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Ph.D. Defense: Patrick Donnelly

Patrick Donnelly successfully defended his Ph.D. titled "Data Locality Techniques in an Active Cluster Filesystem for Scientific Workflows". 

Congratulations to Dr. Donnelly!


The continued exponential growth of storage capacity has catalyzed the broad acquisition of scientific data which must be processed. While today's large data analysis systems are highly effective at establishing data locality and eliminating inter-dependencies, they are not so easily incorporated into scientific workflows that are often complex and irregular graphs of sequential programs with multiple dependencies. To address the needs of scientific computing, I propose the design of an active storage cluster file system which allows for execution of regular unmodified applications with full data
locality.

This dissertation analyzes the potential benefits of exploiting the structural information already available in scientific workflows -- the explicit dependencies -- to achieve a scalable and stable system. I begin with an outline of the design of the Confuga active storage cluster file system and its applicability to scientific computing. The remainder of the dissertation examines the techniques used to achieve a scalable and stable system. First, file system access by jobs is scoped to explicitly defined dependencies resolved at job dispatch. Second, workflow's structural information is harnessed to direct and control necessary file transfers to enforce cluster stability and maintain performance. Third, control of transfers is selectively relaxed to improve performance by limiting any negative effects of centralized transfer management.

This work benefits users by providing a complete batch execution platform joined with a cluster file system. The user does not need to redesign their workflow or provide additional consideration to the management of data dependencies. System stability and performance is managed by the cluster file
system while providing jobs with complete data locality. - See more at: http://cse.nd.edu/events/phd-defense-patrick-donnelly#sthash.4BLYgJYM.dpuf
DATA LOCALITY TECHNIQUES IN AN ACTIVE CLUSTER FILE SYSTEM DESIGNED FOR
SCIENTIFIC WORKFLOWS - See more at: http://cse.nd.edu/events/phd-defense-patrick-donnelly#sthash.4BLYgJYM.dpuf
DATA LOCALITY TECHNIQUES IN AN ACTIVE CLUSTER FILE SYSTEM DESIGNED FOR
SCIENTIFIC WORKFLOWS - See more at: http://cse.nd.edu/events/phd-defense-patrick-donnelly#sthash.4BLYgJYM.dpuf
Wed, 06 Apr 2016 18:38:00 +0000

Searching for Exo-Planets with Makeflow and Work Queue

Students at the University of Arizona made use of Makeflow and Work Queue to build an image processing pipeline on the Chameleon cloud testbed at TACC.

The course project was to build an image processing pipeline to accelerate the research of astronomer Jared Males, who designs instruments to search for exo-planets by observing the changes in appearance of a star.  This results in hundreds of thousands of images of a single star, which must then be processed in batch to eliminate noise and align the images.

The students built a solution (Find-R) which consumed over 100K CPU-hours on Chameleon, distributed using Makeflow and Work Queue.

Read more here:
https://www.tacc.utexas.edu/-/in-search-of-a-planet
Tue, 22 Mar 2016 19:14:00 +0000

Parrot talk at OSG All-hands meeting 2016

Ben Tovar gave a talk on using parrot to access CVMFS as part of the Open Science Grid (OSG) all-hands meeting in Clemson, SC.

Software access with parrot and CVMFS Fri, 18 Mar 2016 22:03:00 +0000

CCTools 5.4.0 released

The Cooperative Computing Lab is pleased to announce the release of version 5.4.0 of the Cooperative Computing Tools including Parrot, Chirp, Makeflow, WorkQueue, Umbrella, SAND, All-Pairs, Weaver, and other software.

The software may be downloaded here:

http://www.cse.nd.edu/~ccl/software/download

This minor release adds several features and bug fixes. Among them:

