Developer Meetings

March 2015

March 13th, 2015

Metrics Server
- deployed on the production server.
- want to do anything on basis of distribution of files
- donald will create a new histogram page ,
Pegasus NSF Report
- sent to Ewa
Pegasus 4.4.2 release
- karan will check in release notes today
Pegasus Tutorial as part of HPC Workshop Series in April
Gideon will be going to the summer school.
Pegasus 4.5.0 release
- Targeting May 1st release
- local-scratch is picked up.
- ensemble manager submission
  - will support both modes
  - bundle mode
  - public ensemble manager. there are security issues. user credentials.
  - the person who starts the service will setup the credentials
- pegasus-analyzer fix for case where jobs eventually succeed after failures
- pegasus-db-admin update
  - ds
- transfer grouping of staging jobs
- Pending items
  - https://jira.isi.edu/issues/?filter=10851
User Questionnaire
- 12 responses for
- a lot of people are interested in a workshop
- better support for loops and branches
- better provenance support .
Workflows on Google and Amazon

March 6th, 2015

metrics server update
- plans to deploy the changes today. fixing last issue
- still has to make the database schema changes required for planner file counts
  - will be done next week
planner reports file breakdowns
pegasus 4.4.2 release
- it has fixes LIGO is interested.
- most probably next week.
pegasus-db-admin
- reorganization of the code and the schema.
pegasus-archive /pegasus-delete
- rafael does not have time to work on these because of proposal work
- will move to either gideon or mats
pegasus-dashboard updates
- has more LIGO requests for pegasus 4.5.0 release
- wsgi script for root mode
LIGO visit
- post 4.5 we will do better organization of files on the file structure
- Pegasus poster for LIGO meeting
ensemble manager
- scec folks will try it
- monitord netlogger bugfix
pegasus-transfer enhancements for panorama
job submission paper in github
- pegasus and job management systems.
online monitoring for pegasus-kickstart
- application sends signal to pegasus-kickstart via libinterpose
pegasus-keg extensions
- the pegasus-mpi-keg is a separate executable
- extensions to the io stuff
- will incorporate in 4.5.0
NSF report
- still waiting to hear from mats and scott
- karan is still updating the metrics page.

February 2015

Feb 20th, 2015

metrics server update
- donald still has to deploy the changes.
pegasus user questionnaire
- gideon will send new links and will update
SCEC update
- scott has debugged his memory
Pegasus Report
- soykb and other iplant workflows ... part of ECSS
- galactic plane
- ahmeds work
pegasus dashboard updates
- pegasus-dashboard is started whenever bamboo is built up
- dashboard show all states for a job now.
pegasus-db-admin tool
- test cases in bamboo
- documentation
- migration notes
- some python errors that need to be fixed.
4.5 release
- still remaining
  - held jobs tracking in monitord
- job retry set to 1 and disable retries for DAX jobs
- decrease the held period from one hour when job is removed.
- improved documentation for output mappers
- ensemble manager todo's
  - we won't have ensemble manger in multiuser mode
  - support both modes ( upload a tar file and finer grained control where he specifies the DAX files and the submit directory )
  - only the dashboard will run in multiuser mode
  - how do we start ensemble manager process
    - run as per user .
- copying of catalog files to submit directory.
input directory copies based on recursive transfers as part of directory
- it won't work in condorio mode because it flattens out
- add type directory in the DAX schema.
pegasus tutorial
environment variable file substitution in site catalog, replica catalog and transformation catalog
XSEDE Tutorial proposal and Posters

January 2015

Jan 14th, 2015

metrics server update
- no update from Donald still away from vacation
Pegasus development
- data configuration for different sites
  - working for steven
- held jobs
- pegasus-dashboard
  - root mode for dashboard and ensemble manager
    - gideon needs to confirm for ensemble manger
    - done for dashboard
- pegasus-analyzer bug fix
- pegasus-db-admin tool update
  - unit tests
  - bamboo pool will break.
- upgrade to newer version of Pegasus
  - what happens to running workflows
- pegasus-statistics with PMC - Mats and Rajiv
  - mats and rajiv will work on it.
- docker based tutorial launcher
  - how to integrate in the build process
  - form
  - candidate machine
    - obelix
  - vmware colo vm
  - obelix.
Pegasus Poster for Si2
- will base on the previous years.
- any particular thing we want to focus on ? or general?
Pegasus Annual Report
- User questionnaire - need to send out.
  - list of people to send it out to . Gideon has one.?

