Using Condor An Introduction Condor Week 2008 http

Using Condor An Introduction Condor Week 2008 http: //www. cs. wisc. edu/condor 1

The Condor Project (Established ‘ 85) Distributed High Throughput Computing research performed by a team of ~35 faculty, full time staff and students. http: //www. cs. wisc. edu/condor 2

The Condor Project (Established ‘ 85) Distributed High Throughput Computing research performed by a team of ~35 faculty, full time staff and students who: face software engineering challenges in a distributed UNIX/Linux/NT environment are involved in national and international grid collaborations, actively interact with academic and commercial users, maintain and support large distributed production environments, and educate and train students. http: //www. cs. wisc. edu/condor 3

Some free software produced by the Condor Project › Condor System › VDT › Metronome › › Class. Ad Library DAGMan Hawkeye GCB › › MW Ne. ST / Lot. Man Stork And others… all as open source http: //www. cs. wisc. edu/condor 4

Full featured system › Flexible scheduling policy engine via Class. Ads Preemption, suspension, requirements, preferences, groups, quotas, settable fair-share, system hold… › Facilities to manage BOTH dedicated CPUs (clusters) and non› › › › dedicated resources (desktops) Transparent Checkpoint/Migration for many types of serial jobs No shared file-system required Federate clusters w/ a wide array of Grid Middleware Workflow management (inter-dependencies) Support for many job types – serial, parallel, etc. Fault-tolerant: can survive crashes, network outages, no single point of failure. Development APIs: via SOAP / web services, DRMAA (C), Perl package, GAHP, flexible command-line tools, MW Platforms: Linux i 386/IA 64, Windows 2 k/XP, Mac. OS, Solaris, IRIX, HP-UX, Compaq Tru 64, … lots. http: //www. cs. wisc. edu/condor 5

Meet Frieda. She is a scientist with a big problem. http: //www. cs. wisc. edu/condor 6

Frieda’s Application … Run a Parameter Sweep of F(x, y, z) for 20 values of x, 10 values of y and 3 values of z 20× 10× 3 = 600 combinations F takes on the average 6 hours to compute on a “typical” workstation (total = 600 × 6 = 3600 hours) F requires a “moderate” (256 MB) amount of memory F performs “moderate” I/O - (x, y, z) is 5 MB and F(x, y, z) is 50 MB http: //www. cs. wisc. edu/condor 7

I have 600 simulations to run. Where can I get help? http: //www. cs. wisc. edu/condor 8

While sharing a beverage with some colleagues, she shares her problem. Somebody asks “Have you tried Condor? It’s free. ” http: //www. cs. wisc. edu/condor 9

Getting Condor › Available as a free download from › http: //www. cs. wisc. edu/condor Download Condor for your operating system Available for most UNIX (including Linux and Apple’s OS/X) platforms Also for Windows XP / 2003 / Vista http: //www. cs. wisc. edu/condor 10

Condor Releases › Stable / Developer Releases Version numbering scheme similar to that of the (pre 2. 6) Linux kernels … Major. minor. release • Minor is even (a. b. c): Stable – Examples: 6. 6. 3, 6. 8. 4, 6. 8. 5 – Very stable, mostly bug fixes • Minor is odd (a. b. c): Developer – New features, may have some bugs – Examples: 6. 7. 11, 6. 9. 2 http: //www. cs. wisc. edu/condor 11

Frieda Installs a “Personal Condor” on her machine… › What do we mean by a “Personal” Condor? Condor on your own workstation No root / administrator access required No system administrator intervention needed › After installation, Frieda submits her jobs to her Personal Condor… http: //www. cs. wisc. edu/condor 12

600 Condor jobs personal your workstation Condor http: //www. cs. wisc. edu/condor 13

Personal Condor? ! What’s the benefit of a Condor “Pool” with just one user and one machine? http: //www. cs. wisc. edu/condor 14

Your Personal Condor will. . . › Keep an eye on your jobs and will keep you › › posted on their progress Implement your policy on the execution order of the jobs Keep a log of your job activities Add fault tolerance to your jobs Implement your policy on when the jobs can run on your workstation http: //www. cs. wisc. edu/condor 15

Definitions › Job The Condor representation of your work › Machine The Condor representation of computers and that can perform the work › Match Making Matching a job with a machine “Resource” http: //www. cs. wisc. edu/condor 16

Job Jobs state their requirements and preferences: I need a Linux/x 86 platform I want the machine with the most memory I prefer a machine in the chemistry department http: //www. cs. wisc. edu/condor 17

Machines state their requirements and preferences: Run jobs only when there is no keyboard activity I prefer to run Frieda’s jobs I am a machine in the physics department Never run jobs belonging to Dr. Smith http: //www. cs. wisc. edu/condor 18

The Magic of Matchmaking › Jobs and machines state their requirements and preferences › Condor matches jobs with machines based on requirements and preferences http: //www. cs. wisc. edu/condor 19

Getting Started: Submitting Jobs to Condor › Overview: Choose a “Universe” for your job Make your job “batch-ready” Create a submit description file Run condor_submit to put your job in the queue http: //www. cs. wisc. edu/condor 20

1. Choose the “Universe” › Controls how Condor handles jobs › Choices include: Vanilla Standard Grid Java Parallel VM http: //www. cs. wisc. edu/condor 21

Using the Vanilla Universe • The Vanilla Universe: – Allows running almost any “serial” job – Provides automatic file transfer, etc. – Like vanilla ice cream • Can be used in just about any situation http: //www. cs. wisc. edu/condor 22

2. Make your job batchready Must be able to run in the background • No interactive input • No GUI/window clicks • No music ; ^) http: //www. cs. wisc. edu/condor 23