  • [Catalog]  Catalog server communication is now done using JSON encoded queries and replies. (Douglas Thain)
  • [Makeflow] --skip-file-check added to mitigate overhead on network file systems. (Nick Hazekamp)
  • [Makeflow] Added amazon batch job interface. (Charles Shinaver)
  • [Resource Monitor] Network bandwidth, bytes received, and sent are now recorded. (Ben Tovar)
  • [Work Queue] Tasks may be grouped into categories, for resource control and fast abort. (Ben Tovar)
  • [Work Queue] work_queue_pool was renamed to work_queue_factory. (Douglas Thain)
  • [Work Queue] --condor-requirements to specify arbitrary HTCondor requirements in worker_queue_factory. (Chao Zheng)
  • [Work Queue] --factory-timeout to terminate worker_queue_factory when no master is active. (Neil Butcher)
  • [Work Queue] Compile-time option to specify default local settings in    sge_submit_workers. (Ben Tovar)
  • [Umbrella]   Several bugfixes. (Haiyan Meng, Alexander Vyushkov)
  • [Umbrella]   Added OSF, and S3 communication. (Haiyan Meng)
  • [Umbrella]   Added EC2 execution engine. (Haiyan Meng)
  • [Parrot] Several bug-fixes for memory mappings. (Patrick Donnelly)
  • [Parrot] All compiled services are shown under / (Tim Shaffer)
  • [Parrot] POSIX directory semantics. (Tim Shaffer)
  • [Parrot] Added new syscalls from Linux kernel 4.3. (Patrick Donnelly)

Thanks goes to the contributors for many features, bug fixes, and tests:

  • Jakob Blomer
  • Neil Butcher
  • Patrick Donnelly
  • Nathaniel Kremer-Herman
  • Nicholas Hazekamp
  • Peter Ivie
  • Kevin Lannon
  • Haiyan Meng
  • Tim Shaffer
  • Douglas Thain
  • Ben Tovar
  • Alexander VyushkovRodney Walker
  • Mathias Wolf
  • Anna Woodard
  • Chao Zheng

Please send any feedback to the CCTools discussion mailing list:

http://ccl.cse.nd.edu/software/help/

Enjoy!

Tue, 16 Feb 2016 20:24:00 +0000

Preservation Talk at Grid-5000

Prof. Thain gave a talk titled Preservation and Portability in Distributed Scientific Applications at the Grid-5000 Winter School on distributed computing in Grenoble, France.  I gave a broad overview of our recent efforts, including distributing software with Parrot and CVMFS, preserving high energy physics applications with Parrot, specifying environments with Umbrella, and preserving workflows with PRUNE.


Wed, 03 Feb 2016 11:31:00 +0000

Summer REU in DISC at Notre Dame

REU in Data Intensive Scientific Computing (DISC) at the University of Notre Dame
DISC combines big data, big science, and big computers at the University of Notre Dame. The only thing missing is you!


We invite outstanding undergraduates to apply for a summer research experience in DISC at the University of Notre Dame.  Students will spend ten weeks learning how to use high performance computing and big data technologies to attack scientific problems.  Majors in computer science, physics, biology, and related topics are encouraged to apply.

For more information:
http://disc.crc.nd.edu

Tue, 12 Jan 2016 19:21:00 +0000

CCTools 5.3.0 released

The Cooperative Computing Lab is pleased to announce the release of version 5.3.0 of the Cooperative Computing Tools including Parrot, Chirp, Makeflow, WorkQueue, Umbrella, SAND, All-Pairs, Weaver, and other software.

The software may be downloaded here:
http://www.cse.nd.edu/~ccl/software/download

This minor release adds several features and bug fixes. Among them:

  • [Makeflow]  Several enhancements in garbage collection. (Nick Hazekamp)
  • [Makeflow]  Better task state handling when recovering execution log. (Nick Hazekamp)
  • [Parrot]    Correct handling of multi-threaded programs. (Patrick Donnelly)
  • [Parrot]    Adds parrot_mount, to set arbitrary mount points while parrot is executing. (Douglas Thain)
  • [Parrot]    Add --fake-setuid option, for executables that request setuid. (Tim Shaffer)
  • [Parrot]    Update cvmfs uri to new convention. (Jakob Blomer)
  • [Parrot]    Add --whitelist to restrict filesystem access. (Tim Shaffer)
  • [Parrot]    Make special file descriptors invisible to tracee. (Patrick Donnelly)
  • [Resource Monitor] Compute approximations of shared resident memory. (Ben Tovar)
  • [Resource Monitor] Remove resource_monitorv for static binaries. resource_monitor now handles all cases.  (Ben Tovar)
  • [Resource Monitor] Working directories are not tracked by default anymore. Use --follow-chdir instead.  (Ben Tovar)
  • [Umbrella]  Support for curateND. (Haiyan Meng)
  • [Umbrella]  Support for installing software from package managers. (Haiyan Meng)
  • [Work Queue] Adds option -C to read a JSON configuration file. (Ben Tovar)
  • [Work Queue] Several bug fixes regarding task/workflow statistics. (Ben Tovar)
  • [Work Queue] Master's shutdown option now correctly terminates  workers. (Ben Tovar)
  • [Work Queue] Adds --sge-paremeter to ./configure script to personalize the sge_submit_workers script. (Ben Tovar)
  • [Work Queue] Adds the executable disk_allocator, to restrict disk usage at the workers. (Nate Kremer-Herman)


Incompatibility warnings:

  • Workers from this release do not work correctly with masters from previous releases.


