Pegasus news feed > Pegasus in the Sky with Data

Pegasus and Ewa Deelman were recently featured in the USC Viterbi School of Engineering magazine. We hope you enjoy the story of Pegasus’ creation and successes as much as we do.

 

Read the Story

 

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News and Announcements from OSG Operations > DNS Migration Tuesday, 23 April, 10:00 EDT

The OSG will be performing a migration of the nameserver for opensciencegrid.org and osgstorage.org next Tuesday, 23 April 2018, starting at 10AM EST.  Given the level of caching within the DNS infrastructure, it may take up to 24 hours for the change to fully propagate.

The migration is expected to be completely transparent to all sites and not require any action.

However, there remains some risk of interruption, particularly around the delivery of email messages to opensciencegrid.org lists.  If you see any issues next Tuesday, kindly reach out to https://support.opensciencegrid.org or, for non-email-related issues, [email protected]

If you have any questions or concerns, feel free to reach out prior to the transition.

OSG Operations and OSG Software Team
https://www.opensciencegrid.org/

News and Announcements from OSG Operations > OSG Statement on Continued Services and Support

As you may have heard, the Open Science Grid (OSG) is undergoing some transitions in its funding model. We have been planning for these changes for some time, and the National Science Foundation is providing clear direction and enthusiastic support now and for the foreseeable future.

We remain committed to providing services and support for our community of resource providers and science users. To that end, we want to tell you about some short-term transitions that are planned between now and the end of May 2018.

OSG operates a fabric of services that form the core of our distributed infrastructure, and we are reviewing all service deployments.  Some services will be retired (e.g., central RSV components, VOMS Admin), most services will be migrated with little planned effect on sites (e.g., OSG Display, CVMFS, perfSONAR monitoring), and some services will be migrated with greater effect on sites (OIM and OSG CA). There will be announcements for each service as it migrates.

In addition, OSG provides support to users, Virtual Organizations (VOs), resource providers, and others through a variety of entry points. Over the next month, we will be retiring one of the three underlying support ticket-tracking systems in use today, but plan to maintain nearly all of the current methods for requesting support (e.g., email addresses).  The LHC community will concentrate its support on the existing GGUS system, and the broader community will use the existing OSG Support system based on the Freshdesk system.  As with services, there will be announcements for specific support entry points as each one migrates.

For OSG resource providers, we have created and will frequently update an OSG Operations Transition document here: https://opensciencegrid.github.io/technology/policy/service-migrations-spring-2018/

Frank Wuerthwein - OSG Executive Director
Miron Livny – OSG Technical Director and Principle Investigator
David Swanson – OSG Council Chair

News and Announcements from OSG Operations > Announcing OSG Software version 3.4.10

We are pleased to announce OSG Software version 3.4.10.

NOTE: See the release notes for known issues with Singularity 2.4.6

Changes to OSG 3.4.10 include:
- Singularity 2.4.6: fixed bind mount security vulnerability
- HTCondor-CE 3.1.1: now accepts InCommon certificates
- HTCondor 8.6.10: fixed handling of grid jobs when submit fails
- cigetcert 1.16: first release in the OSG Software Stack
- BLAHP: Improved input file checks and can save submit info for debugging
- xrootd-lcmaps: fixed crashes on EL6 with HTTPS requests
- frontier-squid: fixed startup problem under SELinux
- osg-configure: several minor bug fixes
- Upcoming: HTCondor 8.7.7
- Upcoming: xrootd-hdfs improved write support

Release notes and pointers to more documentation can be found at:

http://opensciencegrid.github.io/docs/release/3.4/release-3-4-10/

Need help? Let us know:

http://opensciencegrid.github.io/docs/common/help/

We welcome feedback on this release!

News and Announcements from OSG Operations > Applications and letters of recommendation are due Friday, April 20!

Announcing the Open Science Grid User School 2018

If you could access hundreds or even thousands of computers for your
scholarly work, what could you do? How could it transform your work?
What discoveries might you make?

We are seeking applicants for the Open Science Grid (OSG) User School
2018, which takes place July 9-13 at the beautiful University of
Wisconsin in Madison. Participants will learn to use high throughput
computing (HTC) to harness vast amounts of computing power for research,
applicable to nearly any field of study (e.g., physics, chemistry,
engineering, life sciences, earth sciences, agricultural and animal
sciences, economics, social sciences, medicine, and more).