Make your job batch-ready (continued)… Job can still use STDIN, STDOUT, and STDERR (the keyboard and the screen), but files are used for these instead of the actual devices Similar to UNIX shell: • $. /myprogram <input. txt >output. txt http: //www. cs. wisc. edu/condor 24

3. Create a Submit Description File › A plain ASCII text file › Condor does not care about file extensions › Tells Condor about your job: Which executable, universe, input, output and error files to use, command-line arguments, environment variables, any special requirements or preferences (more on this later) › Can describe many jobs at once (a “cluster”), each with different input, arguments, output, etc. http: //www. cs. wisc. edu/condor 25

Simple Submit Description File # Simple condor_submit input file # (Lines beginning with # are comments) # NOTE: the words on the left side are not # case sensitive, but filenames are! Universe = vanilla Executable = my_job Output = output. txt Queue http: //www. cs. wisc. edu/condor 26

4. Run condor_submit › You give condor_submit the name of the submit file you have created: condor_submit my_job. submit › condor_submit: Parses the submit file, checks for errors Creates a “Class. Ad” that describes your job(s) Puts job(s) in the Job Queue http: //www. cs. wisc. edu/condor 27

Class. Ad ? › Condor’s internal data representation Similar to classified ads (as the name implies) Represent an object & its attributes • Usually many attributes Can also describe what an object matches with http: //www. cs. wisc. edu/condor 28

Class. Ad Details › Class. Ads can contain a lot of details The job’s executable is analysis. exe The machine’s load average is 5. 6 › Class. Ads can specify requirements I require a machine with Linux › Class. Ads can specify preferences This machine prefers to run jobs from the physics group http: //www. cs. wisc. edu/condor 29

Class. Ad Details (continued) › Class. Ads are: semi-structured user-extensible schema-free Attribute = Expression http: //www. cs. wisc. edu/condor 30

Class. Ad Example: String My. Type = "Job" Target. Type = "Machine" Number Cluster. Id = 1377 Owner = "roy" Cmd = "sim. exe" Requirements = Boolean (Arch == "INTEL") && (Op. Sys == "LINUX") && (Disk >= Disk. Usage) && ((Memory * 1024)>=Image. Size) … http: //www. cs. wisc. edu/condor 31

The Dog Class. Ad for the “Job” Type = “Dog”. . . Color = “Brown” Requirements = (type == “Dog”) && Price = 12 (color == “Brown”) && (price <= 15). . . http: //www. cs. wisc. edu/condor 32

The Job Queue › condor_submit sends your job’s › Class. Ad(s) to the schedd The schedd (more details later): Manages the local job queue Stores the job in the job queue • Atomic operation, two-phase commit • “Like money in the bank” › View the queue with condor_q http: //www. cs. wisc. edu/condor 33

Example condor_submit and condor_q % condor_submit my_job. submit Submitting job(s). 1 job(s) submitted to cluster 1. % condor_q -- Submitter: perdita. cs. wisc. edu : <128. 105. 165. 34: 1027> : ID OWNER SUBMITTED RUN_TIME ST PRI SIZE CMD 1. 0 frieda 6/16 06: 52 0+00: 00 I 0 0. 0 my_job 1 jobs; 1 idle, 0 running, 0 held % http: //www. cs. wisc. edu/condor 34

Input, output & error files › Controlled by submit file settings › You can define the job’s standard input, standard output and standard error: Read job’s standard input from “input_file”: • Input = input_file • Shell equivalent: program <input_file Write job’s standard ouput to “output_file”: • Output = output_file • Shell equivalent: program >output_file Write job’s standard error to “error_file”: • Error = error_file • Shell equivalent: program 2>error_file http: //www. cs. wisc. edu/condor 35

Email about your job • Condor sends email about job events to the submitting user • Specify “notification” in your submit file to control which events: Notification = complete never error always Default http: //www. cs. wisc. edu/condor 36

Feedback on your job › Create a log of job events › Add to submit description file: log = sim. log › Becomes the Life Story of a Job Shows all events in the life of a job Always have a log file http: //www. cs. wisc. edu/condor 37

Sample Condor User Log 000 (0001. 000) 05/25 19: 10: 03 Job submitted from host: <128. 105. 146. 14: 1816>. . . 001 (0001. 000) 05/25 19: 12: 17 Job executing on host: <128. 105. 146. 14: 1026>. . . 005 (0001. 000) 05/25 19: 13: 06 Job terminated. (1) Normal termination (return value 0). . . http: //www. cs. wisc. edu/condor 38

Example Submit Description File With Logging # Example condor_submit input file # (Lines beginning with # are comments) # NOTE: the words on the left side are not # case sensitive, but filenames are! Universe = vanilla Executable = /home/frieda/condor/my_job. condor Log = my_job. log ·Job log (from Condor) Input = my_job. in ·Program’s standard input Output = my_job. out ·Program’s standard output Error = my_job. err ·Program’s standard error Arguments = -a 1 -a 2 ·Command line arguments Initial. Dir = /home/frieda/condor/run Queue http: //www. cs. wisc. edu/condor 39

“Clusters” and “Processes” › If your submit file describes multiple jobs, we call › › › this a “cluster” Each cluster has a unique “cluster number” Each job in a cluster is called a “process” Process numbers always start at zero A Condor “Job ID” is the cluster number, a period, and the process number (i. e. 2. 1) A cluster can have a single process • Job ID = 20. 0 ·Cluster 20, process 0 Or, a cluster can have more than one process • Job ID: 21. 0, 21. 1, 21. 2 ·Cluster 21, process 0, 1, 2 http: //www. cs. wisc. edu/condor 40