Thanks goes to the contributors for many features, bug fixes, and tests:

  • Jakob Blomer
  • Neil Butcher
  • Patrick Donnelly
  • Nathaniel Kremer-Herman
  • Nicholas Hazekamp
  • Peter Ivie
  • Kevin Lannon
  • Haiyan Meng
  • Tim Shaffer
  • Douglas Thain
  • Ben Tovar
  • Mathias Wolf
  • Anna Woodard

Please send any feedback to the CCTools discussion mailing list:

http://ccl.cse.nd.edu/software/help/

Enjoy!
Mon, 23 Nov 2015 17:24:00 +0000

Analyzing LHC Data on 10K Cores with Lobster

Prof. Thain gave a talk titled Analyzing LHC Data on 10K Cores with Lobster at the Workshop on Data Intensive Computing in the Clouds at Supercomputing 2015.  The talk gave an overview of our collaboration with members of the CMS experiment at Notre Dame.  Together, we have built a data analysis system which can deploy the complex CMS computing environment on large clusters of non-dedicated machines.





Mon, 16 Nov 2015 14:47:00 +0000

Global Filesystems Paper in IEEE CiSE

Our latest paper, in collaboration with Jakob Blomer and the CVMFS team at CERN, describes the evolution of global-scale filesystems to serve the needs of the world-wide LHC experiment collaborations:



Delivering complex software across a worldwide distributed system is a major challenge in high-throughput scientific computing. The problem arises at different scales for many scientific communities that use grids, clouds, and distributed clusters to satisfy their computing needs. For high-energy physics (HEP) collaborations dealing with large amounts of data that rely on hundreds of thousands of cores spread around the world for data processing, the challenge is particularly acute. To serve the needs of the HEP community, several iterations were made to create a scalable, user-level filesystem that delivers software worldwide on a daily basis. The implementation was designed in 2006 to serve the needs of one experiment running on thousands of machines. Since that time, this idea evolved into a new production global-scale filesystem serving the needs of multiple science communities on hundreds of thousands of machines around the world. 

Mon, 09 Nov 2015 19:27:00 +0000

Preservation Talk at iPres 2015

Prof. Thain gave a talk titled "Preserving Scientific Software Executions: Preserve the Mess or Encourage Cleanliness" at the 2015 Conference on Digital Preservation.  This talk gives a high level overview of our work on preservation, encompassing packaging with Parrot, environment specification with Umbrella, and workflow preservation with Prune.

Tue, 03 Nov 2015 19:16:00 +0000

CMS Case Study Paper at CHEP

Our case study work on how to preserve and reproduce a high energy physics (HEP) application with Parrot has been accepted by Journal of Physics: Conference Series (JPCS 2015).

The HEP application under investigation is called TauRoast, and authored by our physics collaborator, Matthias. TauRoast is a complex single-machine application having lots of implicit and explicit dependencies: CVS, github, PyYAML websites, personal websites, CVMFS, AFS, HDFS, NFS, and PanFS. The total size of these dependencies is about 166.8TB.

To make TauRoast reproducible, we propose one fine-grained dependency management toolkit based on Parrot to track the really used data and create a reduced package which gets rid of all the unused data. By doing so, the original execution environment with the size of 166.8TB is reduced into a package with the size of 21GB. The correctness of the preserved package is demonstrated in three different environments - the original machine, one virtual machine from the Notre Dame Cloud Platform and one virtual machine from the Amazon EC2 Platform.

