Resource Management and Job Scheduling · 2016-08-09 · Resource Management and Job Scheduling Jenett Tillotson Senior Cluster System Administrator Indiana University. 18 ... 18

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Resource Management and

Job Scheduling

Jenett TillotsonSenior Cluster System Administrator

Indiana University

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Resource Managers Keep track of resources

Nodes: CPUs, disk, memory, swap, load, etc. Network, licenses, storage, etc.

Keep track of requests Jobs, queues, etc.

Control jobs which use these resources Stop, hold, cancel, monitor, etc.

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Job Scheduler What jobs run on what resources Pretty complicated

Quality of Service/Service Level Agreements Avoid job starvation Job placement

Maximize good stuff Minimize bad stuff

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TORQUE Manager● Terascale Open-source Resource and QUEue Portable Batch System (PBS), NASA, 1991 OpenPBS, open source, 1998 PBSPro, commercial product TORQUE, open source, 2003

Hosted and developed by Adaptive Computing

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Moab Maui, mid 1990s, open sourced 2000 Moab, commercial product, 2001 Dave Jackson, creator of Maui/Moab

Started Cluster Resources Now Adaptive Computing

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Torque Topology Diagram

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Master Node pbs_server Provides

Node tracking Queues and queuing policies Storage for job scripts and tracking of jobs Usage and events logs

pbs_sched: FIFO scheduler

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Compute Nodes pbs_mom: Machine Oriented Mini-server

Starts the job on the compute resources Monitors resource utilizations Notifies pbs_server of job events Facilitates multi-node jobs Spools stdout and stderr

Mother Superior and sister MOMs

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Submit Nodes TORQUE client

qsub, qdel, qhold/qrls, qstat, qalter

trqauthd: TORQUE Authorization Daemon Runs on all nodes

All nodes

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Job Flow

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Job Flow

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Job Flow

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Job Flow

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Job Flow

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Installation Requires libxml2-devel, openssl-devel, Tcl/Tk

for the (optional) GUI, libhwloc for (optional) cpusets, gcc, gcc-c++, make, libtool, boost-devel

configure; make; make install make install_mom, make install_client, make

install_server make rpm -or- make packages

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Configuring TORQUE ./configure options:

--prefix=/usr/local/

--home_server_home=/var/spool/torque/

--with-default-server=$HOSTNAME pbs_server: /var/spool/torque/server_priv/nodes pbs_mom: /var/spool/torque/mom_priv/config /var/spool/torque/server_name

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/var/spool/torque/server_priv/nodes:

node1 np=16 prop1 prop2

node2 np=16 prop1

node3 np=32 prop3 prop2

node4 np=16 prop1 prop2

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/var/spool/torque/mom_priv/config:

$loglevel 3

$spool_as_final_name true

$usecp *:/N/home /N/home

$usecp *:/N/dc2 /N/dc2

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/var/spool/torque/server_name:

myresmgr.domain.edu

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Running TORQUE Startup the first time:

pbs_server -t create pbs_mom, trqauthd

Startup scripts are in $BUILD_DIR/contrib/ Testing

pbsnodes qmgr /var/spool/torque/server_logs /var/spool/torque/mom_logs

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Security Compute nodes and submit hosts must be able

to talk to port 15001 on the pbs_server pbs_server must be able to talk to port 15002

on the compute nodes The compute nodes must be able to talk to port

15003 on the compute nodes

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TORQUE Configuration - qmgrcreate queue foo

set queue foo queue_type = Execution

set queue foo resources_max.nodes = 32

set queue foo resources_max.walltime = 24:00:00

set queue foo resources_default.nodes = 1

set queue foo resources_default.walltime = 1:00:00

set queue foo enabled = True

set queue foo started = True

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TORQUE Configuration (cont.)

set server scheduling = True

set server acl_host_enable = True

set server acl_hosts = myresmgr

set server managers = root@myresmgr

set server operators = root@myresmgr

set server submit_hosts = mysubmithost

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TORQUE Configuration (cont.)set server default_queue = foo

set server log_events = 511

set server mail_from = adm

set server node_check_rate = 150

set server tcp_timeout = 6

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Torque Commands qstat: Used to query the resource manager.

Common usage: “qstat -f $JOBID”: displays full info for $JOBID. “qstat -a”: displays all jobs. “qstat -q”: displays queues status. “qstat -Qf”: display queue definitions.

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TORQUE Commands (cont.) pbsnodes: command used to query the state of

nodes, mark a node offline, or online.– “pbsnodes -o $NODE”: sets the $NODE offline

– “pbsnodes -r $NODE”: clears the offline state

– “pbsnodes -l”: lists all nodes that are down or offline

– “pbsnodes -l $STATE”: lists all node in state $STATE

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Job Script#!/bin/bash

#PBS -l nodes=2:ppn=16

#PBS -l walltime=2:00:00

#PBS -N myjobname

#PBS -m bea

#PBS -M [email protected]

#PBS -j oe

#PBS -k o

#PBS -V

#PBS -q foo

cd $PBS_O_WORKDIR

./runmyjob

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TORQUE Directives● -l resource requests● -N job name● -m when to mail (b: start, e: end, a: abort, n: none)● -M where to mail● -j join output streams● -k keep output stream● -V copy submission environment to compute node● -q queue to submit to