Submit File for a Cluster # Example submit file for a cluster of 2 jobs # with separate input, output, error and log files Universe = vanilla Executable = my_job Arguments = -x 0 log = my_job_0. log Input = my_job_0. in Output = my_job_0. out Error = my_job_0. err Queue ·Job 2. 0 (cluster 2, process 0) Arguments = -x 1 log Input Output Error Queue = = my_job_1. log my_job_1. in my_job_1. out my_job_1. err ·Job 2. 1 (cluster 2, process 1) http: //www. cs. wisc. edu/condor 41

Submitting The Job % condor_submit my_job. submit-file Submitting job(s). 2 job(s) submitted to cluster 2. % condor_q -- Submitter: perdita. cs. wisc. edu : <128. 105. 165. 34: 1027> : ID OWNER SUBMITTED RUN_TIME ST PRI SIZE CMD 1. 0 frieda 4/15 06: 52 0+00: 02: 11 R 0 0. 0 my_job –a 1 –a 2 2. 0 frieda 4/15 06: 56 0+00: 00 I 0 0. 0 my_job –x 0 2. 1 frieda 4/15 06: 56 0+00: 00 I 0 0. 0 my_job –x 1 3 jobs; 2 idle, 1 running, 0 held % http: //www. cs. wisc. edu/condor 42

Back to our 600 jobs… › We could put all input, output, error & log files in the one directory One of each type for each job That’d be 2400 files (4 files × 600 jobs) Difficult to sort through › Better: Create a subdirectory for each run http: //www. cs. wisc. edu/condor 43

Organize your files and directories for big runs › Create subdirectories for each “run” run_0, run_1, … run_599 › Create input files in each of these run_0/simulation. in run_1/simulation. in … run_599/simulation. in › The output, error & log files for each job will be created by Condor from your job’s output http: //www. cs. wisc. edu/condor 44

Frieda’s simulation directory sim. exe sim. sub simulation. in run_0 simulation. out simulation. err simulation. log simulation. in simulation. out run_599 simulation. err simulation. log http: //www. cs. wisc. edu/condor 45

Submit Description File for 600 Jobs # Cluster of Universe = Executable = Log =. . . Arguments = Initial. Dir = Queue 600 jobs with different directories vanilla simulation. log -x 0 run_0 Arguments = -x 1 Initial. Dir = run_1 Queue ·Log, input, output & error files -> run_0 ·Job 3. 0 (Cluster 3, Process 0) ·Log, input, output & error files -> run_1 ·Job 3. 1 (Cluster 3, Process 1) ·Do this 598 more times………… http: //www. cs. wisc. edu/condor 46

Submit File for a Big Cluster of Jobs › We just submitted 1 cluster with 600 › › › processes All the input/output files will be in different directories The submit file is pretty unwieldy (over 1200 lines) Isn’t there a better way? http: //www. cs. wisc. edu/condor 47

Submit File for a Big Cluster of Jobs (the better way) #1 › We can queue all 600 in 1 “Queue” command Queue 600 › Condor provides $(Process) and $(Cluster) $(Process) will be expanded to the process number for each job in the cluster • 0, 1, … 599 $(Cluster) will be expanded to the cluster number • Will be 4 for all jobs in this cluster http: //www. cs. wisc. edu/condor 48

Submit File for a Big Cluster of Jobs (the better way) #2 › The initial directory for each job can be specified using $(Process) Initial. Dir = run_$(Process) Condor will expand these to “run_0”, “run_1”, … “run_599” directories › Similarly, arguments can be variable Arguments = -x $(Process) Condor will expand these to “-x 0”, -x 1”, … “-x 599” http: //www. cs. wisc. edu/condor “ 49

Better Submit File for 600 Jobs # Example condor_submit input file that defines # a cluster of 600 jobs with different directories Universe = vanilla Executable = my_job Log = my_job. log Input = my_job. in Output = my_job. out Error = my_job. err Arguments = –x $(Process) ·–x 0, -x 1, … -x 599 Initial. Dir = run_$(Process) ·run_0 … run_599 Queue 600 ·Jobs 4. 0 … 4. 599 http: //www. cs. wisc. edu/condor 50

Now, we submit it… $ condor_submit my_job. submit Submitting job(s). . . . . . . . . . . . . . . . Logging submit event(s). . . . . . . . . . . . . . . . 600 job(s) submitted to cluster 4. http: //www. cs. wisc. edu/condor 51

And, Check the queue $ condor_q -- Submitter: ID OWNER 4. 0 frieda 4. 1 frieda 4. 2 frieda 4. 3 frieda. . . 4. 598 frieda 4. 599 frieda x. cs. wisc. edu : <128. 105. 121. 53: 510> : x. cs. wisc. edu SUBMITTED RUN_TIME ST PRI SIZE CMD 4/20 12: 08 0+00: 05 R 0 9. 8 my_job -arg 1 –x 0 4/20 12: 08 0+00: 03 I 0 9. 8 my_job -arg 1 –x 1 4/20 12: 08 0+00: 01 I 0 9. 8 my_job -arg 1 –x 2 4/20 12: 08 0+00: 00 I 0 9. 8 my_job -arg 1 –x 3 4/20 12: 08 0+00: 00: 00 I 0 0 9. 8 my_job -arg 1 –x 598 my_job -arg 1 –x 599 600 jobs; 599 idle, 1 running, 0 held http: //www. cs. wisc. edu/condor 52

Removing jobs › If you want to remove a job from the › › Condor queue, you use condor_rm You can only remove jobs that you own Privileged user can remove any jobs “root” on UNIX “administrator” on Windows http: //www. cs. wisc. edu/condor 53

Removing jobs (continued) › Remove an entire cluster: condor_rm 4 ·Removes the whole cluster › Remove a specific job from a cluster: condor_rm 4. 0 ·Removes a single job › Or, remove all of your jobs with “-a” condor_rm -a ·Removes all jobs / clusters http: //www. cs. wisc. edu/condor 54