Jan 7th, 2015

metrics server update
- no update from Donald still away from vacation
4.4.1
- installed on workflow
- OSG and XSEDE submit hosts will be upgraded in 3 weeks
- need to follow up with LIGO
database upgrade tool integration
- documentation and manage left
- import error for properties
- python test case
support for per site data configuration
- mostly done/ still need to figure out worker package staging for that.
pegasus-dashboard
- should we show all job instances for a job.
held jobs logged by pegasus-monitord
user questionnaire

December 2014

Dec 8th, 2014

metrics server update
- minor bugs in the UI... still need to be fixed, especially how the session states are handled
- things remaining to do
  - database/server side pagination
  - figure out the scroll issue for the trend charts
  - move the trends charts from the home page to under planner and download tabs
  - rename run metrics to dagman metrics, and instead of showing the most number of times a workflow was run, we want to see the top applications for which dagman workflows were run
  - for the time bar on the top, have drop down menu for years and months
  - can the maps pin show the actual number, for example in the top downloads map thing
monitord fixes
- for the race issue with postscript handling PM-798
  - had to change the way stdout and stderr is populated for job_instance. It is now populated with the POST_SCRIPT_TERMINATED event happens
pegasus-analyzer fixes
- show the planner log when prescript for sub dax fails. PM-808
we want to release 4.4.1 before the break.
- has monitord fixes that LIGO requires
tracking held jobs
- decided to add a column in the jobstate table to capture why a job was held
changes to pegasus-keg
- to simulate reading in input and writing out of output files
- will also simulate cputime and walltime
- initially pegasus-keg will read in and write out the outputs and then do the sleep for the cpu time duration
- removing the system information that it prints out
- in the mpi version, the IO is solely done by the master.

December 3rd, 2014

Update from Duncan on LIGO dashboard requirements
- run a flask module from apache
- let apache handle authentication
- read only dashboard view
- have a separate flask frontend.
- they are ok with a command line tool to remove workflow entries
- port collisions .. so they prefer apache to do the handling.
failed jdbrc unit test case
glite quoting for the environment
pegasus-dashboard delete workflows capability
failing workflow reporting in the dashboard
monitord to follow condor job log
db admin tool updates

November 2014

November 12th, 2014

DAGMan metrics reporting
- working and completed for 4.5.0cvs
- planned metrics
  - exclude the metrics that never ran.
  - have a drop down menu - planned , planned and run
RPM/ and DEB tracking for downloads
- mats has a script that goes through the download logs to populate the server.
- So we are tracking those now.
Failed data reuse regex test
- make it a planning only test case
hierarchal workflows options forwarding
- have a value of null/none
- --inherit option with a comma separated list of long opts.
higher level DAX API for sub workflows ?
- hack to figure out the command line arguments for the planner
Pegasus Distribute Wrapper
- waiting to hear further from Steven
- a /bin/bash test case
Metrics Server Updates by Donald
- has the geo location running
DB Upgrade tool - Rafael ??
- version upgrades
- specific table version
- https://jira.isi.edu/browse/PM-776

November 5th, 2014

DAGMan metrics reporting
- already in recent DAGMan versions. can be enabled.
- pegasus-run having the duplicate logic.
Pegasus Distribute Wrapper
- Initial implementation done and there is an example for Steven to try out
Metrics Server Updates by Donald
DB Upgrade tool - Rafael ??

October 2014

October 29th, 2014

Upcoming Proposals
- NEESGrid call
  - Robert Flashgun with Nirav..ASU stuff. Do some earthquake stuff
  - frank mckenna for nees type stuff
    - SCEC is part of the proposal
  - December 3rd due date
Pegasus Development
- monitord postscript handling
- dynamic hierarchy stuff
- Condor C with LIGO
- Steven Clarke Distribute Stuff
- pegasus-hpc-cluster ( PHC )
- DAGMan metrics
Kenichi Workflow
- SNS workflow
- Training material.
Metrics UI updates
- Trends over times
- Geo overlay
Darek from Poland - A postdoc 1206
- panorama project
Adaptive Workflows
- adapting workflows... they are not converging.
- templating workflows
- Hopper Site Catalog
- Sample Site Catalogs

September 2014

September 17th, 2014

Checkpointing feature
- tested and implemented into pegasus
- communicated with LIGO and John Veitch will test it next week.
- will be run from a binary install
- kickstart won't enforce non zero exit code for application exit code . we will require application codes to exit with non zero status.
Profile and Properties documentation integration
database schema upgrade tool
- rafael starts working on it
support for google storage
- hassan writes a paper for google storage
- compare S3 with google storage
- parallel uploads of chunks not supported with gsutils.. relies on a very specific python module
- ~/.botoconfig
- uses oath token for authentication
works paper revisions due oct 1st.
dv/dt paper has been submitted as a CS dept tech report.
DOE Oakridge meeting
- interface with ASPEN ( analytical modeling ) - domain specific language for defining code.
- combine aspen model with machine model and come up with estimates of runtimes.
- christopher riggers from RPI models parallel storage systems.
Explore visualization stuff for pegasus-plots and dashboard?

