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?

Notes:
  • For enhanced security, SSH connections that have been idle for 60 minutes will be disconnected. To protect your data from misuse, remember to log off or lock your computer whenever you leave it.
  • 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? 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.

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. 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)?

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.

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.

CPU/memory limits and batch jobs

If your application requires more than 20 minutes of CPU time or has large memory requirements, submit a batch job or request an interactive session using the TORQUE qsub command.

User processes on the login nodes are limited to 20 minutes of CPU time. Processes on the login nodes that run longer than 20 minutes are terminated automatically (without warning). Because of this limit:

  • When running Java programs, add the -Xmx parameter (values must be multiples of 1,024 greater than 2 MB) on the command line to specify the Java Virtual Machine (JVM) maximum heap size. For example, to run a Java program (e.g., Hello_DeathStar) with a maximum heap size of 640 MB , on the command line, enter:
      java -Xmx640m Hello_DeathStar
  • Memory-intensive jobs started on the login nodes will be killed almost immediately. Submit debugging and testing jobs to the INTERACTIVE or DEBUG queue; for example:
    • INTERACTIVE queue:
       qsub -I -q interactive -l nodes=1:ppn=4,vmem=10gb,walltime=4:00:00

      The interactive session will start as soon as the requested resources are available.

    • DEBUG queue:
       qsub -q debug -l nodes=1:ppn=4,vmem=32gb,walltime=00:30:00

Submitting jobs

To submit a TORQUE job script (e.g., job.script) on Carbonate, use the qsub command. If the command exits successfully, it will return a job ID; for example:

 [sgerrera@h1]$ qsub job.script
 123456.m1.Carbonate
 [sgerrera@h1]$

If you need attribute values different from the defaults, but less than the maximum allowed, specify these either in the job script using TORQUE directives, or on the command line with the -l switch. For example, to submit a job (e.g., job.script) that needs more than the default 60 minutes of walltime, use:

 qsub -l walltime=10:00:00 job.script

Jobs on Carbonate default to a per-job virtual memory resource of 16 GB. So, for example, to submit a job (e.g., job.script) that needs 100 GB of virtual memory, use:

 qsub -l nodes=1:ppn=4,vmem=100gb job.script

If you don't provide a virtual memory resource (i.e., omit -l vmem=[n]gb), you will receive a warning, and the default (16 GB) virtual memory will be applied; for example:

 [ersojyn1@h1]$ qsub -l nodes=1:ppn=4 job.script
 warning:vmem resource not provided, default vmem of 16gb will be applied. See
 /etc/motd for details.
 36506.s1
 [ersojyn1@h1]$
Note:

Command-line arguments override directives in the job script, and you may specify many attributes on the command line, either as comma-separated options following the -l switch, or each with its own -l switch. The following two commands are equivalent:

 qsub -l nodes=1:ppn=16,vmem=32gb job.script
 qsub -l nodes=1:ppn=16 -l vmem=32gb job.script

If you need help determining how much memory your jobs are using, TORQUE will report this information when you add the -m e flag to qsub, or when you add the equivalent directive to your submit script:

 #PBS -m e

When you use the -m e parameter, TORQUE/PBS will send you an email message at job completion similar to the following:

 PBS Job Id: 16857.s1
 Job Name:   sleep
 Exec host:  c15/0-3
 Execution terminated
 Exit_status=0
 resources_used.cput=00:00:00
 resources_used.energy_used=0
 resources_used.mem=5464kb
 resources_used.vmem=470124kb
 resources_used.walltime=00:00:33

In the above example, resources_used.vmem=470124kb is the relevant line.

Useful qsub options include:

Option Action
-a YYYYMMDDhhmm.SS Specify the date and time after which the job is eligible to execute (replace YYYY with the year, MM with the month, DD with the day of the month, hh with the hour, and mm with the minute; the .SS to indicate seconds is optional).
-I Run the job interactively. (Interactive jobs are forced to not rerunnable.)
-m e Mail a job summary report when the job terminates.
-q queue_name Specify the destination queue for the job. (On Carbonate, use this only when submitting jobs to the INTERACTIVE or DEBUG queues.)
-r [y|n] Declare whether the job is rerunnable. If the argument is y, the job is rerunnable; if the argument is n, the job is not rerunnable. The default value is y (rerunnable).
-V Export all environment variables in the qsub command's environment to the batch job.

For more, see the qsub manual page.

Monitoring jobs

To monitor the status of a queued or running job, use the TORQUE qstat command. Useful qstat options include:

Option Action
-a Display all jobs.
-f Write a full status display to standard output.
-n List the nodes allocated to a job.
-r Display jobs that are running.
-u user1,user2 Display jobs owned by specified users.

For more, see the qstat manual page.

Deleting jobs

To delete a queued or running job, use the qdel command.

Occasionally, a node will become unresponsive and unable to respond to the TORQUE server's requests to kill a job. In such cases, try using qdel -W <delay> to override the delay between SIGTERM and SIGKILL signals (for <delay>, specify a value in seconds).

For more, see the qdel manual page.

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 2017-11-14 11:44:24.

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