Good News (Boss Fat Cat) The Boss says Frieda can add her co-workers’ desktop machines into her Condor pool as well… but only if they can also submit jobs. http: //www. cs. wisc. edu/condor 55

Adding nodes › Frieda installs Condor on the desktop machines, and configures them with her machine as the central manager The central manager: • Central repository for the whole pool • Performs job / machine matching, etc. › These are “non-dedicated” nodes, meaning that they can't always run Condor jobs http: //www. cs. wisc. edu/condor 56

600 Condor jobs personal your. Pool Condor workstation Condor http: //www. cs. wisc. edu/condor 57

condor_status % condor_status Name Op. Sys Arch State Activ Load. Av Mem antipholus. cs LINUX INTEL Unclaimed Idle 0. 020 511 0+02: 28: 42 coral. cs. wisc LINUX INTEL Claimed Busy 0. 990 511 0+01: 27: 21 doc. cs. wisc. e LINUX INTEL Unclaimed Idle 0. 260 511 0+00: 20: 04 dsonokwa. cs. w LINUX INTEL Claimed Busy 0. 810 511 0+00: 01: 45 ferdinand. cs. LINUX INTEL Claimed Suspe 1. 130 511 0+00: 55 vm 1@pinguino. LINUX INTEL Unclaimed Idle 0. 000 255 0+01: 03: 28 vm 2@pinguino. LINUX INTEL Unclaimed Idle 0. 190 255 0+01: 03: 29 http: //www. cs. wisc. edu/condor Actvty. Time 58

How can my jobs access their data files? http: //www. cs. wisc. edu/condor 59

Access to Data in Condor › Use shared filesystem if available › No shared filesystem? Condor can transfer files • Can automatically send back changed files • Atomic transfer of multiple files • Can be encrypted over the wire Remote I/O Socket Standard Universe can use remote system calls (more on this later) http: //www. cs. wisc. edu/condor 60

Condor File Transfer › Should. Transfer. Files = YES Always transfer files to execution site › Should. Transfer. Files = NO Rely on a shared filesystem › Should. Transfer. Files = IF_NEEDED Will automatically transfer the files if the submit and execute machine are not in the same File. System. Domain Universe = vanilla Executable = my_job Log = my_job. log Should. Transfer. Files = IF_NEEDED Transfer_input_files = dataset. $(Process), common. data Transfer_output_files = The. Answer. dat Queue 600 http: //www. cs. wisc. edu/condor 61

We Always Want More Condor is managing and running our jobs, but § Our CPU requirements are greater than our resources § Jobs are preempted more often than we like http: //www. cs. wisc. edu/condor 62

Happy Day! Frieda’s organization purchased a Dedicated Cluster! › Frieda Installs Condor on all the › › dedicated Cluster nodes Frieda also adds a dedicated central manager She configures her entire pool with this new host as the central manager… http: //www. cs. wisc. edu/condor 63

Frieda’s Condor Pool 600 Condor jobs Condor Pool With the additional resources, Frieda and her co-workers can get their jobs completed even faster. Dedicated Cluster http: //www. cs. wisc. edu/condor 64

Another Universe http: //www. cs. wisc. edu/condor 65

Frieda submits some MPI jobs universe = parallel executable = mp 1 script arguments = my_mpich_linked_executable arg 1 arg 2 machine_count = 4 should_transfer_files = yes when_to_transfer_output = on_exit transfer_input_files = my_mpich_linked_executable queue http: //www. cs. wisc. edu/condor 66

What Condor Daemons are running on my machine, and what do they do? http: //www. cs. wisc. edu/condor 67

condor_master › Starts up all other Condor daemons › If there any problems and a daemon › exits, it restarts the daemon and sends email to the administrator Acts as the server for many Condor remote administration commands: condor_reconfig, condor_restart, condor_off, condor_on, condor_config_val, etc. http: //www. cs. wisc. edu/condor 68

Condor Daemon Layout Personal Condor / Central Manager Master startd schedd negotiator collector = Process Spawned http: //www. cs. wisc. edu/condor 69

Central Manager: condor_collector › Central manager: central repository and match › maker for whole pool Collects information from all other Condor daemons in the pool “Directory Service” / Database for a Condor pool › Each daemon sends a periodic update called a › “Class. Ad” to the collector Services queries for information: Queries from other Condor daemons Queries from users (condor_status) › Only on the Central Manager › At least one collector per pool http: //www. cs. wisc. edu/condor 70

Condor Pool Layout: Collector = Process Spawned = Class. Ad Communication Pathway Central Manager Master Collector http: //www. cs. wisc. edu/condor 71

Central Manager: condor_negotiator › Performs “matchmaking” in Condor › Each “Negotiation Cycle” (typically 5 minutes): Gets information from the collector about all available machines and all idle jobs Tries to match jobs with machines that will serve them Both the job and the machine must satisfy each other’s requirements › Only one negotiator per pool › Only on the Central Manager http: //www. cs. wisc. edu/condor 72

Condor Pool Layout: Negotiator = Process Spawned = Class. Ad Communication Pathway Central Manager negotiator Master Collector http: //www. cs. wisc. edu/condor 73

Execute Hosts: condor_startd › Execute host: machines that run user jobs › Represents a machine to the Condor system › Responsible for starting, suspending, and › › › stopping jobs Enforces the wishes of the machine owner (the owner’s “policy”… more on this in the administrator’s tutorial) Creates a “starter” for each running job One startd runs on each execute node http: //www. cs. wisc. edu/condor 74

Condor Pool Layout: startd = Process Spawned = Class. Ad Communication Pathway Central Manager negotiator Master Collector Cluster Node Master startd http: //www. cs. wisc. edu/condor 75

