Introduction to Makeflow and Work Queue Prof. Douglas Thain, University of Notre Dame

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The Cooperative Computing Lab We collaborate with people who have large scale computing problems in science, engineering, and other fields. We operate computer systems on the O(10,000) cores: clusters, clouds, grids. We conduct computer science research in the context of real people and problems. We develop open source software for large scale distributed computing. 3

Outline Thinking Opportunistically Overview of the Cooperative Computing Tools Makeflow Makeflow + Work Queue Work Queue Native Code Hands-On Tutorial

Thinking Opportunistically

Science Depends on Computing! AGTCCGTACGATGCTATTAGCGAGCGTGA…

Opportunistic Computing Much of scientific computing is done in conventional computing centers with a fixed operating environment with professional sysadmins. But, there exists a large amount of computing power available to end users that is not prepared or tailored to your specific application: – National HPC facility – Campus-level cluster and batch system. – Volunteer computing systems: Condor, BOINC, etc. – Cloud services. Can we effectively use these systems for “long tail” scientific computing?

Opportunistic Challenges When borrowing someone else’s machines, you cannot change the OS distribution, update RPMs, patch kernels, run as root… This can often put important technology just barely out of reach of the end user, e.g.: – FUSE might be installed, but without setuid binary. – Docker might be available, but you aren’t a member of the required Unix group. The resource management policies of the hosting system may work against you: – Preemption due to submission by higher priority users. – Limitations on execution time and disk space. – Firewalls only allow certain kinds of network connections.

Backfilling HPC with Condor at Notre Dame

Users of Opportunistic Cycles

Superclusters by the Hour 11

I can get as many machines on the cloud/grid as I want! How do I organize my application to run on those machines?

The Cooperative Computing Tools

Our Philosophy: Harness all the resources that are available: desktops, clusters, clouds, and grids. Make it easy to scale up from one desktop to national scale infrastructure. Provide familiar interfaces that make it easy to connect existing apps together. Allow portability across operating systems, storage systems, middleware… Make simple things easy, and complex things possible. No special privileges required.

A Quick Tour of the CCTools Open source, GNU General Public License. Compiles in 1-2 minutes, installs in $HOME. Runs on Linux, Solaris, MacOS, Cygwin, FreeBSD, … Interoperates with many distributed computing systems. – Condor, SGE, Torque, Globus, iRODS, Hadoop… Components: – Makeflow – A portable workflow manager. – Work Queue – A lightweight distributed execution system. – All-Pairs / Wavefront / SAND – Specialized execution engines. – Parrot – A personal user-level virtual file system. – Chirp – A user-level distributed filesystem.

16 Makeflow = Make + Workflow Makeflow LocalCondorSGE Work Queue Provides portability across batch systems. Enable parallelism (but not too much!) Fault tolerance at multiple scales. Data and resource management.

17 Work Queue Library #include “work_queue.h” while( not done ) { while (more work ready) { task = work_queue_task_create(); // add some details to the task work_queue_submit(queue, task); } task = work_queue_wait(queue); // process the completed task }

Parrot Virtual File System Unix Appl Parrot Virtual File System Local iRODS Chirp HTTP CVMFS Capture System Calls via ptrace /home = /chirp/server/myhome /software = /cvmfs/cms.cern.ch/cmssoft Custom Namespace File Access Tracing Sandboxing User ID Mapping...

Lots of Documentation

Makeflow: A Portable Workflow System

21 An Old Idea: Makefiles part1 part2 part3: input.data split.py./split.py input.data out1: part1 mysim.exe./mysim.exe part1 >out1 out2: part2 mysim.exe./mysim.exe part2 >out2 out3: part3 mysim.exe./mysim.exe part3 >out3 result: out1 out2 out3 join.py./join.py out1 out2 out3 > result

22 Makeflow = Make + Workflow Makeflow LocalCondorTorque Work Queue Provides portability across batch systems. Enable parallelism (but not too much!) Trickle out work to batch system. Fault tolerance at multiple scales. Data and resource management.