August 2014

August 25th, 2014

Ensemble Manager - User Authentication
- initially gideon is working on a PAM based approach
refactored netlogger dead code
Workflow Checkpointing support - ongoing
Google Compute Engine
- related to google genomics
- put in support for GCE transfer tool to interact with Google Storage ( their S3 equivalent)
- put in credential handling in the planner.
- fits well with long term planning for pegasus.
Replica Catalog Service

August 18th, 2014

Data Reuse Partial Mode
Service integration
Profiles and Properties Documentation
- Scope Column in the properties documentation ( transformation, job and global )
- in profiles documentation corresponding property key
pegasus-service integration
- need to integrate the documentation
redhat 5 builds
- partially... because of 2.4 installed version pegasus-s3 fail
authentication mechanism
pegasus-service-admin migrate option
new tool pegasus-db-admin
get a new 32 bit VM with cents 6.5
also centos 7 VM
add a setup task that cleans $HOME/.pegasus in bamboo infrastructure.
Docker Kernel Problem
- if a docker build running and you stop the build, then the whole thing crashes
- one solution is to upgrade the kernel version.
- cartman OS can be changed or move the docker builds to a VM.

August 11, 2014

August 4th, 2014

how to handle a single job wrapping around PMC
- will add a property to turn the wrapping off.
checkpointing for LIGO . synonym for checkpointing. user level state files.
- create a JIRA item that explains that.
- list the various cases that will be handled
  - a lot of times in case of eviction kill -9 is sent.
pegasus dashboard changes
- multi tenancy for users.

June 2014

June 30th, 2014

pegasus-remove and pegasus-dagman. pegasus-dagman has a wait of 100 seconds before monitord is killed, when pegasus-remove is called.
rafael will add a workflow test case for JDBCRC
Still have to make a slider.
Karan will work on XSEDE poster for Pegasus
IPlant and metadata requirements.
pegasus-dagman / monitord /condor-dagman
- hierarchal
- PMC
- GRAM

June 9th, 2014

4.4 release
- next week
- documentation items remaining
- JDBRC test cases and handover to SCEC
Dashboard improvements
- dashboard improvements
Post Release Activiites
- integrate pegasus service back into the main codebase

May 2014

May 12th, 2014

PM-747
- will be used for soykb
- test case
Development releases
- 4.4
  - plan for June 20th
  - automatic data dependencies
  - wrap up existing stuff
  - documentation
  - JDBCRC change
  - documentation of FAQ's
- 4.5
  - pegasus-service
    - some form of multi tenancy
    - python dependencies especially for external stuff is tricky
    - rename of dashboard database tables
  - pegasus-dashboard enhancements
  - separate the planning job from the prescript
  - checkpointing
  - software cleanup
  - transfers with hierarchies
  - leverage condor asynch transfers in pegasus lite
  - try for before christmas
  - 5 minute youtube video
- 4.6
  - metadata
  - dax annotation
  - enhanced notifications
    - monitord
  - PMC data locality
  - globus online support ??
    - get credentials . at least do more research.
  - skipping symbolic links

May 5th, 2014

Condor week

Lauren
- Karan needs to provide more documentation for her
Kent Wenger
- dagman reporting
  - dagman metrics files is created by newer versions of DAGMan in the submit directory.
- retry immediate parent
  - CMS has a requirement for this also. The most important thing on Kent's plate

dynamic workflows
- node expansion . may not be that worthwhile

pegasus lite asynch transfers
- using condor chirp in the pegasus lite shell script once the main computations are done. that way we can pipeline
- does not work with partitionable slots
- does not work with condor file io

Bamboo Test Cases

Job got hung for a long time??

User Survey

Developer Meeting will be moved to 1PM for

April 2014

April 21st, 2014

April 14th, 2014

JIRA Policy Document or page
Pegasus Metrics
Pegasus Survey
- Develop a list of questions .
- Forward to Duncan CBC Group
New Default Transfer Refiner - BalancedCluster

March 2014

March 31st, 2014

Gideon changed the tutorial VM.
Put in backward support for old credential handling.
Mats started on an outline for the optimizations chapter.
next week's developer meeting is cancelled.
general Pegasus dependencies
- python > 2.4 and less 3.0
- in general, easier to build from source rather than from source RPMs
update Pegasus README
change the build.xml to say default build without docs. remove the dist-nodoc target. instead we will have ant dist-release as the default target
also we should start having documentation per minor release and not per major release as we do now.