Submit Hosts: condor_schedd › Submit hosts: machines that users can submit › › › jobs on Maintains the persistent queue of jobs Responsible for contacting available machines and sending them jobs Services user commands which manipulate the job queue: condor_submit, condor_rm, condor_q, condor_hold, condor_release, condor_prio, … › Creates a “shadow” for each running job › One schedd runs on each submit host http: //www. cs. wisc. edu/condor 76

Condor Pool Layout: schedd = Process Spawned = Class. Ad Communication Pathway Central Manager negotiator schedd Master Collector Cluster Node Master startd Cluster Node Master Desktop Master startd schedd Desktop startd Master startd schedd http: //www. cs. wisc. edu/condor 77

Condor Pool Layout: master = Process Spawned = Class. Ad Communication Pathway Cluster Node Central Manager negotiator schedd Master startd Cluster Node Collector Master Desktop Master startd schedd Desktop startd Master startd schedd http: //www. cs. wisc. edu/condor 78

Now what? › Some of the machines in the pool can’t run my jobs Not enough RAM Not enough scratch disk space Required software not installed Etc. http: //www. cs. wisc. edu/condor 79

Specify Requirements › An expression (syntax similar to C or Java) › Must evaluate to True for a match to be made Universe = Executable = Log = Initial. Dir = Requirements Queue 600 vanilla my_job. log run_$(Process) = Memory >= 256 && Disk > 10000 http: //www. cs. wisc. edu/condor 80

Advanced Requirements › Requirements can match custom attributes in your Machine Ad Can be added by hand to each machine Or, automatically using the “Hawkeye” mechanism Universe = vanilla Executable = $$(My. Prog. Path) Log = my_job. log Initial. Dir = run_$(Process) Requirements = Memory >= 256 && Disk > 10000 && ( My. Prog. Path =!= UNDEFINED) ) Queue 600 http: //www. cs. wisc. edu/condor 81

And, Specify Rank › All matches which meet the requirements › can be sorted by preference with a Rank expression. Higher the Rank, the better the match Universe = vanilla Executable = my_job Log = my_job. log Arguments = -arg 1 –arg 2 Initial. Dir = run_$(Process) Requirements = Memory >= 256 && Disk > 10000 Rank = (KFLOPS*10000) + Memory Queue 600 http: //www. cs. wisc. edu/condor 82

My jobs aren’t running!! http: //www. cs. wisc. edu/condor 83

Check the queue › Check the queue with condor_q: bash-2. 05 a$ condor_q -- Submitter: x. cs. wisc. edu : <128. 105. 121. 53: 510> : x. cs. wisc. edu ID OWNER SUBMITTED RUN_TIME ST PRI SIZE CMD 5. 0 frieda 4/20 12: 23 0+00: 00 I 0 9. 8 my_job -arg 1 –n 0 5. 1 frieda 4/20 12: 23 0+00: 00 I 0 9. 8 my_job -arg 1 –n 1 5. 2 frieda 4/20 12: 23 0+00: 00 I 0 9. 8 my_job -arg 1 –n 2 5. 3 frieda 4/20 12: 23 0+00: 00 I 0 9. 8 my_job -arg 1 –n 3 5. 4 frieda 4/20 12: 23 0+00: 00 I 0 9. 8 my_job -arg 1 –n 4 5. 5 frieda 4/20 12: 23 0+00: 00 I 0 9. 8 my_job -arg 1 –n 5 5. 6 frieda 4/20 12: 23 0+00: 00 I 0 9. 8 my_job -arg 1 –n 6 5. 7 frieda 4/20 12: 23 0+00: 00 I 0 9. 8 my_job -arg 1 –n 7 6. 0 frieda 4/20 13: 22 0+00: 00 H 0 9. 8 my_job -arg 1 –arg 2 8 jobs; 8 idle, 0 running, 1 held http: //www. cs. wisc. edu/condor 84

Look at jobs on hold % condor_q –hold -- Submiter: x. cs. wisc. edu : <128. 105. 121. 53: 510> : x. cs. wisc. edu ID OWNER HELD_SINCE HOLD_REASON 6. 0 frieda 4/20 13: 23 Error from starter on skywalker. cs. wisc. edu 9 jobs; 8 idle, 0 running, 1 held Or, See full details for a job % condor_q –l 6. 0 http: //www. cs. wisc. edu/condor 85

Check machine status › Verify that there are idle machines with condor_status: bash-2. 05 a$ Name vm 1@tonic. c vm 2@tonic. c vm 3@tonic. c vm 4@tonic. c INTEL/LINUX Total condor_status Op. Sys Arch State LINUX INTEL Claimed Activity Busy Load. Av Mem 0. 000 501 0. 040 501 0. 000 501 Actvty. Time 0+00: 20 0+00: 19 0+00: 17 0+00: 05 Total Owner Claimed Unclaimed Matched Preempting 4 0 4 0 0 0 http: //www. cs. wisc. edu/condor 86

Look in Job Log › Look in your job log for clues: bash-2. 05 a$ cat my_job. log 000 (031. 000) 04/20 14: 47: 31 Job submitted from host: <128. 105. 121. 53: 48740>. . . 007 (031. 000) 04/20 15: 02: 00 Shadow exception! Error from starter on gig 06. stat. wisc. edu: Failed to open '/scratch. 1/frieda/workspace/v 67/condortest/test 3/run_0/my_job. in' as standard input: No such file or directory (errno 2) 0 - Run Bytes Sent By Job 0 - Run Bytes Received By Job. . . http: //www. cs. wisc. edu/condor 87

Still not running? Exercise a little patience › On a busy pool, it can take a while to match and start your jobs › Wait at least a negotiation cycle or two (typically a few minutes) http: //www. cs. wisc. edu/condor 88