 

Tue, 20 Oct 2015 16:15:00 +0000

OpenMalaria Preservation with Umbrella

Haiyan worked together with Alexander from CRC, successfully preserved and reproduced a C++ application, openMalaria, using Umbrella. The data dependencies of openMalaria include packages from yum repositories, OS images from the CCL websites, software and data dependencies from curateND. Through a JSON-format specification, Umbrella allows the user to specify the complete execution environment for his application: hardware, kernel, OS, software, data, packages supported by package managers, environment variables, and command. Each dependency in an Umbrella specification also comes with its metadata information - size, format, checksum, downloading urls, and mountpoints. During runtime, Umbrella tries to construct the execution environment specified in the specification with the help of different sandboxing techniques such as Parrot and Docker, and run the user's task. Mon, 19 Oct 2015 20:54:00 +0000

DAGVz Paper at Visual Performance Analysis Workshop

An Huynh will be presenting a paper on the visualization of task-parallel programs at the Visual Performance Analysis workshop at Supercomputing 2015.  (He is a student of Kenjiro Taura at the University of Tokyo who spent a semester working with us in the Cooperative Computing Lab.)

An developed DAGViz, a tool for exploring the rich structure of task parallel programs, which requires associating DAG structure with performance measures at multiple levels of detail.  This allows the analyst to zoom in to trouble spots and view exactly where and how each basic block of a program ran on a multi-core machine.




Tue, 13 Oct 2015 15:01:00 +0000

Virtual Wind Tunnel in IEEE CiSE

Some of our recent work on a system for collaborative engineering design was recently featured in the September issue of IEEE Computing in Science and Engineering focused on "Open Simulation Laboratories"  This project was part of a collaboration between faculty in the computer science and civil engineering departments, Open Sourcing the Design of Civil Infrastructure.

CCL grad student Peter Sempolinski led the design and implementation of an online service enabling collaborative design and evaluation of structures, known as the "Virtual Wind Tunnel".  This service enables structural designs to be uploaded and shared, then evaluated for performance via the OpenFOAM CFD package.  The entire process is similar to that of collaborative code development, where the source (i.e. a building design) is kept in a versioned repository, automated builds (i.e. building simulation) are performed in a consistent and reproducible way, and test results (i.e. simulation metrics) are used to evaluate the initial design.  Designs and results can be shared, annotated, and re-used, making it easy for one engineer to build upon the work of another.

The prototype system has been used in a variety of contexts, most notably to demonstrate the feasibility of crowdsourcing design and evaluation work via Amazon Turk.








Wed, 09 Sep 2015 13:27:00 +0000

Three Papers at IEEE Cluster in Chicago

This week, at the IEEE Cluster Computing conference in Chicago, Ben Tovar will present some of our work on automated application monitoring:

(PDF)Gideon Juve, Benjamin Tovar, Rafael Ferreira da Silva, Dariusz Krol, Douglas Thain, Ewa Deelman, William Allcock, and Miron Livny, Practical Resource Monitoring for Robust High Throughput Computing, Workshop on Monitoring and Analysis for High Performance Computing Systems Plus Applications at IEEE Cluster Computing, September, 2015. 

Matthias Wolf will present our work on the Lobster large scale data management system:

(PDF)Anna Woodard, Matthias Wolf, Charles Mueller, Nil Valls, Ben Tovar, Patrick Donnelly, Peter Ivie, Kenyi Hurtado Anampa, Paul Brenner, Douglas Thain, Kevin Lannon and Michael Hildreth,
Scaling Data Intensive Physics Applications to 10k Cores on Non-Dedicated Clusters with Lobster, IEEE Conference on Cluster Computing, September, 2015.

Olivia Choudhury will present some work on modelling concurrent applications, trading off thread-level parallelism against task-level parallelism at scale:

(PDF)Olivia Choudhury, Dinesh Rajan, Nicholas Hazekamp, Sandra Gesing, Douglas Thain, and Scott Emrich,
Balancing Thread-level and Task-level Parallelism for Data-Intensive Workloads on Clusters and Clouds,
IEEE Conference on Cluster Computing, September, 2015.


Mon, 07 Sep 2015 19:07:00 +0000

CCTools 5.2.0 released

The Cooperative Computing Lab is pleased to announce the release of version 5.2.0 of the Cooperative Computing Tools including Parrot, Chirp, Makeflow, WorkQueue, SAND, All-Pairs, Weaver, and other software.