For more background:
https://research.cs.wisc.edu/htcondor/htc.html
https://www.opensciencegrid.org/news/research-highlights-list/
https://docs.google.com/presentation/d/1KeI-ZGfPya6S9WQ7Wzo7lRhU5fr0N_gIHRgRtK3tlIc/

Using lectures, discussions, roleplays, and lots of hands-on work with
OSG experts in HTC, participants will learn how HTC systems work, how to
run and manage many jobs and huge datasets, how to implement a realistic
scientific computing workflow, and where to turn for help and more info.

Worried about costs? We pay all basic travel, hotel, and food costs for
applicants who are selected to attend. This is a valuable offer!

Ideal candidates are graduate students whose research involves or could
involve large-scale computing - work that cannot be done on one laptop
or a handful of computers. Also, we accept some post-doctoral students,
faculty, staff, and advanced undergraduates, so make a strong case for
yourself regardless of your current role!

IMPORTANT DATES

Application Period (OPEN NOW): 15 March - 20 April 2018
OSG User School: 9-13 July 2018

MORE INFORMATION AND APPLICATIONS

Web: https://www.opensciencegrid.org/UserSchool
Email: [email protected]
Facebook: https://www.facebook.com/OSGUserSchool
Twitter: https://twitter.com/OSGUserSchool

Please forward this announcement to anyone who might benefit from the
OSG User School. And consider posting our flyer where appropriate:

https://opensciencegrid.github.io/user-school-2018/files/osg-user-school-2018-flyer.pdf

Pegasus news feed > Developing Pegasus Workflows via Jupyter Notebooks

We will be holding regular online Pegasus Office Hours starting Friday April 13th at 11AM Pacific.
Initially, they will be held on a bi-monthly basis on second Friday of the month, and will address user questions and also apprise the community of new developments.

We will have an overview presentation on how to develop Pegasus workflows via Jupyter Notebooks.
Support for Jupyter Notebooks was first introduced in Pegasus 4.8.0 released in September 2017

We hope to see you online on April 13th. Please feel to forward to interested people.
Blue Jeans Contact Information

To join the meeting on a computer or mobile phone : 
https://bluejeans.com/240192441 

Just want to dial in on your phone?
1) +1.408.740.7256 (United States)
   +1.888.240.2560 (US Toll Free)
   +1.408.317.9253 (Alternate number)
    Global Numbers: http://bluejeans.com/numbers
2) Enter Meeting ID: 240 192 441
3) Press # 
Developing Pegasus Workflows via Jupyter Notebooks (presentation slides)
Recording of Seminar
See the Online Office Hours Series Page
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News and Announcements from OSG Operations > Operations Service Update - Thursday, April 12th, 2018 at 13:00 UTC

The GOC will upgrade the following services beginning Thursday, April 12th, 2018 at 13:00 UTC. Grid Operations reserves 8 hours in the unlikely event unexpected problems are encountered.

Repo
  * Remove el5 and osg 3.1 support

OIM
  * Downtime add/editing permission integration update
  * SSO update

Pegasus news feed > Pegasus related talks and topics at the 2018 OSG All Hands Meeting

Last week, Open Science Grid held its annual All Hands Meeting, this time hosted by University of Utah. It was a pleasure to meet Pegasus users and see their talks. A big thank you to those projects and presenters, for sharing their experiences and continued use of Pegasus. Here are some highlights:

  • VERITAS – “VERITAS and Its computational challenges”, presented by Udara Abeysekara, University of Utah. [slides]
  • XENON1T – “XENON1T Computing on OSG – An Update”, presented by Benedikt Reidel, University of Chicago. [slides]
  • Daniel Katz, California State University, Northridge. “Rudin-Shapiro-Like Sequences with Low Correlation” [slides]
  • Ariella Gladstein, University of Arizona. “Inference of Evolutionary History with Approximate Bayesian Computation” [slides]
  • Alex Feltus, Clemson University. “Mining Huge Collections of Genomics Datasets for Genes Controlling Complex Traits from Humans to Legumes” [slides]

The All Hands meeting also covered some technologies which either are supported in Pegasus and/or are of interest to the Pegasus community. For example:

  • StashCache [slides] – A very efficient way to get data to your OSG jobs. Pegasus already has support for StashCache using stash:// URLs.
  • HostedCE. “Expanding the Reach and Scope of Hosted CEs” [slides]. This enables you to access XSEDE allocations from the managed OSG infrastructure and provides an easy approach to run high throughput workloads across XSEDE machines.

 

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Miha's Blog > Interview with Monika Madlen Vetter, Ph.D.