Look to condor_q for help: condor_q -analyze bash-2. 05 a$ condor_q -ana 29 --029. 000: Run analysis summary. Of 1243 machines, 1243 are rejected by your job's requirements 0 are available to run your job WARNING: Be advised: No resources matched request's constraints Check the Requirements expression below: Requirements = ((Memory > 8192)) && (Arch == "INTEL") && (Op. Sys == "LINUX") && (Disk >= Disk. Usage) && (TARGET. File. System. Domain == MY. File. System. Domain) http: //www. cs. wisc. edu/condor 89

Better analysis (Linux only): condor_q –better-analyze bash-2. 05 a$ condor_q -better-ana 29 The Requirements expression for your job is: ( ( target. Memory > 8192 ) ) && ( target. Arch == "INTEL" ) && ( target. Op. Sys == "LINUX" ) && ( target. Disk >= Disk. Usage ) && ( TARGET. File. System. Domain == MY. File. System. Domain ) Condition Machines Matched Suggestion ------------1 ( ( target. Memory > 8192 ) ) 0 MODIFY TO 4000 2 ( TARGET. File. System. Domain == "cs. wisc. edu" )584 3 ( target. Arch == "INTEL" ) 1078 4 ( target. Op. Sys == "LINUX" ) 1100 5 ( target. Disk >= 13 ) 1243 http: //www. cs. wisc. edu/condor 90

Learn about available resources: bash-2. 05 a$ condor_status –const 'Memory > 8192' (no output means no matches) bash-2. 05 a$ condor_status -const 'Memory > 4096' Name Op. Sys Arch State Activ Load. Av Mem Actvty. Time vm 1@s 0 -03. cs. LINUX X 86_64 Unclaimed Idle 0. 000 5980 1+05: 35: 05 vm 2@s 0 -03. cs. LINUX X 86_64 Unclaimed Idle 0. 000 5980 13+05: 37: 03 vm 1@s 0 -04. cs. LINUX X 86_64 Unclaimed Idle 0. 000 7988 vm 2@s 0 -04. cs. LINUX X 86_64 Unclaimed Idle 0. 000 7988 13+06: 03: 47 1+06: 00: 05 Total Owner Claimed Unclaimed Matched Preempting X 86_64/LINUX 4 0 0 Total 4 0 0 http: //www. cs. wisc. edu/condor 91

Job Policy Expressions › User can supply job policy expressions in › the submit file. Can be used to describe a successful run. on_exit_remove = <expression> on_exit_hold = <expression> periodic_remove = <expression> periodic_hold = <expression> http: //www. cs. wisc. edu/condor 92

Job Policy Examples › Do not remove if exits with a signal: on_exit_remove = Exit. By. Signal == False › Place on hold if exits with nonzero status or ran for less than an hour: on_exit_hold = ( (Exit. By. Signal==False) && (Exit. Signal != 0) ) || ( (Server. Start. Time - Job. Start. Date) < 3600) › Place on hold if job has spent more than 50% of its time suspended: periodic_hold = Cumulative. Suspension. Time > (Remote. Wall. Clock. Time / 2. 0) http: //www. cs. wisc. edu/condor 93

Insert Class. Ad attributes › Special purpose usage › In the submit description file, introduce an attribute for the job +Department = “biochemistry” causes the Class. Ad to contain Department = “biochemistry” http: //www. cs. wisc. edu/condor 94

We’ve seen how Condor can: Keep an eye on your jobs and will keep you posted on their progress Implement your policy on the execution order of the jobs Keep a log of your job activities http: //www. cs. wisc. edu/condor 95

Another Universe http: //www. cs. wisc. edu/condor 96

My new jobs run for 20 days… › What happens when a job is forced off it’s CPU? Preempted by higher priority user or job Vacated because of user activity › How can I add fault tolerance to my jobs? http: //www. cs. wisc. edu/condor 97

Condor’s Standard Universe to the rescue! › Support for transparent process checkpoint and restart › Remote system calls (remote I/O) Your job can read / write files as if they were local http: //www. cs. wisc. edu/condor 98

Remote System Calls in the Standard Universe › I/O system calls are trapped and sent back to the submit machine Examples: open a file, write to a file › No source code changes typically required › Programming language independent http: //www. cs. wisc. edu/condor 99

Process Checkpointing in the Standard Universe › Condor’s process checkpointing provides a › mechanism to automatically save the state of a job The process can then be restarted from right where it was checkpointed After preemption, crash, etc. http: //www. cs. wisc. edu/condor 100

Checkpointing: Process Starts checkpoint: the entire state of a program, saved in a file § CPU registers, memory image, I/O time http: //www. cs. wisc. edu/condor 101

Checkpointing: Process Checkpointed time 1 2 3 http: //www. cs. wisc. edu/condor 102

Checkpointing: Process Killed time Killed! 3 3 http: //www. cs. wisc. edu/condor 103

Checkpointing: Process Resumed goodput badput time goodput 3 3 http: //www. cs. wisc. edu/condor 104

When will Condor checkpoint your job? › Periodically, if desired For fault tolerance › When your job is preempted by a higher › › priority job When your job is vacated because the execution machine becomes busy When you explicitly run condor_checkpoint, condor_vacate, condor_off or condor_restart command http: //www. cs. wisc. edu/condor 105

Making the Standard Universe Work › The job must be relinked with Condor’s › standard universe support library To relink, place condor_compile in front of the command used to link the job: % condor_compile gcc -o myjob. c - OR % condor_compile f 77 -o myjob filea. f fileb. f - OR % condor_compile make –f My. Makefile http: //www. cs. wisc. edu/condor 106

Limitations of the Standard Universe › Condor’s checkpointing is not at the kernel level. Standard Universe the job may not: • Fork() • Use kernel threads • Use some forms of IPC, such as pipes and shared memory › Must have access to source code to relink › Many typical scientific jobs are OK http: //www. cs. wisc. edu/condor 107