The software may be downloaded here:

http://www.cse.nd.edu/~ccl/software/download

This minor release considers the following issues from version 5.1.0:

  • [Chirp]     Fix mkdir python binding. (Ben Tovar)
  • [Chirp]     Adds 'ln' for file links. (Nate Kremer-Herman)
  • [Chirp/Confuga] Kill a job even on failure. (Patrick Donnelly)
  • [Debug]     Fix log rotation with multiple processes. (Patrick Donnelly)
  • [Makeflow]  Better support for Torque and SLURM for XSEDE. (Nick Hazekamp)
  • [Parrot]    Fix bug where cvmfs alien cache access was sequential. (Ben Tovar)
  • [Parrot]    Allow compilation with iRODS 4.1. (Ben Tovar)
  • [WorkQueue] Improvements to statistics when using foremen. (Ben Tovar)
  • [WorkQueue] Fix bug related to exporting environment variables. (Ben Tovar)
  • [WorkQueue] Task sandboxes where not being deleted at workers. (Ben Tovar)

Thanks goes to our contributors:

Patrick Donnelly
Nathaniel Kremer-Herman
Nicholas Hazekamp
Ben Tovar

Please send any feedback to the CCTools discussion mailing list:

http://ccl.cse.nd.edu/software/help/

Enjoy! Wed, 19 Aug 2015 12:05:00 +0000

Recent CCL Grads Take Faculty Positions

Peter Bui is returning to Notre Dame this fall, where he will be a member of the teaching faculty and will be teaching undergraduate core classes like data structures, discrete math, and more.  Welcome back, Prof. Bui!






Hoang Bui completed a postdoc position at Rutgers University with Prof. Manish Parashar, and is starting as an assistant professor at Western Illinois University.  Congratulations, Prof. Bui!

Tue, 18 Aug 2015 15:16:00 +0000

CMS Analysis on 10K Cores Using Lobster

We have been working closely with the CMS physics group at Notre Dame for the last year to build Lobster, a data analysis system that runs on O(10K) cores to process data produced by the CMS experiment at the LHC.  At peak, Lobster at ND delivers capacity equal to that of a dedicated CMS Tier-2 facility!

Existing data analysis systems for CMS generally require that the user be running in a cluster that has been set up just so for the purpose: exactly the right operating system, certain software installed, various user identities present, and so on. This is fine for the various clusters dedicated to the CMS experiment, but it leaves unused the enormous amount of computing power that can be found at university computing centers (like the ND CRC), national computing resources (like XSEDE or the Open Science Grid), and public cloud systems.

Lobster is designed to harness clusters that are not dedicated to CMS.  This requires solving two problems:
  1. The required software and data are not available on every node.  Instead, Lobster must bring them in at runtime and create the necessary execution system on the fly.
  2. A given machine may only be available for a short interval of time before it is taken away and assigned to another user, so Lobster must be efficient at getting things set up, and handy at dealing with disconnections and failures.
To do this, we build upon a variety of technologies for distributed computing.  Lobster uses Work Queue to dispatch tasks to thousands of machines, Parrot with CVMFS to deliver the complex software stack from CERN, XRootD to deliver the LHC data, and Chirp and Hadoop to manage the output data.

Lobster runs effectively on O(10K) cores so far, depending on the CPU/IO ratio of the jobs.  These two graphs show the behavior of a production run on top of HTCondor at Notre Dame hitting up to 10K cores over the course of a 48-hour run.  The top graph shows the number of tasks running simultaneously, while the bottom shows the number of tasks completed or failed in each 10-minute interval.  Note that about two thirds of the way through, there is a big hiccup, due to an external network outages.  Lobster accepts the failures and keeps on going.

Lobster has been a team effort between Physics, Computer Science, and the Center for Research Computing: Anna Woodard and Matthias Wolf have taken the lead in developing the core software; Ben Tovar, Patrick Donnelly, and Peter Ivie have improved and debugged Work Queue, Parrot, and Chirp along the way; Charles Mueller, Nil Valls, Kenyi Anampa, and Paul Brenner have all worked to deploy the system at scale in production; Kevin Lannon, Michael Hildreth, and Douglas Thain provide the project leadership.


Anna Woodard, Matthias Wolf, Charles Nicholas Mueller, Ben Tovar, Patrick Donnelly, Kenyi Hurtado Anampa, Paul Brenner, Kevin Lannon, and Michael Hildreth, Exploiting Volatile Opportunistic Computing Resources with Lobster, Computing in High Energy Physics, January, 2015.