March 24th, 2014

Pegasus 4.3.2 release done last week
storage constraints paper - gideon, rafael and karan worked on it.
karan worked on the hpc-pegasus setup.. has workflows running through PMC
karan and mats have a XSEDE tutorial proposal that will be submitted today
dv/dt paper rejected for HPDC. Will try for a middleware conference due mid may
4.4 release
- checkpointing solution
- leaf cleanup for hierarchal workflows
- md5checksum option for guc transfers
  - we won't follow up on kickstart generating the checksums, but tracking checksums in replica catalog.

March 17th, 2014

Agenda

XSEDE poster and tutorial proposal
- will get it done this week. mats and karan will work on it.
idafen will work on a workshop paper for xsede on reproducibility
- 4 page limit
- deadline is april 5th.
energy simulation for SC 2014
- measure energy when running workflows
- try to check if energy usage changes whether data is transferred to a site, or everything is executed at one site.
sane defaults for 4.4 for transfer jobs, pre scripts etc
- transfer jobs
  - how many stage in jobs - 2 jobs and each job with 2 threads.
  - how many threads each transfer jobs - pegasus-transfer has a default to 2
  - pegasuslite job
    - change sls name ? property name change
    - control the number of threads
  - add a chapter called tuning workflows
    - mats will add about a section on tuning transfers.
    - setting clustering parameters.
  - changing back the default refiner to bundle???
- cleanup job
- change hold release time to one hour.
new transfer refiner
- maybe can use k means clustering ?
leaf cleanup for hierarchal workflows
- --cleanup leaf,inplace,none
- tell the planner to throw a warning when
sudharshan's paper
- emphasize that the goal is not improving the makespan.
4.3.2 release
- release notes checked in on friday
- mats will tag after the release.
- the service should be installed in the tutorial VM image.
Condor Categories
- similar to dagman categories.
- will condor accounting groups work??

March 10th, 2014

Agenda

Should we stage sub-workflow output files to parent workflow scratch? (related to leaf cleanup)
Should we enable DAX jobs to have input and output uses, and distinguish between planner inputs and sub-workflow inputs?
SUB DAG keyword to make pegasus generated subdag submit files match with dagman version alway
- From Kent, Wenger
  Hey, I just wanted to touch base and find out whether you guys have made any progress towards making Pegasus-generated sub-DAG submit files match
  the "normal" DAGMan format.
  (See https://htcondor-wiki.cs.wisc.edu/index.cgi/tktview?tn=3891,4.)
data reuse edge case
- have fix for it and have added unit test cases
altassian licenses expiring?
plan for a pegasus workshop / meeting for 2nd week of January 2015

March 3rd, 2014

monitord fix for LIGO
- pegasus plan prescripts were not logged in the database.
checkpointing files
- karan will create a JIRA item and send it to ligo folks for comment.
transfer fix
held jobs ?
separate pegasus plan planning jobs
- throttle jobs via category.
real full ahead planning
- plan full ahead -
- will help in debugging workflows
hierarchal workflows planner arguments in the prescript wrapper shell scripts.
final cleanup job for the workflow
fix for iplant workflows cleanup. previously generated files whose locations are determined in the replica catalog should not be cleaned up

Workflow reproducability ( idafen )

here for 3 months - march/april and may
document the infrastructure that was used to generate the workflows
created ontologies to describe infrastructure.
precip API
- expressed an interest in it .
- he focuses not on how to deploy, but instead to describe the infrastructure
- then do experiments that take in his description and deploy it using precept
target two conferences
- one systems
- other semantic

Pegasus Submit Node on HPCC

waiting on glite recommendations from condor-admin

Feb 2014

February 24th, 2014

SCEC Transfer Issues

hpc login crashed for scec workflows because of too many stageout jobs
there were too many connections open at xinetd level
also the stageout jobs were starving all the other local universe jobs in the workflows
so the workflows were getting bunched at the stageout level
- we solved it by moving only the transfers to the vanilla universe on shock
- ran into credential handling backward compatibility we put in 4.4 after new credential handling.

Transfer Configuration for 4.4

by default the number of threads will be 2
we will expose a way via properties to increase the number if users want to have better bandwidth
in case of any failures, pegasus-transfer will revert back on a single thread

February 10th, 2014

Postscript handling

————————————————————————————————

- We have implemented a solution in PM-737 to get around condor quoting rules.

- MPI code are not kickstart wrapped

- Pegasus should indicate whether a clustered job or a kickstart job.