Connecting Condors › Frieda knows people with › their own Condor pools, and gets permission to use their computing resources… How can Condor help her do this? http: //www. cs. wisc. edu/condor 108

Connect Condors with Flocking › Frieda configures her Condor pool › to “flock” flock to her friend’s pool. Flocking is a Condor-specific technology. http: //www. cs. wisc. edu/condor 109

Frieda’s Condor Pool 600 Condor jobs Condor Pool Friendly Condor Pool http: //www. cs. wisc. edu/condor 110

Frieda meets The Grid › Frieda also has access to grid resources she wants to use She has certificates and access to Globus or other resources at remote institutions › But Frieda wants Condor’s queue › management features for her jobs! She installs Condor so she can submit “Grid Universe” jobs to Condor http: //www. cs. wisc. edu/condor 111

“Grid” Universe › All handled in your submit file › Supports a number of “back end” types: Globus: GT 2, GT 4 Nordu. Grid UNICORE Condor PBS LSF EC 2 NQS http: //www. cs. wisc. edu/condor 112

Grid Universe & Globus 2 › Used for a Globus GT 2 back-end “Condor-G” › Format: Grid_Resource = gt 2 Head-Node Globus_rsl = <RSL-String> › Example: Universe = grid Grid_Resource = gt 2 beak. cs. wisc. edu/jobmanager Globus_rsl = (queue=long)(project=atom-smasher) http: //www. cs. wisc. edu/condor 113

Grid Universe & Globus 4 › Used for a Globus GT 4 back-end › Format: Grid_Resource = gt 4 <Head-Node> <Scheduler-Type> Globus_XML = <XML-String> › Example: Universe = grid Grid_Resource = gt 4 beak. cs. wisc. edu Condor Globus_xml = <queue>long</queue><project>atomsmasher</project> http: //www. cs. wisc. edu/condor 114

Grid Universe & Condor › Used for a Condor back-end “Condor-C” › Format: Grid_Resource = condor <Schedd-Name> <Collector-Name> Remote_<param> = <value> “Remote_” part is stripped off › Example: Universe = grid Grid_Resource = condor beak condor. cs. wisc. edu Remote_Universe = standard http: //www. cs. wisc. edu/condor 115

Grid Universe & Nordu. Grid › Used for a Nordu. Grid back-end Grid_Resource = nordugrid <Host-Name> › Example: Universe = grid Grid_Resource = nordugrid ngrid. cs. wisc. edu http: //www. cs. wisc. edu/condor 116

Grid Universe & UNICORE › Used for a UNICORE back-end › Format: Grid_Resource = unicore <USite> <VSite> › Example: Universe = grid Grid_Resource = unicore uhost. cs. wisc. edu vhost http: //www. cs. wisc. edu/condor 117

Grid Universe & PBS › Used for a PBS back-end › Format: Grid_Resource = pbs › Example: Universe = grid Grid_Resource = pbs http: //www. cs. wisc. edu/condor 118

Grid Universe & LSF › Used for a LSF back-end › Format: Grid_Resource = lsf › Example: Universe = grid Grid_Resource = lsf http: //www. cs. wisc. edu/condor 119

Credential Management › Condor will do The Right Thing™ with your › X 509 certificate and proxy Override default proxy: X 509 User. Proxy = /home/frieda/other/proxy › Proxy may expire before jobs finish executing Condor can use My. Proxy to renew your proxy When a new proxy is available, Condor will forward the renewed proxy to the job This works for non-grid jobs, too http: //www. cs. wisc. edu/condor 120

My jobs have dependencies… Can Condor help solve my dependency problems? http: //www. cs. wisc. edu/condor 121

Condor Universes: Scheduler and Local › Scheduler Universe Plug in a meta-scheduler Developed for DAGMan (more later) Similar to Globus’s fork job manager › Local Very similar to vanilla, but jobs run on the local host Has more control over jobs than scheduler universe http: //www. cs. wisc. edu/condor 122

Frieda learns DAGMan › Directed Acyclic Graph Manager › DAGMan allows you to specify the dependencies between your Condor jobs, so it can manage them automatically for you. › (e. g. , “Don’t run job “B” until job “A” has completed successfully. ”) http: //www. cs. wisc. edu/condor 123

What is a DAG? › A DAG is the data structure Job A used by DAGMan to represent these dependencies. › Each job is a “node” in the DAG. › Each node can have any number of “parent” or “children” nodes – as long as there are no loops! Job B Job C Job D http: //www. cs. wisc. edu/condor 124

Defining a DAG › A DAG is defined by a. dag file, listing each of its nodes and their dependencies: # diamond. dag Job A a. sub Job B b. sub Job C c. sub Job D d. sub Parent A Child B C Parent B C Child D Job A Job B Job C Job D › each node will run the Condor job specified by its accompanying Condor submit file http: //www. cs. wisc. edu/condor 125

Submitting a DAG › To start your DAG, just run condor_submit_dag with your. dag file, and Condor will start a personal DAGMan daemon which to begin running your jobs: % condor_submit_dag diamond. dag › condor_submit_dag is run by the schedd DAGMan daemon itself is “watched” by Condor, so you don’t have to http: //www. cs. wisc. edu/condor 126

Running a DAG › DAGMan acts as a “meta-scheduler”, managing the submission of your jobs to Condor based on the DAG dependencies. A Condor A Job Queue B C . dag File DAGMan D http: //www. cs. wisc. edu/condor 127

Running a DAG (cont’d) › DAGMan holds & submits jobs to the Condor queue at the appropriate times. A Condor B Job Queue C B C DAGMan D http: //www. cs. wisc. edu/condor 128

Running a DAG (cont’d) › In case of a job failure, DAGMan continues until it can no longer make progress, and then creates a “rescue” file with the current state of the DAG. A Condor Job Queue B X DAGMan D http: //www. cs. wisc. edu/condor Rescue File 129

