Daily Bulletin Archive

July 30, 2018

Globus team members will present a workshop at NCAR from 8:30 a.m. to 5 p.m. MDT on Wednesday, September 5, for system administrators who have deployed or are planning to deploy Globus, developers building applications for research, and others who are  interested in learning more about the service for research data management.

Place: Center Green Campus, CG1-1210-South-Auditorium, 3080 Center Green Drive, Boulder
Agenda: https://www.globusworld.org/tour/program?c=14  
Registration: https://www.globusworld.org/tour/register
Registration: No charge to attend; space is limited so register early

The session will include hands-on walkthroughs of:

  • Using Globus for file transfer, sharing and publication

  • Installing and configuring Globus endpoints

  • Incorporating Globus capabilities into your own data portals, science gateways, and other web applications

  • Automating research data workflows using Globus CLI and API — including how to automate scripted transfers to and from the new NCAR Campaign Storage

  • Using Globus in conjunction with the Jupyter platform

  • Integrating Globus services into your institutional repository and data publication workflows

  • Using Globus Auth authentication and fine-grained authorization for accessing your own services

Globus (www.globus.org) is a research data management service developed by the University of Chicago and used by hundreds of thousands of researchers at institutions in the U.S. and abroad.

July 30, 2018

Cheyenne, Geyser, and Caldera users can now get a quick look at what software environment modules are installed on those systems before they log in. These two documentation pages are updated daily with the output of module spider commands:

For more information about module commands, see our environment modules documentation.

July 24, 2018

The Globus interface for transferring data does not handle symbolic links and does not create a symbolic link on a destination endpoint. This is true in both the web and command line interfaces. If you explicitly request a transfer of a symbolic link, Globus will follow that link and transfer the data that the link points to. More important, if you have symbolic links inside a directory which you copy recursively with Globus, the links will be ignored entirely. You can run the following command to determine if you have symbolic links in your transfer:

find /path/to/folder -type l

Because symbolic links are common in working directories, CISL recommends using the cp or rsync commands to move data between various spaces on GLADE. To move data from old work spaces to new work spaces, for example, use the following recursive copy:

cp -a -r /glade/p_old/work/${USER}/data_directory /glade/work/${USER}

For transfers to and from the new Campaign Storage, and for large transfers to file systems at other sites, CISL still recommends Globus as the easy, fast, and secure option to move data. However, it is important to prepare your data for transfer by identifying and managing your symbolic links. There are two approaches you can take:

  1. If you wish to preserve the linked data, simply replace the symbolic link with the target data using cp.

  2. If you wish to preserve the symbolic links themselves, the easiest approach is to create a tarball containing all of the files you want to copy (including the symbolic links), and then use Globus to transfer that tarball to the target file system.

If you need guidance on which approach is the best for your particular data transfer, please contact cislhelp@ucar.edu with questions.


July 20, 2018

The Cheyenne, Geyser, and Caldera clusters will be unavailable Tuesday, July 24, starting at approximately 6 a.m. MDT to allow CISL staff to update key system software components. The outages are expected to last until approximately 6 p.m. Tuesday evening but every effort will be made to return the systems to service as soon as possible.

To minimize impact to running jobs, all Cheyenne batch queues will be suspended at approximately 6:00 p.m. tonight. Running jobs will not be interrupted. After the queues are suspended users will be still able to submit batch jobs but those jobs will be held until the system is returned to service Tuesday evening.  A system reservation will be created on Geyser and Caldera to prevent batch jobs from executing past 6:00 a.m. Tuesday morning.

All batch jobs and interactive processes that are still executing when the outages begin will be killed.  The clusters’ login nodes will be unavailable throughout the outages.

CISL will inform users through the Notifier service when the systems are restored.

July 16, 2018

Containers are a hot topic in high-performance and scientific computing, but while they can provide significant advantages they don't always live up to the hype. That’s why CISL is offering a hands-on class, “Containers and How They Work,” from 9 a.m. to noon MDT on Friday, July 20, at the NCAR Mesa Lab in Boulder.

The course explains what containers are and how they work, and it surveys some popular implementations with an eye toward supporting scientific workloads. Security and other operational concerns will also be covered for cluster administrators who are thinking about supporting containerized workloads on their systems. Topics to be covered include:

  • What are containers and how do they work?

  • Image formats (tar/filesystem/overlayfs/dense filesystem image/singularity)

  • Build vs. run [singularityhub]

  • Platform independence/reproducibility

  • User namespaces and rootless containers

  • Scheduler integration

  • Container runtimes (Docker, Charliecloud, Inception, Singularity, others)

  • OCI/Standards/runc

  • Applications

  • Education/outreach

  • Cloud

  • Reproducible science

The class is intended for anyone who is planning to deploy applications and create application environments using containers; developers and systems support staff getting started with containers; and others interested in learning about containers. Participants should be familiar with Linux and system operations and should bring a laptop and authentication token for connecting to Geyser and Caldera. Laptops should be fully charged as there may not be enough power receptacles in the seminar room.

Please use this form to register so CISL knows how many participants to expect. Space is limited to 50 participants and registration is open through July 16.

July 13, 2018

HPSS downtime: Tuesday, July 17th 7:30 a.m. - 10:00 a.m.

No downtime: Cheyenne, GLADE, Geyser_Caldera

July 12, 2018

The CISL Help Desk and Consulting support will close at 3:00 p.m. Friday so staff members can attend a UCAR function.

July 11, 2018

A new and larger work space is now available for GLADE. The new /glade2/work file space has a total capacity of 2 PB. The default quota for individual users 1 TB. Users can access the new space as /glade/work.

The older /glade/p/work file space (where users’ default quota is 512 GB) will become read-only within the next two months. The date will be announced soon. The /glade/p/work space will be retired by the end of 2018.

Users are encouraged to begin using the new space soon and move all of their active files and directories from the old space to their individual /glade/work directories at their earliest convenience.

Based on input from users, the new /glade/work spaces will remain unpurged. We apologize for the incorrect info in yesterday's Daily B item.

July 11, 2018

Changes to the GLADE project space being implemented on Tuesday, July 10, continue the evolution of CISL’s storage architecture and user environment as announced in April. Users should take note of the changes for their impact on workflows and scripts.

Here are the key changes to be aware of:

  • On July 10, the present /glade/p/ spaces will become /glade/p_old/ and be made read/write-only for a period of 30 days. After 30 days, the old spaces will be read-only until they are decommissioned at the end of 2018.

  • Also on July 10, new /glade/p/<entity>/ spaces will be in place for existing projects so users can move their files from /glade/p_old/ to the new file system. An entity can be univ, uwyo, cesm, cisl, nsc, or other designated NCAR lab or special program.


  • NCAR Lab: /glade/p/P12345678 becomes /glade/p_old/P12345678 and the new space is /glade/p/cisl/P12345678

  • University: /glade/p/UABC1234 becomes /glade/p_old/UABC1234 and the new space is /glade/p/univ/UABC1234

CISL recommends using Globus as the most efficient way to transfer files. The system monitors progress and automatically validates correctness of each file transfer. Users are asked to remove files from /glade/p_old/ once their transfers are complete.

July 10, 2018

A recording of the July 9 tutorial, “Using Globus and Campaign Storage,” is now available on the CISL web site. See the course page to review the presentation and download the slides. The 45-minute tutorial familiarizes users with the Globus file transfer system and the new Campaign Storage resource.