- DAGMan exitcode

checkpoint jobs

- 10% of runtimes

- pegasus-transfer will have to be changed

- link is set to type checkpoint

- transaction support for checkpoint

- timeout is job runtime - process

- pegasus-kickstart timeout method

- also has dv/dt implications for monitoring.

pegasus-exitcode assumes success and checks for failure

- refactored the script for unit tests as a library

- pegasus-statistics

- pegasus-analyzer ( maybe some commonality)

- pegasus python library has to be included in worker package

pegasus-transfer

- threads are handled similar to pegasus-s3

- default threading

-

- expose options end to end

- initial threads to irods

- what options to set

pegasus-config will now work with a source checkout

December 2013

December 16th, 2013

TODO: Talk about ADAMANT design

December 3rd, 2013

4.3.1 release
- just need to send the announcement.
- gideon has updated the build infrastructure in bamboo to build the release
- to do
  - do a drupal snippet, to update the downloads page automatically.
    - dynamically render the page using the shared directory in drupal.
- pegasus-analyzer will have a recurse option.
identity management for pegasus service
- portal use case
- user authentications
- website
  - put a token in a cookie.
- draw bigger pictures on the identity stuff.
Unicore Testing

November 2013

November 11th, 2013

4.4 Planning
- according to proposal, we need pegasus as a service, metadata registration, enhanced notifications on long runtimes etc.
- ligo realtime analysis?
  - scott and kent mentioned that real time analysis is a priority.
  - gstreamer interface.
  - investigate streaming workflows
- unicore testing support
Pegasus Tutorial on (Mats VM on oregon region)
Pegasus as a service
Ensemble Manager
- an ensemble has no end state currently.
- update documentation on the website
- gideon plans to remove the upload catalog options. instead the clients will read in the properties and automatically upload.
NSF Cloud Proposal
- Experiment management.... maybe does not align itself with NSF Cloud.
Adamant Demo
- workflows are setup and done.

November 4th, 2013

Tutorial format finalized for November 14th meeting. similar to software carpentry layout
4.4 release things
- pegasus metadata support
  - dax schema changes
  - irods - support for metadata attributes
  - s3 objects - they can have tags associated with it.
- transient replica catalog.
- unicore support
- for JIRA items move to the next one.
- moteur support.
- dv/dt wrapper support ( probably in a separate dv/dt branch)
move to VMWare for hosting websites
- pegasus.isi.edu will be as a VM in a VMWARE ESX pool.
  - initially 4 VM's for Bamboo BNT
  - retire the machine for PAGE QC
- long term we are moving to ESX

October 2013

October 1st, 2013

Pegasus 4.3 release

dashboard is separate
prepare rpm for ligo
ssh submission for 4.3
tutorial vm almost done
- the clock issue remains. probably an issue with how virtualbox does the time.
need to hear back from scott
sepiddeh working on make flow compatible code generator.

September 2013

September 23rd, 2013

Software Carpentry followup

Create a pegasus youtube channel.
See if that can be linked from the ISI webcast page.

ISI Pegasus Workshop

Submit host setup at HPCC
specs are similar to workflow.isi.edu
gideon will mail to HPCC admins today about this

Tutorial VM

networking issue
- persistent rules file /etc/udev/rules/70-persistent-networking.rules
- instead of deleting it lets just disable it in our VM's
X with virtual box guest additions for enabling copy paste
turn on ntp
larger virtual disk - will increase the size to 8GB
X should just add couple of hundred MB's

Pegasus Release

JDBC RC
Tutorial VM
pegasus-statistics
pick up a release date
tentatively next friday i.e the 4th.

September 9th, 2013

Software Carpentry

Karan will prepare introductory slides for Pegasus.
Talk to John about providing a Pegasus submit node.
Rajiv will be working on the Pegasus RNASeq VM.
John Mehringer will go first in the second day.
Parking is in Levy structure in southwest corner.
Inquire about shuttle from Health Science Campus.
Still do - RNASeq module.
Put Information about parking and HSC Shuttle.
- Parking Center.

Pegasus Release

waiting for Scott to do release testing.

Pegasus Lite Paper

Karan will send the camera ready version today.

Precip

using netlogger for logging.
replace python logging framework
incorporating events from the remote site
AMQP ?
- Getting events into a common file.
Run montage using precip

Condo of Condos Workshop

Laurent and Gideon have 10 minutes each.
Bosco new name is MyHTC.

August 26th, 2013

Pegasus 4.3 release

dagman metrics not implemented yet by kent. still in design phase.
testing stuff
- unit tests running in bamboo.
add missing data dependencies
- still checks and produces errors

Precip Logging

getting the metrics back

Pegasus Hold

how to get dagman stop submitting jobs
idle jobs need to go on hold.
we can send sigusr1 to dagman.
need to handle hierarchal workflows.
JDBC RC stuff

JDBC RC

we will just update the existing version one.
have a python based RC for Replica Catalog.

Ensemble Manager Paper

Gideon will be working on it.

DAGMan replacement??

Software engg stuff.