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Job Environment Variables PBS_O_HOST - The machine that submitted the job. PBS_O_LOGNAME - The user who submitted the job. PBS_O_HOME - The home directory of the user who submitted the job. PBS_O_WORKDIR - The working directory from where the qsub was run. PBS_ENVIRONMENT - Set to PBS_BATCH for batch jobs and to

PBS_INTERACTIVE for interactive jobs. PBS_O_QUEUE - The original queue to which the job was submitted. PBS_JOBID - The identifier that PBS assigns to the job. PBS_JOBNAME - The name of the job. PBS_NODEFILE - The file which contains the list of nodes assigned to

the job.

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Job Control qsub – submit a job to the queues qdel – delete a job from the queues qhold – put a job on hold qrls – release a hold qstat – job status qalter – alter the attributes of an idle job

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Submitting a Job qsub -I

Submits an interactive job qsub $JOB_SCRIPT_FILE qsub -l nodes=1:ppn=16 -l walltime=2:00:00 -q

foo -N myname $JOB_SCRIPT_FILE Directives on the command line will override the

directives in the job script Jobs spooled in /var/spool/torque/server_priv/jobs

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Job Scheduling “pbs_sched”: Simple FIFO scheduler “qrun”

Terminating TORQUE “qterm -t quick”: Leave jobs running “qterm -t immediate”: Terminate all jobs as well

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Troubleshooting “tracejob -n $NUMB_OF_DAYS $JOB_ID”

Logs /var/spool/torque/server_logs /var/spool/torque/mom_logs /var/spool/torque/client_logs /var/spool/torque/server_priv/accounting /var/spool/torque/job_logs

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Moab Workload Manager

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Installation Download from Adaptive Computing libcurl, perl, perl-cpan, libxml2-devel, torque configure; make; make install Configure options

--prefix=/opt/moab

--with_homedir=/opt/moab

--with-serverhost=$HOSTNAME

--with-torque=/usr/local

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moab.cfgSCHEDCFG[mysched] SERVER=mysched:42559

ADMINCFG[1] USERS=root

ADMINCFG[3] USERS=all

RMCFG[myresmgr] TYPE=PBS

RMCFG[myresmgr] SUBMITCMD=/usr/local/bin/qsub

RMCFG[myresmgr] TIMEOUT=00:05:00

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moab.cfgLOGLEVEL 3

LOGFILEMAXSIZE 100000000

LOGFILEROLLDEPTH 10

RMPOLLINTERVAL 15

DISABLESCHEDULING TRUE

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moab.cfgJOBNODEMATCHPOLICY EXACTNODE

NODEALLOCATIONPOLICY PRIORITY

NODEACCESSPOLICY SINGLEJOB

JOBREJECTPOLICY HOLD

DEFERTIME 00:15:00

DEFERCOUNT 5

JOBACTIONONNODEFAILURE REQUEUE

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moab.cfgPROCWEIGHT 10

XFACTORWEIGHT 1000

FSWEIGHT 3

FSUSERWEIGHT 1000

FSPOLICY DEDICATEDPS

FSDEPTH 7

FSINTERVAL 24:00:00

FSDECAY 0.80

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moab.cfgRESERVATIONPOLICY CURRENTHIGHEST

RESERVATIONDEPTH 10

BACKFILLPOLICY FIRSTFIT

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moab.cfg

USERCFG[DEFAULT] FSTARGET=10.0

USERCFG[DEFAULT] MAXIJOBS=16

CLASSCFG[foo] HOSTLIST=node1[0-9]$

CLASSCFG[foo] MAXNODEPERUSER=4

CLASSCFG[foo] MAXJOB[USER]=1

NODECFG[DEFAULT] PRIORITYF=-LOAD

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Running moab “mdiag -C”: Will check moab.cfg for errors “/opt/moab/sbin/moab” Startup scripts are in $BUILD_DIR/contrib

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Troubleshooting “mdiag -R”: Shows what moab thinks is the status of

the resource manager “showq”: shows jobs in the Running, Idle, and Blocked

moab queues “checkjob -v $JOB_ID” “checknode $NODE_ID” “showstart $JOB_ID” Logs are in /opt/moab/log

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Controlling moab “mschedctl -p”: Pauses moab “mschedctl -r”: Starts moab “mschedctl -R”: Re-reads moab.cfg “mschedctl -k”: Kill moab “mschedctl -L 7”: Sets log level

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Moab Client● Installed just like on the server● Requires just the following line in moab.cfg:

SCHEDCFG[mysched] SERVER=mysched:42559● msub, mjobctl – submit and control jobs through moab

instead of the resource manager

● ADMINCFG[3] users allowed to run query commands (checknode, checkjob, etc.)

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Examples

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External Resources● Moab Information, Download, and Docs:

http://www.adaptivecomputing.com/products/hpc-products/moab-hpc-suite-basic-edition/

● Torque Information, Download, Docs and User Community Lists:

http://www.adaptivecomputing.com/products/open-source/torque