Carbonate at Indiana University

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Note:
For help determining which of IU's research supercomputing systems is best suited to meet your needs, use the UITS Supercomputing Pathfinder.

System overview

Carbonate (carbonate.uits.iu.edu) is Indiana University's replacement for Mason and is available to IU students, faculty, and staff. Carbonate fully supports high-performance, data-intensive computing, and provides an eighteenfold increase in processing capability over Mason. Carbonate can handle computing tasks for researchers using genome assembly software, large-scale phylogenetic software, and other genome analysis applications that require large amounts of computer memory.

Carbonate has 72 general-purpose compute nodes, each with 256 GB of RAM, and eight large-memory compute nodes, each with 512 GB of RAM. Each node is a Lenovo NeXtScale nx360 M5 server equipped with two 12-core Intel Xeon E5-2680 v3 CPUs and four 480 GB solid-state drives. All nodes are housed in the IU Bloomington Data Center, run Red Hat Enterprise 7.x, and are connected to the IU Science DMZ via 10-gigabit Ethernet.

Carbonate uses the TORQUE resource manager integrated with Moab Workload Manager to coordinate resource management and job scheduling. The Data Capacitor II and Data Capacitor Wide Area Network (DC-WAN) parallel file systems are mounted for temporary storage of research data. The Modules environment management package on allows users to dynamically customize their shell environments.

System access

IU students, faculty, and staff can request accounts on Carbonate by following the instructions in At IU, if I already have some computing accounts, how do I get others?

Non-IU collaborators must have IU faculty sponsors. For details, see the Research system accounts (all campuses) section of What computing accounts are available at IU, and for whom?

NSF-funded life sciences researchers can apply to the National Center for Genome Analysis Support (NCGAS) allocations committee to request accounts on Carbonate. To request an allocation, submit the NCGAS Allocations Request Form. If you have questions, email NCGAS.

Once your account is created, you can use your IU username and passphrase to log into Carbonate (carbonate.uits.iu.edu) with any SSH2 client. Public key authentication also is permitted; see How do I set up SSH public-key authentication to connect to a remote system?

Note:
The scheduled monthly maintenance window for Carbonate is the first Tuesday of each month, 7am-7pm.

Available software

For a list of software available on Carbonate, log in, and then, on the command line, enter:

  module avail
Note:
Carbonate users are free to install software in their home directories and may request the installation of software for use by all users on the system. Only faculty or staff can request software. If students require software packages on Carbonate, their advisors must request them. For details, see At IU, what is the policy about installing software on Carbonate and Mason? To request software, use the HPC software request form.

Setting up your user environment

On the research computing resources at Indiana University, the Modules environment management system provides a convenient method for dynamically customizing your software environment.

For more about using Modules to configure your user environment, see On the research computing systems at IU, how do I use Modules to manage my software environment?

File storage options

For file storage information, see On IU's research systems, how much allocated and short-term storage capacity is available to me?

Note:
Before storing data on this system, make sure you understand the information in the Working with data containing PHI section (below).

Working with data containing PHI

The Health Insurance Portability and Accountability Act of 1996 (HIPAA) established rules protecting the privacy and security of individually identifiable health information. The HIPAA Privacy Rule and Security Rule set national standards requiring organizations and individuals to implement certain administrative, physical, and technical safeguards to maintain the confidentiality, integrity, and availability of protected health information (PHI).

This system meets certain requirements established in the HIPAA Security Rule that enable its use for research involving data that contain protected health information (PHI). You may use this resource for research involving data that contain PHI only if you institute additional administrative, physical, and technical safeguards that complement those UITS already has in place. For more, see When using UITS Research Technologies systems and services, what are my legal responsibilities for protecting the privacy and security of data containing protected health information (PHI)? If you need help or have questions, contact UITS HIPAA Consulting.