August 19th, 2013

Pegasus 4.3 release
- output mapper stuff implemented.
- pegasus-statistics changes checked in by Rajiv
- app metrics associated with the metrics report
  - pegasus.metrics.app
  - can be used for RNASeq tracking and other applications
  - the metrics UI will be able to filter on the name.
Globus Online Support - move to 4.4 release
- can only do certain parts of transfers.
- for transfers from local submit host , we need to use globus connect
  - credentials issue
  - for submit host, there needs a local endpoint.
LIGO testing ?
- prepare a pre release RPM for LIGO

August 12th, 2013

Pegasus Lite Paper
- Wait for the Big Data and Science Workshop
4.3 Release
- - Output Mapper Submission
    - error if output site and a output mapper replica catalog specified
  - Globus Online Support in pegasus-transfer
    - OAuth tokens issue.. when to get the token
    - support for multi end point with different credentials
    - probably need to do a pegasus-globus-online
      - the client needs to be blocking .
  - SSH Submission
    - Will use RNASeq for that.
  - Boto downgrade worked.
    - did not build on RHEL 5
  - Test Suite
    - Suite of integration tests
      - checksum the files
Ensemble Manager
- Almost done with the first version
- Will work on the Galactic Plane version
General JUnit Tests for Pegasus
Galactic Plane Paper

July 2013

July 29th, 2013

Software Carpentry

Workflows Tutorial
- 1 hours overview of HPCC if HPCC folks are interested.
- Pegasus Tutorial ( 2 hours )
- An info part on where to run jobs
  - OSG
  - HPCC
  - XSEDE
Pegasus Development
- Rajiv will complete the pegasus-statistics part
- error messages ( give more hints on what went wrong on site selection )
Monitoring API
- wants a jar with a simple API to monitor workflows
- wrap it up in a jar
- provide interface
- portal integration
  - rest interface for the pegasus service

July 8th, 2013

gideon has changes checked in dax2dot based on the closures and reductions
karan has checked in the LCA approach. But does not scale for our performance test case.
Also changed the way edges added for the create dir nodes. that will go in for 4.3.
Precip Paper
- deadline extended to the 19th of July.
Posters to be made for XSEDE
Sudharshan will make a poster on his cleanup work on Monday.
- Sudharshan will be going on Monday to campus to present the poster around 1-3PM
- Will give a talk to CCG group Tuesday July 16th at 11:00AM
Currently, sudharshan's algo takes 15 seconds on a 1000 node montage workflow.

July 1st, 2013

monitord bug fix checked in
algorithm to remove extra graph dependencies
backups
- we need to update the pegasus machine
  - jira, svn , website ( website and svn need to move at the same time ) , crowd updates
  - confluence was moved to another . also coordinate with action to do the move.
  - mats already updated crowd today
    - there is secret number of conf files... apache on top of tomcat
  - update to debian machines
    - obelix, cartman and stewie, and the ccg worker nodes.
mats has updated the bamboo tests to use new filesystem paths
ADAS abstract
- for galactic plane on Amazon. if accepted due in september.
4.3 release
- fix error messages. see what can be done to improve them .
- output replica catalog
- pegasus-transfer tests.
- updates to cleanup algorithm based on sudharshan's work ??
- release notes will be updated to indicate the dashboards move to pegasus-services thing.
Precip Paper
- mats will do the zotero work.
- submitting to cloud com in bristol uk.
- seppideh has some data on openstack. could not get all instances started up.
- seppideh will release the token to gideon to do an edit pass
Cleanup Algorithm

June 2013

June 24th, 2013

Pegasus Development
- Monitord issue https://jira.isi.edu/browse/PM-712
- karan has a fix that works for him.
- needs to test the replay mode.
Update on SCEC visit
- pegasus-archive tool
  - archive everything other than the stampede db and braindump file
- scott will try to cluster rupture variations for the same rupture in one task based on runtime estimates
- the SGT will become 16 times bigger and post processing 8 times bigger on move to 1HZ. clustering rupture variations in scec code will help in reducing the number of jobs in the DAX
- Scott tried to generate a single DAX for the post processing worklfow. Was unable to do so. Has generated two dax'es
Galactic Plane
- Cut out service. Slow times on retrieving the image from S3. Small bandwith between S3 and EC2
- Will need to have monitoring etc... Not fast enough for a webpage to be responsive.. will need some queuing up
- Backups
  - Mats working on Kepler data.
  - mats tried backup with S3. does not like symlinks. will change the way backups are managed. the transfer times can be long.
Update from Sudharshan
- Good progress. showed some simulations
Adamant Update
- we are on hook for providing the interfaces in pegasus-transfer that will talk to the exo planner service
- also provide shadow queue service, that gives estimates on jobs that will be in the queue.
- supercomputing demo?
Precip Paper
- majeick si doing some experiments