Makeflow Syntax [output files] : [input files] [command to run] sim.exe in.dat calib.dat out.txt sim.exe in.dat –p 50 > out.txt out.txt : in.dat sim.exe –p 50 in.data > out.txt One Rule Not Quite Right! out.txt : in.dat calib.dat sim.exe sim.exe –p 50 in.data > out.txt

You must state all the files needed by the command.

sims.mf out.10 : in.dat calib.dat sim.exe sim.exe –p 10 in.data > out.10 out.20 : in.dat calib.dat sim.exe sim.exe –p 20 in.data > out.20 out.30 : in.dat calib.dat sim.exe sim.exe –p 30 in.data > out.30

How to run a Makeflow Run a workflow locally (multicore?) – makeflow -T local sims.mf Clean up the workflow outputs: – makeflow –c sims.mf Run the workflow on Torque: – makeflow –T torque sims.mf Run the workflow on Condor: – makeflow –T condor sims.mf

Visualization with DOT makeflow_viz –D example.mf > example.dot dot –T gif example.gif DOT and related tools:

Makeflow Shapes a Workflow Make Flow Transaction Log Batch System Concurrency Control Millions of Tasks Thousands of Nodes T T T T Precise Cleanup Performance Monitoring

Makeflow Shapes a Workflow Make Flow Batch System Millions of Tasks Thousands of Nodes T T T T --wrapper-input mycode.jar JAR

Batch System Makeflow Shapes a Workflow Make Flow Millions of Tasks Thousands of Nodes --docker ubuntu T T T T

Example: Biocompute Portal Generate Makefile Make flow Run Workflow Progress Bar Transaction Log Update Status Condor Pool Submit Tasks BLAST SSAHA SHRIMP EST MAKER …

Makeflow Applications

Makeflow + Work Queue

Private Cluster Campus Condor Pool Public Cloud Provider FutureGrid Torque Cluster Makefile Makeflow Local Files and Programs Makeflow + Batch System makeflow –T torque makeflow –T condor ???

FutureGrid Torque Cluster Campus Condor Pool Public Cloud Provider Private Cluster Makefile Makeflow Local Files and Programs Makeflow + Work Queue W W W ssh WW W W torque_submit_workers W W W condor_submit_workers W W W Thousands of Workers in a Personal Cloud submit tasks

Advantages of Work Queue Harness multiple resources simultaneously. Hold on to cluster nodes to execute multiple tasks rapidly. (ms/task instead of min/task) Scale resources up and down as needed. Better management of data, with local caching for data intensive tasks. Matching of tasks to nodes with data.

Makeflow and Work Queue To start the Makeflow % makeflow –T wq sims.mf Could not create work queue on port % makeflow –T wq –p 0 sims.mf Listening for workers on port 8374… To start one worker: % work_queue_worker master.hostname.org 8374

Start 25 Workers in Batch System Submit workers to Condor: condor_submit_workers master.hostname.org Submit workers to SGE: sge_submit_workers master.hostname.org Submit workers to Torque: torque_submit_workers master.hostname.org

Keeping track of port numbers gets old fast…

Project Names Worker work_queue_worker –N myproject Catalog connect to india:4057 advertise “myproject” is at india:4057 query Makeflow (port 4057) makeflow … –N myproject query work_queue_status

Project Names Start Makeflow with a project name: % makeflow –T wq –N myproject sims.mf Listening for workers on port XYZ… Start one worker: % work_queue_worker -N myproject Start many workers: % torque_submit_workers –N myproject 5

work_queue_status

Resilience and Fault Tolerance MF +WQ is fault tolerant in many different ways: – If Makeflow crashes (or is killed) at any point, it will recover by reading the transaction log and continue where it left off. – Makeflow keeps statistics on both network and task performance, so that excessively bad workers are avoided. – If a worker crashes, the master will detect the failure and restart the task elsewhere. – Workers can be added and removed at any time during the execution of the workflow. – Multiple masters with the same project name can be added and removed while the workers remain. – If the worker sits idle for too long (default 15m) it will exit, so as not to hold resources idle.

Writing Work Queue Programs

Makeflow vs. Work Queue Makeflow – Directed Acyclic Graph programming model. – Static structure known in advance. – All communication through files on disk. Work Queue – Submit-Wait programming model. – Dynamic structure decided at run-time. – Communicate through buffers or files. – More detailed knowledge of how tasks ran.

46 Work Queue API #include “work_queue.h” queue = work_queue_create(); while( not done ) { while (more work ready) { task = work_queue_task_create(); // add some details to the task work_queue_submit(queue, task); } task = work_queue_wait(queue); // process the completed task }

Work Queue Applications Nanoreactor MD Simulations Adaptive Weighted Ensemble Scalable Assembler at Notre Dame ForceBalance Lobster HEP

Replica Exchange T=10KT=20K T=30KT=40K Replica Exchange Work Queue Simplified Algorithm: Submit N short simulations at different temps. Wait for all to complete. Select two simulations to swap. Continue all of the simulations. Dinesh Rajan, Anthony Canino, Jesus A Izaguirre, and Douglas Thain, Converting A High Performance Application to an Elastic Cloud Application, Cloud Com 2011.

