HUBbub 2013:Developing hub tools that submit

HPC jobs

Rob CampbellPurdue University

Thursday, September 5, 2013

Example “SubmitR” tool running on the DiaGrid hub

• DiaGrid: distributed research computing network

• SubmitR: hub tool for running R scripts on DiaGrid

SubmitR Move files, run job on remote system, view results

Hub

Building a job:Files, options/arguments, job parameters

Job Types

One process

Multiple processes, communicating

(parameter sweep)independent processes

The “submit” command: Runs user command on a remote system

submit

1.Connect to remote system

2.Transfer input files and program

3.Create script for user’s command

4.Talk to batch or workflow system

5.Output periodic status updates

6.Transfer files back to hub

For SubmitR, submit uses:•PBS job scheduling on Purdue’s Hansen cluster (single or parallel jobs) •Pegasus workflow management with HTCondor (parameter sweeps)

submit options:• VENUES - remote systems• MANAGERS - commands that can be run on remote systems

Building the submit command:

submit -n 2 -w 60 -v hansen -M -i inp.dat R-2.15.1 CMD BATCH -q “--args inp.dat” myscipt.R

Use manager “R-2.15.1”. Causes “R” interpreter to run on remote system.

Job should use 2 processors, 60 minutes walltime, run on Hansen cluster, and collect metrics. File “inp.dat” should be included

(transported to remote system).

Options for the R interpreter. Note: submit detects that “myscript.R” is used and transports it to remote system.

Executing the submit command, getting status updates:

Tips for using submit:

Test submit from the hub’s command line (workspace):

$> submit -n 1 -w 5 -v hansen -M R-2.15.1 CMD BATCH -q "--args 1 2" testargs.R" =SUBMIT-METRICS=> job=1214144 (5073894) Job Submitted at hansen-a Mon Sep 2 17:38:54 2013 (5073894) Simulation Queued at hansen-a Mon Sep 2 17:39:04 2013 (5073894) Simulation Complete at hansen-a Mon Sep 2 17:39:20 2013 (5073894) Simulation Done at hansen-a Mon Sep 2 17:39:30 2013 =SUBMIT-METRICS=> job=1214144 venue=1:sshPBS:5073894:diagrid-a@hansen.rcac.purdue.edu status=0 cpu=3.290000 real=3.000000 wait=14.000000 (end of output)

Use submit’s email notification feature to alert user when job finishes:

$> submit mail2self –s ‘Hey’ –t ‘Your job is done.’

Additional submit feature: Automatic breakout of parameter combinations (for sweeps)

“ submit … -p @@p1=1-3;@@p2=7,9 … ”

User wants six runs.

Parameters:•1 7•1 9•2 7•2 9•3 7•3 9

Directories: “Run” directory:•A tool-specific directory under hub’s session directory.•Current working directory for executing submit .•Isolates job-related files.•Ex. “~/data/sessions/6716/submitr”

Parameter sweep output:•Job directory created under run directory.•Pegasus puts each run’s (sub-job’s) output in separate directory under job directory.•Pegasus bookkeeping files in job directory.

Exiting the tool, canceling the job:

Moving files:

1. Browse - moving files between directories on hub (“os.rename(pathname,newpath”)

2. Upload / download - moving files between workstation and hub

• Hub commands: importfile and exportfile .

• Execute importfile from separate thread to handle user-canceled uploads

Concept: File “import / export” • Bringing files into and out of tool. • Two flavors:

Resource LinkRob Campbell mailto:rcampbel@purdue.edu

Research Computingat Purdue http://www.rcac.purdue.edu

DiaGrid Hub http://diagrid.org

SubmitR https://diagrid.org/tools/submitr

Tool Developers Guide http://hubzero.org/documentation/1.1.0/tooldevs

The submit command http://hubzero.org/documentation/1.1.0/tooldevs/grid.submitcmd

Pegasus http://pegasus.isi.edu/

HTCondor http://research.cs.wisc.edu/htcondor/

Information