Recovering a DAG › Once the failed job is ready to be re-run, the rescue file can be used to restore the prior state of the DAG. A Condor Job Queue C B C Rescue File DAGMan D http: //www. cs. wisc. edu/condor 130

Recovering a DAG (cont’d) › Once that job completes, DAGMan will continue the DAG as if the failure never happened. A Condor Job Queue D B C DAGMan D http: //www. cs. wisc. edu/condor 131

Finishing a DAG › Once the DAG is complete, the DAGMan job itself is finished, and exits. A Condor Job Queue B C DAGMan D http: //www. cs. wisc. edu/condor 132

Additional DAGMan Features › Provides other handy features for job management… nodes can have PRE & POST scripts failed nodes can be automatically re- tried a configurable number of times job submission can be “throttled” http: //www. cs. wisc. edu/condor 133

› › › › › General User Commands condor_status View Pool Status condor_q View Job Queue condor_submit Submit new Jobs condor_rm Remove Jobs condor_prio Intra-User Prios condor_history Completed Job Info condor_submit_dag Submit new DAG condor_checkpoint Force a checkpoint condor_compile Link Condor library http: //www. cs. wisc. edu/condor 134

Condor Job Universes • • • Vanilla Universe Standard Universe Grid Universe Scheduler Universe Local Universe Virtual Machine Universe • Java Universe • Parallel Universe • • MPICH-1 MPICH-2 LAM … http: //www. cs. wisc. edu/condor 135

Why have a special Universe for Java jobs? › Java Universe provides more than just inserting “java” at the start of the execute line of a vanilla job: Knows which machines have a JVM installed Knows the location, version, and performance of JVM on each machine Knows about jar files, etc. Provides more information about Java job completion than just JVM exit code • Program runs in a Java wrapper, allowing Condor to report Java exceptions, etc. http: //www. cs. wisc. edu/condor 136

Universe Java Job › Example Java Universe Submit file: Universe = java Executable = Main. class jar_files = My. Library. jar Input = infile Output = outfile Arguments = Main 1 2 3 Queue http: //www. cs. wisc. edu/condor 137

Java support, cont. bash-2. 05 a$ Name abulafia. cs acme. cs. wis adelie 01. cs adelie 02. cs … condor_status –java Java. Vendor Ver State Sun Microsy 1. 5. 0_ Claimed Sun Microsy 1. 5. 0_ Unclaimed Sun Microsy 1. 5. 0_ Claimed INTEL/LINUX INTEL/WINNT 50 SUN 4 u/SOLARIS 28 X 86_64/LINUX Total Actv Busy Idle Busy Load. Av Mem 0. 180 503 0. 000 1002 Total Owner Claimed Unclaimed Matched Preempting 965 179 516 250 20 0 102 6 65 31 0 0 128 2 106 20 0 0 1196 187 687 302 http: //www. cs. wisc. edu/condor 20 0 138

Frieda wants Condor features on remote resources › She wants to run standard universe jobs on Grid-managed resources For matchmaking and dynamic scheduling of jobs For job checkpointing and migration For remote system calls http: //www. cs. wisc. edu/condor 139

Condor Glide. In › Frieda can use the Grid Universe to run › › › Condor daemons on Grid resources When the resources run these Glide. In jobs, they will temporarily join her Condor Pool She can then submit Standard, Vanilla, PVM, or MPI Universe jobs and they will be matched and run on the remote resources Currently only supports Globus GT 2 We hope to fix this limitation http: //www. cs. wisc. edu/condor 140

Globus Grid 600 Condor jobs personal your. Pool Condor workstation Condor PBS LSF glide-in jobs Friendly Condor Pool Condor http: //www. cs. wisc. edu/condor 141

Glide. In Concerns › What if the remote resource kills my Glide. In job? That resource will disappear from your pool and your jobs will be rescheduled on other machines Standard universe jobs will resume from their last checkpoint like usual › What if all my jobs are completed before a Glide. In job runs? If a Glide. In Condor daemon is not matched with a job in 10 minutes, it terminates, freeing the resource http: //www. cs. wisc. edu/condor 143

In Review With Condor’s help, Frieda can: Manage her compute job workload Access local machines Access remote Condor Pools via flocking Access remote compute resources on the Grid via “Grid Universe” jobs Carve out her own personal Condor Pool from the Grid with Glide. In technology http: //www. cs. wisc. edu/condor 144

› › › › Administrator Commands condor_vacate Leave a machine now condor_on Start Condor condor_off Stop Condor condor_reconfig Reconfig on-the-fly condor_config_val View/set config condor_userprio User Priorities condor_stats View detailed usage accounting stats http: //www. cs. wisc. edu/condor 145

My boss wants to watch what Condor is doing http: //www. cs. wisc. edu/condor 146

Use Condor. View! › Provides visual graphs of current and past › › › utilization Data is derived from Condor's own accounting statistics Interactive Java applet Quickly and easily view: How much Condor is being used How many cycles are being delivered Who is using them Utilization by machine platform or by user http: //www. cs. wisc. edu/condor 147

Condor. View Usage Graph http: //www. cs. wisc. edu/condor 148

› › › I could also talk lots about… GCB: Living with firewalls & private networks Federated Grids/Clusters APIs and Portals MW Database Support (Quill) High Availability Fail-over Compute On-Demand (COD) Dynamic Pool Creation (“Glide-in”) Role-based prioritization and accounting Strong security, incl privilege separation Data movement scheduling in workflows … http: //www. cs. wisc. edu/condor 149

Thank you! Check us out on the Web: http: //www. condorproject. org Email: condor-admin@cs. wisc. edu http: //www. cs. wisc. edu/condor 150