June 17th, 2013

Pegasus Development
- the dax job handling is completed.
- update on ligo front.
- condor priorities for local universe jobs
  - not handled right now.
  - gideon has a ticket open for them.
- gideon observation of s3
  - scalable but not good latency or
Pegasus Lite Paper
- mats is almost done with the runs. to grep through the runs to get the intermediate files in and out of S3
- not done the S3 caching for rosetta as yet. still not sure. too much work for the time remaining.
- mats did do the runs with task clustering. he got better numbers and saw a difference in case of rosetta.
- interleaving of compute jobs and transfers. may help montage.. but won't help rosetta
- whether we should include the new pegasus 4.2 features.
Cleanup Algorithm
Glacier Backups for NFS?
- instead of using two qnaps, just have one and use other for duplicates
- we need a place for backups
- currently the QNAPS are 18TB each with raid 6. Raid 10 is a better configuration on the QNAP according to the forums. This means though we will have half the space.
  - have one qnap for scratch
  - have other qnap for storage - the storage will be backed upto glacier. right now QNAP only support S3. Support for glacier is coming.
- ewa and richard think glacier backups are a good option.
  - there might be a purge policy required on glacier.
Precip Paper
- change tracking on
- use dropbox
- broadcast when you making a new version.

June 10th, 2013

- Pegasus Development

- change to dax handling

- fix of stdout

- regex based replica catalog.

- changes to pegasus-statistics for aggregate statistics

Pegasus Lite Paper

- compute data between s3 and local disk.

- compute costs for the runs ?

- have data outside

- local cache for the S3 client ?? could affect the rosette cache.

- change the rosetta workflow.

- if there are a lot of small files.

- reading parts of files.

- Ewa will send her version of the changes.

Sudharshan Algorithm for Cleanup

Greedy appraoch planned
will try implementing a version and show the different executable workflows created

June 3rd, 2013

Pegasus Lite Paper

Breakdown of the runtimes , experiments
- In case of sharedfs, the kickstart runtimes in the breakdown file will be longer
- for the S3 case we can calculate the S3 transfer time by calculating the difference between the cumulative runtimes
- doing two experiments rosetta(cpu intensive) and montage( io intensive)

Pegasus Development

Java DAX API issues
- might be some bugs in there.

Precip Paper

Ewa wants a link to pegasus website in the paper.
have more logical thinking in the paper, like reliability and repeatability
Sepideh adding some new figures to the paper.
Maciek will provide an experiment use-case for the paper.

Stampede and Corral Annual Reports

Karan and Mats will be working on these

Sudarshan's Project

Going to look into providing a cleanup algorithm that meets a given storage constraint
Will look at the static problem of inserting dependencies into the workflow to achieve a solution

PMC Paper

on amazon
with clustering and pmc

Shirts

Should get the logo sample this week, once we approve then we can order shirts

dV/dT

Rafael is working on a draft of the data collection and modeling paper
We are planning on publishing data, will start drafting a format this week

May 2013

May 20th, 2013

Confluence is going slow. Mats is going to look.

Analytics are set up on Confluence now.

Pegasus Transfer

Mats committed a new version that has support for 2-stage transfers

Pegasus S3 Client

Gideon changed .s3cfg to .pegasus/s3cfg

Pegasus Lite Paper

Mats is working on the experiments
We have two weeks to the deadline

PMC Paper

Experiments on Amazon comparing Pegasus, Pegasus w/ Clustering, PMC alone

Pegasus Service

Finished setting up users and test suite
Next is a quick-and-dirty ensemble manager implementation
Gideon is going to commit a change to Pegasus that removes the dashboard components. They will live in the pegasus-service repository from now on.

Summer Student

Need to think up a project. Needs to be research-oriented and relatively small.
Cleanup? Precip?

Contacting users

Find out if they need anything.

Examples

Simple examples in Perl, Python and Java
Gideon will add them to the examples in the pegasus Git repo

April 2013

April 22nd, 2013

Pegasus 4.2.1 Release

monitord prescript handling fixed
- pegasus-analyzer should detect prescript failures, and the prescript exitstatus should be logged in the database
- pegasus-statistics was updated for the job instance report
pegasus planner
- need to confirm all checkin's are complete
do we want to get LIGO to do a test or just release?

Pegasus statistics across workflows - Rajiv

Pegasus Lite Paper

Mats will do the runs on Amazon
Karan will work on paper when he comes back

pegasus-hold and pegasus-release

any difference between doing a hold on the dagman directly or pegasus-dagman
we need to do more investigations on monitord

BOSCO

Mats is trying to run on HPCC
a single job is running fine.

April 8th, 2013

Pegasus 4.2.1 Release

Work on it towards this week
monitord prescript issue to fix

Pegasus 4.3

pegasus statistics extensions
- across root workflows
- https://jira.isi.edu/browse/PM-507
- condor temp file

Pegasus Posters

One at XSEDE
joint one with BOSCO team

Pegasus Lite Paper

Submission to IEEE Big Data

New Programmer Hire

expanded posting on confluence
New Programmer Hire
will send out to HPC Wire , RENCI and USC SC Connect

April 1st, 2013

Pegasus Lite Paper

Waiting on Ewa
Not much we can do about the IEEE conference. The page limit is 8 , the current size of the paper.