Monika Madlen Vetter, PhD,  works at  University of Chicago · Department of Ecology and Evolution. Marco Mambelli and I interviewed her as part of our "Going out of the door" strategy to learn what R Statistical project users do. The product we delivered in Beta is Bosco R We wanted to discover the data scientist, but Dr. Vetter is much more than just a Data Scientist. I always look around for what fascinates and her story is amazing. She explains  science in simple words but the genomic studies of plants is a complex science, normally hidden to the casual observer.

How important is the usage of statistics in your research?


MV: Very important! My work has two components: conducting an experiment in the laboratory or green house and later analyzing the gathered data. I use R for most of my statistical and graphical analysis. More specifically, I use a method called genome wide association (GWA) study to identify the genetic loci controlling the interactions between plants and bacteria.

What is a GWA?

MV: A genome-wide association study aims to identify genes controlling the variation in a trait.   Most traits, however, are complex – most diseases for instance. Many genes contribute to hypertension or diabetes in humans. Statistical methods help elucidate these complex genetic traits. Scientific knowledge progressed a lot since the first human genome was sequenced in 2000. We have begun to understand the genetic basis of many diseases using genome-wide association studies.

You work on the innate immunity of plants. We live in a world where particle physics dominate the headlines, this is not a widely covered theme in the media


MV: *laughs* Yes, if I talk about my research, many people react with surprise when realizing that plants actually DO HAVE an immune system. Plants cannot run away to escape pathogens, which constantly threaten their survival and reproduction. They do not have antibodies and we therefore often describe the plant immune system as simple. Yet, it does a pretty good job, which is evident by a green world around us.

I investigate the evolution of innate immunity in plants. Immune receptors of the plant model species Arabidopsis thaliana recognize molecular signals, which are unique to bacteria. The perception of these signals triggers a general and effective defense response but is also accompanied with reduction in plant growth. My current work identified several genetic loci, which control these growth changes upon stimulation of the immune system. Another project investigates how plants shape the bacterial community within their leaves.


What is your biggest challenge on a daily basis?

MV:  [thinking a bit]. Perhaps the biggest challenge is to stay focused on the problem and one specific research questions. So many interesting possibilities and questions distract me. I guess having many new thoughts and a creative mind is also what makes a good scientist.



Does your work move in the direction pharmaceutical research?



MV: I am especially fascinated by how plants modulate their immune responses and growth in response to biotic and abiotic environments but it does not directly aim at developing an application or product. Basic knowledge does lead to innovation on the long run. A crop breeder might use this knowledge to make a plant more resistant against pests while maintaining yield for instance.

What motivated you to select this career?

MV: I like to get to the bottom of things and I was interested in plant biology early in my childhood. My parents would have liked me to be a physician but I could not get around cutting someone open – even for the prospect of helping them. I was interested in lichens instead. Three totally different organisms come together to create a form of life with properties which none of them has by itself. How cool is that!


All creatures struggle to let in nutrients and vent wastes. We know a lot at human level. What about the plant level?




MV: We declare waste as unwanted materials but one’s waste is another’s necessity. The photosynthesis of plants produces sugars from water and sunlight. What they release – their waste so to speak, is oxygen, which is crucial to most other life forms on the planet. Otherwise plants do not consume living matter so they do not have unwanted by-products they would need to get rid of.

Heavy metals can be a problem in plants. They either need an excretion system or a high tolerance when growing in soil contaminated by heavy metals such as cadmium, arsenic, mercury or lead. If the plant accumulates those metals, humans can harvest and depose the plants to clean soil. However, it can also be a problem to human health if we eat these plants. Some plants accumulate heavy metals to get resistant to herbivores. There is a lot of fun research ongoing.

In terms of nutrients, plants struggle just as much as other organisms. Their growth will be limited if they lack certain minerals. You might know that from a ‘sad looking’ plant on your windowsill. It might not get all nutrients from its regular water supply. You need to fertilize or re-pot it, too.


How U of Chicago stimulated your work?



MV: The University of Chicago supplies fantastic research facilities, helps with bureaucracy and provides a stimulating research environment. My co-workers come from diverse  (biological) disciplines, which leads to different viewpoints and lively discussions.


What would be in your opinion the biggest achievement as a scientist?



MV: *laughs* Perhaps I am not idealistic enough to think that my research can solve grandiose  humanity problems. However, my research has relevance to food safety, pathogen resistance and stability of yield in crops. On a smaller scale I am happy to share my passion about biological processes with students or lay people.