Anna Woodard, Matthias Wolf, Charles Mueller, Nil Valls, Ben Tovar, Patrick Donnelly, Peter Ivie, Kenyi Hurtado Anampa, Paul Brenner, Douglas Thain, Kevin Lannon and Michael Hildreth, Scaling Data Intensive Physics Applications to 10k Cores on Non-Dedicated Clusters with Lobster, IEEE Conference on Cluster Computing, September, 2015.

Fri, 14 Aug 2015 15:19:00 +0000

Haipeng Cai Defends Ph.D.

Haipeng Cai successfully defended his dissertation, "Cost-effective Dependence Analyses for Reliable Software Evolution", which studied methods for efficiently determining the scope of complex software system that is affected by a given change.

Haipeng will be taking a postdoctoral research position at Virginia Tech under the supervision of Prof. Barbara Ryder.

Congratulations to Dr. Haipeng Cai!


Thu, 16 Jul 2015 17:42:00 +0000

CCTools 5.1.0 released

The Cooperative Computing Lab is pleased to announce the release of version 5.1.0 of the Cooperative Computing Tools including Parrot, Chirp, Makeflow, WorkQueue, SAND, All-Pairs, Weaver, and other software.

The software may be downloaded here:
download

This minor release adds a couple of small features, and fixes the following
issues of version 5.0.0:

  • [Prune]     Fix installation issue. (Haiyan Meng)
  • [Umbrella]  Fix installation issue. (Haiyan Meng)
  • [WorkQueue] Worker's --wall-time to specify maximum period of time a worker may be active. (Andrey Tovchigrechko, Ben Tovar)
  • [WorkQueue] work_queue_status's --M to show the status of masters by name. (Names may be regular expressions). (Ben Tovar)
  • [WorkQueue] Fix missing priority python binding.
  • [WorkQueue] Fix incorrect reset of workers when connecting to different masters. (Ben Tovar)
  • [WorkQueue] Fix segmentation fault when cloning tasks. (Ben Tovar)
  • [WQ_Maker]  Cleanup, and small fixes. (Nick Hazekamp)

Thanks goes to our contributors:

Nicholas Hazekamp
Haiyan Meng
Ben Tovar
Andrey Tovchigrechko

Please send any feedback to the CCTools discussion mailing list:

mailing list

Enjoy!

~ Thu, 16 Jul 2015 16:42:00 +0000

CCTools 5.0.0 released

The Cooperative Computing Lab is pleased to announce the release of version 5.0.0 of the Cooperative Computing Tools including Parrot, Chirp, Makeflow, WorkQueue, SAND, All-Pairs, Weaver, and other software.
The software may be downloaded here: CCTools download
This is a major release that incorporates the preview of three new tools:
  • [Confuga] An active storage cluster file system built on top of Chirp. It is used as a collaborative distributed file system and as a platform for execution of scientific workflows with full data locality for all job dependencies. (Patrick Donnelly)
  • [Umbrella] A tool for specifying and materializing comprehensive execution environments. Once a task is specified, Umbrella determines the minimum mechanism necessary to run it such as, direct execution, a system container, a local virtual machine, or submission to a cloud or grid environment. (Haiyan Meng).
  • [Prune] A system for executing and precisely preserving scientific workflows. Collaborators can verify research results and easily extend them at a granularity determined by the user. (Peter Ivie)
This release adds several features and several bug fixes. Among them:
  • [AllPairs] Support for symmetric matrices. (Haiyan Meng)
  • [Chirp] Perl and python bindings. (Ben Tovar)
  • [Chirp] Improvements to the job interface. (Patrick Donnelly)
  • [Makeflow] Improved Graphviz's dot output. (Nate Kremer-Herman)
  • [Makeflow] Support for command wrappers. (Douglas Thain)
  • [Parrot] Several bug fixes for CVMFS-based applications. (Jakob Blomer, Patrick Donnelly)
  • [Parrot] Valgrind support. (Patrick Donnelly)
  • [Resource Monitor] Library for polling resources. (Ben Tovar)
  • [WorkQueue] Signal handling bug fixes. (Andrey Tovchigrechko)
  • [WorkQueue] Log visualizer. (Ryan Boccabella)
  • [WorkQueue] work_queue_worker support for Docker. (Charles Zheng)
  • [WorkQueue] Improvements to perl bindings. (Ben Tovar)
  • [WorkQueue] Support to blacklist workers. (Nick Hazekamp)
Incompatibility warnings: Workers from 5.0 do not work with masters pre 5.0.
Thanks goes to the contributors for many features and bug fixes: Matthew Astley, Jakob Blomer, Ryan Boccabella, Peter Bui, Patrick Donnelly, Nathaniel Kremer-Herman, Victor Hawley, Nicholas Hazekamp, Peter Ivie, Kangkang Li, Haiyan Meng, Douglas Thain, Ben Tovar, Andrey Tovchigrechko, and Charles Zheng.
Please send any feedback to the CCTools discussion mailing list: mailing list
Enjoy!