Note:
Although PHI is one type of institutional data classified as Critical at IU, other types of institutional data classified as Critical are not permitted on Research Technologies systems. Except for PHI, the most sensitive classification of institutional data allowed on Research Technologies resources is Restricted. For help determining which institutional data elements classified as Critical are considered PHI, see Which data elements in the classifications of institutional data are considered protected health information (PHI)?

Running jobs on Carbonate

IU's research computing clusters use the TORQUE resource manager (based on OpenPBS) and the Moab Workload Manager to manage and schedule batch jobs. Moab uses fairshare scheduling to track usage and prioritize jobs.

Queue information

Carbonate employs a default routing queue that funnels jobs, according to their resource requirements, into two execution queues configured to maximize job throughput and minimize wait times (i.e., the amount of time a job remains queued, waiting for required resources to become available). Depending on the resource requirements specified in either your batch job script or your qsub command, the routing queue (BATCH) automatically places your job into the NORMAL or LARGEMEMORY queue:

  • NORMAL queue: Jobs requesting up to 251 GB of virtual memory (qsub -l vmem=251gb)
  • LARGEMEMORY queue: Jobs requesting from 251 GB up to 503 GB of virtual memory (qsub -l vmem=503gb)
Note:
To best meet the needs of all research projects affiliated with Indiana University, the High Performance Systems (HPS) team administers the batch job queues on UITS Research Technologies supercomputers using resource management and job scheduling policies that optimize the overall efficiency and performance of workloads on those systems. If the structure or configuration of the batch queues on any of IU's supercomputing systems does not meet the needs of your research project, fill out and submit the Research Technologies Ask RT for Help form (for "Select a group to contact", select High Performance Systems).

You do not have to specify a queue in your job script or in your qsub command to submit your job to one of the two batch execution queues; your job will run in the NORMAL or LARGEMEMORY queue unless you specifically submit it to the DEBUG or INTERACTIVE queue, the properties of which are as follows:

  • DEBUG: The DEBUG queue is intended for short, quick-turnaround test jobs requiring less than 1 hour of wall time.
  • Maximum wall time: 1 hour
    Maximum nodes per job: 2
    Maximum cores per job: 48
    Maximum number of jobs per user: 2
    Direct submission: Yes

    To submit a batch job to the DEBUG queue, either add the #PBS -q debug directive to your job script, or enter qsub -q debug on the command line.

    Note:
    For longer debugging or testing sessions, submit an interactive job to the INTERACTIVE queue instead.
  • INTERACTIVE: Interactive jobs submitted to the INTERACTIVE queue should experience less wait time (i.e., start sooner) than interactive jobs submitted to the batch execution queues.
  • Maximum wall time: 8 hours
    Maximum cores per job: 8
    Maximum number of jobs per queue: 128
    Maximum number of jobs per user: 2
    Direct submission: Yes

    To submit an interactive job to the INTERACTIVE queue, on the command line, enter qsub with the -I and -q interactive options added; for example:

      qsub -I -q interactive -l nodes=1:ppn=1,walltime=4:00:00
    
    Note:
    If you enter qsub without the -q interactive option, your interactive job will be placed in the routing queue for submission to the NORMAL or LARGEMEMORY batch execution queue, which most likely will entail a longer wait time for your job.

Requesting single user time

Although UITS Research Technologies cannot provide dedicated access to an entire compute system during the course of normal operations, "single user time" is made available by request one day a month during each system's regularly scheduled maintenance window to accommodate IU researchers with tasks requiring dedicated access to an entire compute system. To request such single user time, complete and submit the Research Technologies Ask RT for Help form, requesting to run jobs in single user time on HPS systems. If you have questions, email the HPS team.

Support

For an overview of Carbonate documentation, see Getting started on Carbonate.

For tutorials on how to effectively use Carbonate's large memory compute nodes, see Supercomputing quick start guides.

Support for IU research computing systems, software, and services is provided by various UITS Research Technologies units. For help, see Research computing support at IU.

This is document aolp in the Knowledge Base.
Last modified on 2017-09-20 15:56:06.

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