genomic data.

Command line resources

Command line guides

Guides for Transcriptome applications on the command line

Get help

For more information or help getting started, contact NCGAS.

This is document axgn in the Knowledge Base.
Last modified on 2023-03-22 15:11:04.