Data-driven Workflow Planning in Cluster management Systems

1. Data-driven Workflow Planning in Cluster management Systems Srinath Shankar David J DeWitt Department of Computer Sciences University of Wisconsin-Madison, USA

2. Data explosion in science • Scientific applications – Traditionally considered as compute-intensive • Data explosion in recent years • Astronomy – hundreds of TB • Sloan Digital Sky Survey • LIGO – Laser Interferometry Gravitational-wave observer • Bioinformatics – • BIRN – Biomedical informatics research network • SwissProt – Protein database

3. Scientific workflows and files Jobs with dependencies organized in Directed Acyclic Graphs Large number of similar DAGs make up a workflow A, B, C and D are programs File1 and File2 are pipeline (intermediate) files FileInput is a batch input file -- common to all DAGs

4. Distributed scientific computing • Scientists have exploited distributed computing to run their programs and workflows • One popular distributed computing system is Condor • Condor harvests idle CPU cycles on machines in a network • Condor has been installed on roughly 113,000 machines across 1,600 clusters around the world

5. But … • Several advances have been made since the development of Condor in the `80s • Machines are getting cheaper • Organizations no longer rely solely on idle desktop machines for computing cycles • The proportion of machines dedicated to Condor computing in a cluster is increasing • Disk capacities are increasing • A single machine may have 500 GB of disk space • Thus, desktop machines may also have a lot of free disk space • Dedicated and desktop machines have unused disk space • Half a petabyte of disk space spread over a modest cluster of 1000 machines

6. Focus • The volume of data processed by scientific applications is increasing. • How can we leverage distributed disk space to improve data management in cluster computing systems (like Condor) ? • Step 1: Store workflow data across the disks of machines in a cluster • Step 2: Schedule workflows based on data location – Exploit disk space to improve workflow execution times

7. Overview of Condor Machine info Job info Planner Job info Machine info Execute Machine Submit Machine User input data Output data User Process User Data Data flow Control flow

8. Job and workflow submission • To submit a job, the user provides a “submit” file containing • Complete job description – The input, output and error files, when to transfer these files etc. • Machine preferences like OS, CPU speed and memory • Workflows are managed in a separate layer • The user specifies dependencies between jobs in a separate “DAG description” file • A DAG manager process (DAGMan) on the submit machine continuously monitors job completion events • This process submits a job only when all its parents have completed

9. Limitations of Condor • The “source” of files in Condor is the submit machine, or perhaps a shared or third-party file system • Inefficient handling of files during workflow execution • Files always transferred to and from the submit machine • The planner only handles single jobs • It has no direct knowledge of job dependencies. • It only sees a job after DAGMan submits it.

10. Distributed file caching • Keep the files of a job on the disk of machines after execution • Utilize local disks on execute machines as sources of files • Schedule dependent jobs on same machine whenever feasible • Avoid network file transfer • Reduce overall workflow execution time

11. Disk aware planning • Goal – reduce workflow execution time by minimizing file transfers • Planner must be aware of the locations of cached files • Requires a planner that is also aware of workflow structure

12. Two phase planning algorithm • AssignDAGs : Each DAG in a workflow tentatively assigned to the best machine based on disk cache contents • But, assigning whole DAGs ignores inter-job parallelism • Parallelize : Exploit parallelism in DAG to distribute load • Cost-benefit analysis used when scheduling dependent jobs on different machines

13. Planning example B A F2 F1 C Suppose we have 4 machines available to run the workflow shown below Sample DAG B A A A A A A C C C C C C Sample Workflow (6 DAGs)

14. Assignment of DAGs • For each DAG in the workflow, we determine the machine that will result in earliest completion time for that DAG, and assign it to that machine. • DAG runtime = Sum of job runtimes and file transfer times • File transfer times depends on cache contents of the machine • Effectively, each DAG is treated like a single job in this phase.

15. Schedule after AssignDAGs Jobs in the same DAG are of the same color M1 M2 M3 M4 A A A A B B B B Time The schedule produced after AssignDAGs entails no transfer of intermediate files C C C C A A B B C C

16. Assignment phase (contd.) • While DAGs are being assigned, a cumulative runtime is maintained for each machine • Once a DAG has been scheduled on a machine, we assume that machine caches the workflow batch input (common to all DAGs) • Thus, batch input transfer times are not included in calculations of the runtime of other DAGs on that machine

17. Parallelization of DAGs • After assignment phase, uneven load on machines • There are “extra” DAGs on a few heavily loaded machines • There are some machines with a much lighter load • Exploit inter-job parallelism to distribute load • The “extra” DAGs are examined in turn. • If two jobs in a DAG can be run in parallel, we try to move one of them to a lightly loaded machine.