Genome Assembly Christopher Moretti, Andrew Thrasher, Li Yu, Michael Olson, Scott Emrich, and Douglas Thain, A Framework for Scalable Genome Assembly on Clusters, Clouds, and Grids, IEEE Transactions on Parallel and Distributed Systems, 2012 Using WQ, we could assemble a human genome in 2.5 hours on a collection of clusters, clouds, and grids with a speedup of 952X. SAND filter master SAND align master Celera Consensus W W W W W W W Sequence Data Modified Celera Assembler

Adaptive Weighted Ensemble 50 Proteins fold into a number of distinctive states, each of which affects its function in the organism. How common is each state? How does the protein transition between states? How common are those transitions?

AWE on Clusters, Clouds, and Grids 51

Application Local Files and Programs Work Queue Architecture Worker Process Cache Dir A C B Work Queue Master Library 4-core machine Task.1 Sandbox A B T 2-core task Task.2 Sandbox C A T 2-core task Send files Submit Task1(A,B) Submit Task2(A,C) A B C Submit Wait Send tasks

Basic Queue Operations #include “work_queue.h” struct work_queue *queue; struct work_queue_task *task; // Creates a new queue listening on a port, use zero to pick any port. queue = work_queue_create( port ); // Submits a task into a queue. (non-blocking) work_queue_submit( queue, task ); // Waits for a task to complete, returns the complete task. task = work_queue_wait( queue, timeout ); // Returns true if there are no tasks left in the queue. work_queue_empty( queue ); // Returns true if the queue is hungry for more tasks. work_queue_hungry( queue );

Basic Task Operations #include “work_queue.h” struct work_queue_task *task; // Create a task that will run a given Unix command. task = work_queue_task_create( command ); // Indicate an input or output file needed by the task. work_queue_task_specify_file( task, name, remote_name, type, flags ); // Indicate an input buffer needed by the task. work_queue_task_specify_buffer( task, data, length, remote_name, flags); // Destroy the task object. work_queue_task_delete( task );

Run One Task in C #include “work_queue.h” struct work_queue *queue; struct work_queue_task *task; queue = work_queue_create( 0 ); work_queue_specify_name( “myproject” ); task = work_queue_task_create(“sim.exe –p 50 in.dat >out.txt”); /// Missing: Specify files needed by the task. work_queue_submit( queue, task ); while(!work_queue_empty(queue)) { task = work_queue_wait( queue, 60 ); if(task) work_queue_task_delete( task ); }

Run One Task in Perl use work_queue; $queue = work_queue_create( 0 ); work_queue_specify_name( “myproject” ); $task = work_queue_task_create(“sim.exe –p 50 in.dat >out.txt”); ### Missing: Specify files needed by the task. work_queue_submit( $queue, $task ); while(!work_queue_empty($queue)) { $task = work_queue_wait( $queue, 60 ); if($task) work_queue_task_delete( $task ); }

Run One Task in Python from work_queue import * queue = WorkQueue( port = 0 ) queue.specify_name( “myproject” ); task = Task(“sim.exe –p 50 in.dat >out.txt”) ### Missing: Specify files needed by the task. queue.submit( task ) While not queue.empty(): task = queue.wait(60)

C: Specify Files for a Task work_queue_task_specify_file( task,“in.dat”,”in.dat”, WORK_QUEUE_INPUT, WORK_QUEUE_NOCACHE ); work_queue_task_specify_file( task,“calib.dat”,”calib.dat”, WORK_QUEUE_INPUT, WORK_QUEUE_CACHE ); work_queue_task_specify_file( task,“out.txt”,”out.txt”, WORK_QUEUE_OUTPUT, WORK_QUEUE_NOCACHE ); work_queue_task_specify_file( task,“sim.exe”,”sim.exe”, WORK_QUEUE_INPUT, WORK_QUEUE_CACHE ); sim.exe in.dat calib.dat out.txt sim.exe in.dat –p 50 > out.txt

Perl: Specify Files for a Task sim.exe in.dat calib.dat out.txt sim.exe in.dat –p 50 > out.txt work_queue_task_specify_file( $task,“in.dat”,”in.dat”, $WORK_QUEUE_INPUT, $WORK_QUEUE_NOCACHE ); work_queue_task_specify_file( $task,“calib.dat”,”calib.dat”, $WORK_QUEUE_INPUT, $WORK_QUEUE_NOCACHE ); work_queue_task_specify_file( $task,“out.txt”,”out.txt”, $WORK_QUEUE_OUTPUT, $WORK_QUEUE_NOCACHE ); work_queue_task_specify_file( $task,“sim.exe”,”sim.exe”, $WORK_QUEUE_INPUT, $WORK_QUEUE_CACHE );

Python: Specify Files for a Task task.specify_file( “in.dat”, ”in.dat”, WORK_QUEUE_INPUT, cache = False ) task.specify_file( “calib.dat”, ”calib.dat”, WORK_QUEUE_INPUT, cache = False ) task.specify_file( “out.txt”, ”out.txt”, WORK_QUEUE_OUTPUT, cache = False ) task.specify_file( “sim.exe”, ”sim.exe”, WORK_QUEUE_INPUT, cache = True ) sim.exe in.dat calib.dat out.txt sim.exe in.dat –p 50 > out.txt

You must state all the files needed by the command.

