CCS Data Center Migration – August 3, 2017

CCS resources will be unavailable starting August 3, 2017 at 20:00. All CCS systems and networks will be affected.
Details and updates on the CCS AC website here: http://ccs.miami.edu/ac/migration

2017-02-17 CCS Advanced Computing – Slack community

CCS Advanced Computing invites you to connect with the Advanced Computing community on Slack: http://umadvancedcomputing.slack.com
The Advanced Computing community Slack channels provide a place for user discussions, information sharing, and informal announcements about CCS resources and developments. All users with an @miami.edu or @umiami.edu email address can create a Slack account in UM Advanced Computing.

2017-01-18 CCS Portal – portal.ccs.miami.edu

CCS Advanced Computing is excited to announce the launch of our newly redesigned Portal: http://portal.ccs.miami.edu
The new CCS Portal home page showcases up-to-date information about our clusters. Click the title for more details.

2016-09-29 Pegasus /scratch purge policy violations

Files on /scratch are subject to purging after 21 days. Circumventing this purge is a violation of University of Miami Acceptable Use Policies and the account responsible for it will be suspended. Using ‘touch’ to thwart /scratch purge is not allowed.

2016-04-15 Parallel Queue Debut

CCS AC debuts the new ‘parallel’ Pegasus cluster job queue for parallel jobs requiring 16 cores from the same host, or MPI jobs requiring 16+ CPUs.
Click title for details.

Support & FAQ

Links & Forms

FAQ – Frequently Asked Questions

Detailed information for FAQ topics is available in our Policies and Documentation.

How do I reset my CCS password?
Via the CCS Portal: http://portal.ccs.miami.edu/portal
Click on “Reset Password”

How do I connect to CCS resources from off-site?
To access CCS resources while offsite, open a VPN connection first.
CCS does not administer VPN accounts.

FAQ Pegasus Software

Pegasus Software

Software on Pegasus

What software is available?
Software Modules list on the CCS Portal: http://portal.ccs.miami.edu/portal/resources/modules
Software Modules from the command line: $ module avail

How do I view my currently loaded modules?
$ module list

How do I use software modules?
Software on Pegasus

How do I request global software installation on Pegasus?
Request new global software via the CCS Portal: http://portal.ccs.miami.edu/portal/resources/soft/new

When will my global software request be approved/installed?
When a minimum of 20 users require it. Software requests are reviewed quarterly.

How can I increase Java memory on Pegasus?
Load the java module, then change the value of _JAVA_OPTIONS.

[username@pegasus ~]$ module load java
[username@pegasus ~]$ echo $_JAVA_OPTIONS
-Xmx512m
[username@pegasus ~]$ export _JAVA_OPTIONS="-Xmx4g"

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FAQ Pegasus Projects

Pegasus Projects

Projects on Pegasus

How do I join a project?
Request membership to an existing project via the CCS Portal: http://portal.ccs.miami.edu/portal
Click on Forms and Access -> Projects -> List, then the project name to access the membership request form.

How do I request a new project?
Any PI or faculty member may request a new project via the CCS Portal: http://portal.ccs.miami.edu/portal/project/req/edit

When will my project be created?
When the allocations committee has reviewed and approved it. Check your request status via the CCS Portal under My Pegasus -> My Requests. Scratch requests over 2TB can take a month for the allocations committee to review as availability is limited.

How do projects work?
Projects

How can I manage my Projects and Groups?
Manage owned Projects and Groups via the CCS Portal: http://portal.ccs.miami.edu/portal
Click on My Pegasus -> My Projects or My Groups
See Project Management for more information.

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FAQ Pegasus Jobs

Pegasus Job Scheduling

Scheduling Jobs

May I run resource-intensive jobs on Pegasus login nodes?
No. Resource-intensive jobs must be submitted to LSF.

How do I submit jobs to Pegasus?
With bsub command: LSF

How do I check on my submitted jobs?
With bjobs command: LSF

How do I monitor job progress?
With bpeek command: LSF

Is there a limit on how many jobs I can run?
No. Users are limited by number of simultaneous CPUs used. Individual users can run on up to 512 CPUs at a time, projects on up to 1000 CPUs at a time.

How can I see pending and running job counts for Pegasus queues?
With bqueues command: LSF

Why is my job still pending?
Jobs wait for enough resources to satisfy requirements. When the cluster is under heavy user load, jobs will wait longer. Use $ bsub -l jobID to see PENDING REASONS. Check your resource requirements for accuracy and feasibility.

If your job has been pending for more than 24 hours and is not requesting exclusive access or all cores on a node, you may e-mail hpc@ccs.miami.edu for assistance.

Are other users’ pending jobs slowing my job?
No. The number of pending jobs is irrelevant to job performance in LSF. The scheduler can handle hundres of thousands of jobs.

How do I submit jobs to my Project?
With the -P flag: LSF

How do I submit an interactive job?
With the -Is -q interactive flags: LSF Interactive

How do I submit an interactive X11 job?
With the -Is -q interactive -XF flags: LSF X11

Why was my job killed?
Jobs are killed to protect the cluster and preserve system performance. Common reasons include:
– running on a login node
– using more memory than reserved
– using all the memory on a compute node
– using more CPUs than reserved
– needing more time to complete than reserved
– using more /tmp space than available on compute nodes

See LSF for assistance with appropriate resource reservations and Pegasus Queues for default wall times.

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FAQ Linux

Linux

Linux Primers

How can I check my shell?
$ echo $SHELL or $ echo $0

How can I view my environment variables?
$ env or $ env | sort

How can I check command/software availability and location?
$ which executable, for example $ which vim

How can I get help with commands/software?
Use the Linux manual pages: $ man executable, for example $ man vim

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Suggest Edit

Office Hours

Advanced Computing offers office hours to provide assistance with usage issues on the Pegasus cluster. The team is able to provide onsite assistance with queuing inquiries, software installation, and technical troubleshooting. The team is also able to help answer questions regarding grant proposals and can provide resource information about the Advanced Computing environment.

  • Coral Gables Campus:    Wednesdays 2:00-4:00 PM | Ungar 330E Dr. Zongjun Hu
  • RSMAS Campus:     Wednesdays 9:00-11:00 AM | MSC 223 Mr. Warner Baringer

Contact

Request help via email to hpc@ccs.miami.edu. Provide detailed descriptions of the problem, paths to your job file and any outputs, the software modules you have loaded, and your job ID when appropriate.

Suggestions:

  • computer and operating system you are using
  • your CCS account ID
  • complete path to your job script file, program, or job submission
  • complete path to output files (if any)
  • error message(s) received
  • module(s) loaded ($ module list)
  • whether this job ran previously and what has changed since it last worked
  • steps you may have already taken to address your issues