18. Parallelization – Costs and benefits • Cost of parallelization – When you move a job to a different machine than its parents and children, its input and output files have to be transferred to and from that machine. • Cost = (input_size +output_size)/net_BW. • Input_size and output_size are the sizes of the input files and output files for the job • Net_BW is the network bandwidth • Cost is the time taken to perform data transfers to and from the different machines • Benefit = Time saved due to parallel execution of jobs

19. Final Schedule B B B B F2 F2 C C C C M1 M2 M3 M4 A A A A B B B B In the final schedule, files are transferred from M2 to M1 and from M4 to M3 Time C C C C A A Network file transfer

20. Parallelization (contd.) • In the formula for the cost of parallelization, input_size and output_size are adjusted for files already cached on either machine • If a job being considered for parallelization has no children, output_size is taken as 0 since its output files do not need to be transferred back

21. Implementation • Main feature is a database used to store • File information – checksums, sizes, file type, file locations • Job information – Files used by jobs, job dependencies • Workflow schedules – Produced by the planner • The Condor daemons were modified to directly connect to the database and perform insert/updates/queries

22. Role of database Planner Workflow, file info Schedule Execute Machine Submit Machine Data- base Cache info Workflow and file info File Cache User Data

23. Implementation – versioning • Versions of input and executables are determined by checksums computed at submission time • The versions of intermediate and output files are “derived” from the versions of the inputs and executables that produce them

24. Implementation – Distributed Storage • Before a job executes on a machine, its input files are retrieved • Files available in the machine’s local cache are used directly • Unavailable files are retrieved from other machines in the cluster. Any machine can serve as a file server • After a job completes, its executable, input and output files are saved in the execute machine’s disk cache. • Once a job has completed, the database is updated with the new status and cache information.

25. Implementation – Workflow submission • An entire workflow is submitted at one time • The workflow submission tools directly update the database with job and workflow information • This information includes files used by the workflow as well as job dependencies in the workflow • The planner directly uses the information in the database. Thus • It has knowledge of job dependencies during planning • It has knowledge of the locations of the relevant files during planning

26. Performance testing • Comparison of three systems • ORIG – The original Condor system • DAG-C – Our caching and DAG-oriented planning framework • Job-C • Same caching mechanism as DAG-C • No DAG-based planning. When a job is ready, it is matched to the machine that caches most input

27. Description of setup • Tested on BLAST and synthetic workflows with varying branch-in factor and pipeline volume • Cluster of 25 execute machines – all files were in the same network • Two submit machines • Network bandwidth was 100 Mbps • No shared file system was used • All experiments run with initially clean disk caches

28. The BLAST workflow Batch input :(~4GB) nr_db.psq nr_db.pin nr_db nr_db.phr nr.gz nr_db.psq (986 MB) nr_db.pin (23 MB) seq seq.csv seq.blast blastall (3.1 MB) java- wrap (1KB) seq.bin nr_db.psq (986 MB) nr_db.pin (23 MB) Pipeline volume: seq.blast (~2MB) BLAST is a sequence alignment workflow. Given a protein sequence “seq”, blastall checks a database of known proteins for any similarities. Proteins with similar sequences are expected to have similar properties. Javawrap converts the results into CSV and binary format for later use.

29. BLAST results

30. Sensitivity to pipeline volume • F1, F2, G1 and G2 are distinct files • 10 minutes per job • Varying size per file – 100MB, 1GB, 1.5 GB, 2GB • 50 DAGs per workflow

31. Pipeline I/O results

32. DAG breadth • File Fi, Gi are distinct • Varied branching factor (n) from 3 to 6 • 10 min per job • Tested a 50 DAG workflow with 1GB per file

33. DAG breadth results (1GB)

34. Varying computation time • Size of each file set to 1GB • Varied the time per job from 10 to 30 minutes. (i.e. time per DAG from 80 to 240 min) • Tested a 50 DAG workflow

35. Increasing computation

36. Results – Summary • Job-C and DAG-C are better than ORIG • In ORIG, all file traffic through submit machine • In Job-C and DAG-C, files can be retrieved from multiple locations • Thus, caching helps • DAG-C is significantly better than Job-C when pipeline volume, branching factor are high • In Job-C parent jobs often run on different machines • Output files have to be transferred to the machine where their child executes • Thus, DAG-oriented planning helps

37. Distributed file caching – other benefits • Scientists frequently reuse files (such as executables) – These can be used directly at their stored locations. • Maintaining user data • ‘What were the programs run to obtain this output ?’ • ‘When did I last use a particular version of a file?’

38. Ongoing work • Planning • Evaluating planning overhead, dependence on DB size • Make planning scheme more responsive to job failure, machine failure • A cache replacement policy based on an LRFU scheme has been implemented, but not validated (See paper for details). Ongoing work includes • Validating the cache replacement policy and determining the best policy for a workflow depending on user’s submission pattern • Including the time needed for generating a file in estimates of its “cache-worthiness”

39. Related work • ZOO, GridDB – data centric workflow management systems • Thain et al. – Pipeline and batch sharing in Grid workloads – HPDC 2003 • Romosan et al. – Coscheduling of computation and data on computer clusters – SSDBM 2005 • Bright et al. – Efficient scheduling and execution of scientific workflow tasks – SSDBM 2005

40. Questions ?