Running a Work Queue Program gcc work_queue_example.c -o work_queue_example -I $HOME/cctools/include/cctools -L $HOME/cctools/lib -lwork_queue -ldttools -lm./work_queue_example Listening on port 8374 … In another window:./work_queue_worker master.host.name.org 8374

… for Python setenv PYTHONPATH ${PYTHONPATH}: (no line break) ${HOME}/cctools/lib/python2.6/site-package./work_queue_example.py Listening on port 8374 … In another window:./work_queue_worker master.host.name.org 8374

… for Perl setenv PERL5LIB ${PERL5LIB}: (no line break) ${HOME}/cctools/lib/perl5/site_perl./work_queue_example.pl Listening on port 8374 … In another window:./work_queue_worker master.host.name.org 8374

Start Workers Everywhere Submit workers to Condor: condor_submit_workers master.hostname.org Submit workers to SGE: sge_submit_workers master.hostname.org Submit workers to Torque: torque_submit_workers master.hostname.org

Use Project Names Worker work_queue_worker –N myproject Catalog connect to india:9037 advertise “myproject” is at india:9037 query Work Queue (port 9037) query work_queue_status

Specify Project Names in Work Queue Specify Project Name for Work Queue master: Python: Perl: C: q.specify_name (“myproject”) work_queue_specify_name ($q, “myproject”); work_queue_specify_name (q, “myproject”);

Start Workers with Project Names Start one worker: $ work_queue_worker -N myproject Start many workers: $ sge_submit_workers -N myproject 5 $ condor_submit_workers -N myproject 5 $ torque_submit_workers -N myproject 5

Advanced Features (in the docs) Submit / remove tasks by tag / name. Auto reschedule tasks that take too long. Send in-memory data as a file. Log and graph system performance Much more!

Managing Your Workforce SGE Cluster Master A Master B Master C Condor Pool W W W W W W Submits new workers. Restarts failed workers. Removes unneeded workers. WQ Pool 100 work_queue_pool –T sge 100 WQ Pool 200 work_queue_pool –T condor 200

Multi-Slot Workers Master Worker work_queue_worker --cores 8 --memory core task 1 core task 1 core task 1 core task 1 core task 4 cores 512 MB specify_cores(4); specify_memory(512); Worker work_queue_worker (implies 1 task, 1 core)

Using Foremen Master T TTTTT T TTTTT W W W W W W W W W Approx X1000 at each fanout. Fore man $$$ work_queue_worker --foreman $MASTER $PORT Fore man $$$ California Chicago

Makeflow vs. Work Queue Makeflow – Directed Acyclic Graph programming model. – Static structure known in advance. – All communication through files on disk. Work Queue – Submit-Wait programming model. – Dynamic structure decided at run-time. – Communicate through buffers or files. – More detailed knowledge of how tasks ran.

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Extra Slides

Containers Pro: Are making a big difference in that users now expect to be able to construct and control their own namespace. Con: Now everyone will do it, thus exponentially increasing efforts for porting and debugging. Limitation: Do not pass power down the hierarchy. E.g. Containers can’t contain containers, create sub users, mount FUSE, etc… Limitation: No agreement yet on how to integrate containers into a common execution model.

Where to Apply Containers? Worker Process Cache A C B Task.1 A B T Task.2 C A T Worker in Container Worker Process Cache A C B Task.1 A B T Task.2 C A T Worker Starts Containers Cache Task.1 A B T Task.2 Worker Process A C B C A T C A T Task Starts Container

Abstract Model of Makeflow and Work Queue data calib code output output: data calib code code –i data –p 5 > output If inputs exist, then: Make a sandbox. Connect the inputs. Run the task. Save the outputs. Destroy the sandbox. Ergo, if it’s not an input dependency, it won’t be present. data calib code output

Clearly Separate Three Things: Inputs/Outputs: The items of enduring interest to the end user. Code: The technical expression of the algorithms to be run. Environment: The furniture required to run the code.