XSEDE Poster

Pegasus Poster. Karan will send update
Also a joint Pegasus BOSCO poster
Also as part of that we will get the MPI workflows up and running through Pegasus and BOSCO

Pegasus Development

Bypass of staging input files for Pegasus Lite Case
Inplace cleanup bug fixes done.
pegasus-s3
- gideon checked in changes of copy from one file to another
- mats adds a pegasus transfer
workflow cleanup nodes
- separate cleanup node in the workflow
- for hierarchal workflows we only delete the outermost workflow
- what happens if no output-site specified
  - the ligo case!
backward compatiblity for LIGO
Pegasus Dashboard
- general javascript updates
Generic Pegasus Slides
- 2-3 slides.

March 2013

March 25th, 2013

Pegasus Lite Paper Submission
- We will try for https://sites.google.com/site/sweetworkshop2013/
- Karan will move the paper to the ACM format
Pegasus-statisitcs
- Waiting on Scott to get back with the list of metrics
- Rajiv will be working on it
pegasus-s3 changes
- we want to be able to copy output files from one s3 bucket to another
- requires changes to pegasus-transfer and pegasus-s3
final node for cleaning up remote directories
- also related is getting the cleanup algorithm working when we bypass first level staging.

March 18th, 2013

Mats has an RPM almost sorted out for LIGO that does not require us to have PYTHONPATH set. Instead the libraries go into standard locations
Karan is testing this RPM at on spice-dev1 and has setup a page with instructions on how to submit a test workflow to VIRGO
- https://www.lsc-group.phys.uwm.edu/ligovirgo/cbcnote/aLIGOaVirgo/130307121559GeneralInstructions%20For%20Submitting%20Workflows%20on%20VIRGO
Statistics across root workflows
- earlier gaurang had generated statistics for scec runs by hand... executiing queries on the msql command line
- he does not have the queries documented anywhere
- this is something we have talked about in context of 4.3 with Rajiv
- will follow up with scott on wednesday's call
4.2.1 release
- backward compatibility for LIGO . still to be done
- probably next week after the pegasus annual report
- RPM to handle native python installation
Pegasus Annual Report
- Karan will work on it this week
- Try to follow the same template as earlier.

March 4th, 2013

Sent link on DAGMan metrics to DAGMan Metrics Reporting to Ewa
Metrics for Rob Quick's workflow
Gideon pushed out kickstart changes
Rajiv has pushed changes to the queries for the dashboard.
Setup meeting with Jaime and Derrick at OSG AHM to discuss
- remote_initialdir
- extra attributes for glite/bosco submissions
- mpi workflows.
OSG Poster to be made this week. And 4.2 Release slides.

February 2013

February 11th, 2013

Direct submission of workflows to PBS

Glite submission in Condor. We setup a VM that hosts a PBS scheduler and using that too test
Karan prepared an example for 4.2 that can be used to submit directly to local PBS using the glite interfaces in Condor
- the remote_initialdir / +remote_iwd does not work
  - problem for MPI codes
  - for the time being, the example prepared relies on kickstart to change the directory before launching a job
- there is also a ssh style that allows us to use BOSCO to do remote submissions using SSH to a PBS cluster
  - that one also has the issue of remote initialdir

- jobstate.log refactoring.

- data transfer ( support for globus online)

- lightweight tracing

- task stats. net link socket pegasus-kickstart . how much memory the task used and io used.

- add task stats to kickstart

- ptrace

- trace linux equivalent is system tap

- dashboard improvements

- single api for clients

- last week drop down

- performance run on large workflows.

February 4th, 2013

CCGrid / Pegasus Lite Paper
- Performance section
- remove the experiments section?
- OR
- extra experiments section
- have the squid proxy cache
- find a workshop to submit the paper

Cloud Paper
- Ewa is working on it.
Git HUB Migration
- - couple of branches like monitord , pmc and dang are branches
- - svn will be made read only .
- - update the website with all the development information
- - bamboo scripts
- - documentation ( long term )
- - nightly builds

SSH Submission
- - gsissh submission for blue waters
- - ssh to blue waters is required for OTP
- - passing of parameters to PBS
- - SSH key
- - ssh agent.
- - queue keyword
- - Batch session
- - submit jobs to HPCC
- - Gideon will do that.
monitord memory explosion
- - long term for monitord
- - pegasus-dagman replacement
minor release 4.2.1
- - potential monitord bug issue
- - long term dagman replacement
Response time for metrics page
- - occasionally it is slow

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