August 8, 2013 in Chicago




News and Announcements from OSG Operations > Operations Service Update - Tuesday, March 27th, 2018 at 13:00 UTC

The GOC will upgrade the following services beginning Tuesday, March 27th, 2018 at 13:00 UTC. Grid Operations reserves 8 hours in the unlikely event unexpected problems are encountered.

REPO
 *Update repository maintenance scripts

Oasis
 *Update to cvmfs-servermon-1.7+

OIM
 *Python script updates
 *Database configuration changes

Myosg
 *Jquery update

Ticket Exchange
 *Fermilab format update  

News and Announcements from OSG Operations > Operations Service Update - Tuesday, March 27th, 2018 at 13:00 UTC

The GOC will upgrade the following services beginning Tuesday, March 27th, 2018 at 13:00 UTC. Grid Operations reserves 8 hours in the unlikely event unexpected problems are encountered.

REPO
 *Update repository maintenance scripts

Oasis
 *Update to cvmfs-servermon-1.7+

OIM
 *Python script updates
 *Database configuration changes

Myosg
 *Jquery update

Ticket Exchange
 *Fermilab format update  

News and Announcements from OSG Operations > ANNOUNCING THE OPEN SCIENCE GRID USER SCHOOL 2018!

If you could access hundreds or even thousands of computers for your
scholarly work, what could you do? How could it transform your work?
What discoveries might you make?

We are seeking applicants for the Open Science Grid (OSG) User School
2018, which takes place July 9-13 at the beautiful University of
Wisconsin in Madison. Participants will learn to use high throughput
computing (HTC) to harness vast amounts of computing power for research,
applicable to nearly any field of study (e.g., physics, chemistry,
engineering, life sciences, earth sciences, agricultural and animal
sciences, economics, social sciences, medicine, and more).

For more background:
https://research.cs.wisc.edu/htcondor/htc.html
https://www.opensciencegrid.org/news/research-highlights-list/

Using lectures, discussions, roleplays, and lots of hands-on work with
OSG experts in HTC, participants will learn how HTC systems work, how to
run and manage many jobs and huge datasets, how to implement a realistic
scientific computing workflow, and where to turn for help and more info.

Worried about costs? We pay all basic travel, hotel, and food costs for
applicants who are selected to attend. This is a valuable offer!

Ideal candidates are graduate students whose research involves or could
involve large-scale computing - work that cannot be done on one laptop
or a handful of computers. Also, we accept some post-doctoral students,
faculty, staff, and advanced undergraduates, so make a strong case for
yourself regardless of your current role!

IMPORTANT DATES

Application Period (OPEN NOW): 15 March - 20 April 2018
OSG User School: 9-13 July 2018

MORE INFORMATION AND APPLICATIONS

Web: https://www.opensciencegrid.org/UserSchool
Email: [email protected]
Facebook: https://www.facebook.com/OSGUserSchool
Twitter: https://twitter.com/OSGUserSchool

Please forward this announcement to anyone who might benefit from the
OSG User School. And consider posting our flyer where appropriate:

https://opensciencegrid.github.io/user-school-2018/files/osg-user-school-2018-flyer.pdf

Condor Project News > HTCondor 8.7.7 released! ( March 13, 2018 )

The HTCondor team is pleased to announce the release of HTCondor 8.7.7. This development series release contains new features that are under development. This release contains all of the bug fixes from the 8.6.10 stable release. Enhancements in the release include: condor_ssh_to_job now works with Docker Universe jobs; A 32-bit condor_shadow is available for Enterprise Linux 7 systems; Tracks and reports custom resources, e.g. GPUs, in the job ad and user log; condor_q -unmatchable reports jobs that will not match any slots; Several updates to the parallel universe; Spaces are now allowed in input, output, and error paths in submit files; In DAG files, spaces are now allowed in submit file paths. Further details can be found in the Development Version History and the Stable Version History. HTCondor 8.7.7 binaries and source code are available from our Downloads page.

Condor Project News > HTCondor 8.6.10 released! ( March 13, 2018 )

The HTCondor team is pleased to announce the release of HTCondor 8.6.10. A stable series release contains significant bug fixes. Highlights of this release are: Fixed a problem where condor_preen would crash on an active submit node; Improved systemd configuration to clean up processes if the master crashes; Fixed several other minor problems. More details about the fixes can be found in the Version History. HTCondor 8.6.10 binaries and source code are available from our Downloads page.


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