Tue, 07 Jul 2015 17:21:00 +0000

Preservation Framework for Computational Reproducibility at ICCS 2015

Haiyan Meng presented our work on Preservation Framework for Computational Reproducibility at the International Conference on Computational Science (ICCS) in Reykjavik, Iceland. This is a collaborative work between University of Notre Dame and University of Chicago for the DASPOS project both of these two universities are working on.


The preservation framework proposed in this paper includes three parts: 
  • First, how to use light-weight application-level virtualization techniques to create a reduced package which only includes all the necessary dependencies; 
  • Second, how to organize the data storage archive to preserve these packages; 
  • Third, how to distribute applications through standard software delivery mechanisms like Docker and deploy applications through flexible deployment mechanisms such as Parrot, PTU, Docker, and chroot.

 

Wed, 01 Jul 2015 16:04:00 +0000

Umbrella and Containers at VTDC 2015

Two CCL students presented their latest work at the Virtualization Technologies in Distributed Computing (VTDC) at the Symposium on High Performance Distributed Computing (HPDC) in Portland, Oregon.

Haiyan Meng presented her work on Umbrella, a system for specifying and materializing execution environments in a portable and reproducible way.  Umbrella accepts a declarative specification for an application, and then determines the minimum technology needed to deploy it.   The application will be run natively if the local execution environment is compatible, but if not, Umbrella will deploy a container, a virtual machine, or make use of a public cloud if necessary.

(PDF)Haiyan Meng and Douglas Thain,
Umbrella: A Portable Environment Creator for Reproducible Computing on Clusters, Clouds, and Grids,
Workshop on Virtualization Technologies in Distributed Computing (VTDC) at HPDC, June, 2015. DOI: 10.1145/2755979.2755982

Charles Zheng presented his work on integrating Docker containers into the Makeflow workflow engine and the Work Queue runtime system, each with different tradeoffs in performance and isolation.  These capabilities will be included in the upcoming 5.0 release of CCTools.

(PDF) Charles Zheng and Douglas Thain,
Integrating Containers into Workflows: A Case Study Using Makeflow, Work Queue, and Docker,
Workshop on Virtualization Technologies in Distributed Computing (VTDC), June, 2015. DOI: 10.1145/2755979.2755984
Fri, 19 Jun 2015 18:21:00 +0000

Lobster Talk at Condor Week 2015

Ben Tovar gave an overview of Lobster in the talk High-Energy Physics workloads on 10k non-dedicated opportunistic cores with Lobster. The talk was part of Condor Week 2015, at the University of Wisconsin-Madison.

Lobster is a system for deploying data intensive high-throughput science applications on non-dedicated resources. It is build on top Work Queue, Parrot, and Chirp, which are part of CCTools.


Wed, 27 May 2015 18:47:00 +0000

Parrot and Lobster at CHEP 2015

CCL students gave two poster presentations at the annual Computing in High Energy Physics (CHEP) conference in Japan.  Both represent our close collaboration with the CMS HEP group at Notre Dame:


Haiyan Meng presented A Case Study in Preserving a High Energy Physics Application.  This poster describes the complexity of preserving a non-trivial application, the shows how Parrot packaging technology can be used to capture a program's
dependencies, and then re-execute it using a variety of technologies.





Anna Woodard and Matthias Wolf won the best poster presentation award for Exploiting Volatile Opportunistic Computing Resources with Lobster, which was rewarded with a lightning plenary talk.  Lobster is an analysis workload management system which has been able to harness 10-20K opportunistic cores at a time for large workloads at Notre Dame, making the facility comparable in size to the dedicated Tier-2 facilities of the WLCG!


Tue, 19 May 2015 14:57:00 +0000