Wolfgang Friebel, 15.10.2001 HEPiX Meeting Berkeley Installing and Running SGE at DESY (Zeuthen)
Wolfgang Friebel,15.10.2001HEPiX Meeting Berkeley
Installing and Running SGE at DESY (Zeuthen)
Oct 15, 2001 SGEEE Zeuthen 2
Introduction Motivations for using a batch system
more effective usage of available computers (e. g. more uniform load) usage of resources 24h/day assignment of resources according to policies (who gets how much CPU when) quicker execution of tasks (system knows most powerful least loaded nodes)
Our goal: You tell the batch system a script name and what you need in terms of disk space, memory, CPU timeThe batch system guarantees fastest possible turnaround
Could even be used to get xterm windows on least loaded machines for interactive use
Oct 15, 2001 SGEEE Zeuthen 3
Batch Systems Overview Condor targeted at using idle workstations (not used at DESY) NQS public domain and commercial versions, basic functionality.
Used for APE100 projects Loadleveler mostly found on IBM machines, used at DESY LSF popular, rich set of features, licensed software, used at DESY PBS public domain and commercial versions, origin: NASA
rich set of features, became popular recently, used in H1 Codine/GRD batch system similar to LSF in functionality, used in HERA-B
and for all farms at DESY Zeuthen SGE/SGEEE Sun Grid Engine (Enterprise Edition), open source
successors of Codine/GRD. Became the only batch system at Zeuthen (except for the legacy APE 100 batch system)
Oct 15, 2001 SGEEE Zeuthen 4
The old Batch System Concept Each group runs a separate cluster with separate
instances of GRD or Codine Project priorities within a group are maintained by
configuring several queues reflecting the priorities Queue names were named after priority, e.g. long, medium, short, idle, ... Could also be named according to task, e.g. simulation, production, test, ... Individuals had to obey group dependent rules to submit jobs
Priorities between different groups were realized by the cluster size (CPU power)
Urgent tasks were tried to carry out by asking other groups to temporarily use their cluster
Administrative overhead to enable accounts on machines Users had to adapt their batch jobs to the new environment
There were always heavily overloaded clusters next to machines with lots of idle CPU cycles
Oct 15, 2001 SGEEE Zeuthen 5
A new Scheme for Batch Processing Two factors led us design a new batch processing scheme
shortcomings of the old system, especially the non uniform usage pattern licensing situation, our GRD license ended, wanted to go to the open source
successor of GRD
One central batch system for all groups dynamic allocation of resources according to the current needs of groups more uniform configuration of batch nodes
Very few queue types basically only two types: Queue for ordinary batch jobs and idle queue most of the scheduling decisions based on other mechanisms (see below)
Resource requests for jobs determine queuing Resource definition based on the concept of complexes (explained later) User should request resources if the defaults are not well suited for the jobs
Bookkeeping of resources within the batch system
Oct 15, 2001 SGEEE Zeuthen 6
The Sun Grid Engine ComponentsComponents of the system
Queues contain information on number of jobs and job characteristics thatare allowed on a given host. Jobs need to fit into a queue to getexecuted. Queues are bound to specific hosts.
Resources Features of hosts or queues that are known to SGE. Resourceattributes are defined in so called (global, host, queue and user defined) complexes
Projectscontain lists of users (usersets) that are working together. Therelative importance to other projects may be defined using shares.
Policies Algorithms that define, which jobs are scheduled to which queuesand how the priority of running jobs has to be set. SGEEE knowsfunctional, share based, urgency based and override policies
Shares SGEEE can use a pool of tickets to determine the importance ofjobs. The pool of tickets owned by a project/job etc. is called share
Oct 15, 2001 SGEEE Zeuthen 7
Benefits Using the SGEEE Batch System For users:
jobs get executed on the most suitable (least loaded, fastest) machine fair scheduling according to defined sharing policies no one else can overuse the system and provoke system degradation users need no knowledge of host names where their jobs can run quick access to load parameters of all managed hosts
For administrators: one time allocation of resources to users, projects, groups no manual intervention to guarantee policies reconfiguration of the running system (to adapt to changing usage
pattern) easy monitoring of hosts and jobs
Oct 15, 2001 SGEEE Zeuthen 8
Policies for the Job handling within SGEEE Within SGEEE tickets are used to distribute the workload User based functional policy
Tickets are assigned to projects, users and jobs. More tickets mean higher priority and faster execution (if concurrent jobs are running on a CPU)
Share based policy Certain fractions of the system resources (shares) can be assigned to projects
and users. Projects and users receive that shares during a configurable moving time
window (e.g. CPU usage for a month based on usage during the past month)
Deadline policy By redistributing tickets the system can assign jobs an increasing weight to
meet a certain deadline. Can be used by authorized users only
Override policy Sysadmins can give additional tickets to jobs, users or projects to temporarily
adjust their relative importance.
Oct 15, 2001 SGEEE Zeuthen 9
Classes of Hosts and Users Submit Host node that is allowed to submit jobs (qsub) and query its
status Exec Host node that is allowed to run (and submit) jobs
Admin Host node from which admin commands may be issued
Master Host node controlling all SGE activity, collecting statusinformation, keeping access control lists etc.
A certain host can have any mixture of the roles above Administrator user that is allowed to fully control SGE
Operator user with admin privileges, who is not allowed tochange the queue configuration
Owner user that is allowed to suspend jobs in queues he ownsor disable owned queues
User can manipulate only his own jobs
Oct 15, 2001 SGEEE Zeuthen 10
The Zeuthen SGEEE Installation
SGEEE built from the source with AFS support Another system (SGE with AFS) was built for the HERA-B experiment
Two separate clusters (no mix of operating systems) 95 Linux nodes in default SGEEE cell Other Linux machines (public login) used as submit hosts 17 HP-UX nodes in cell hp
A cell is a separate pool of nodes controlled by a master node
Oct 15, 2001 SGEEE Zeuthen 11
The Zeuthen SGEEE Installation
In production since 9/2001 Smooth migration from the old system
Two batch systems were running in parallel for a limited time Coexistence of old queue configuration scheme and the new one
Ongoing tuning of the new system Initial goal was to reestablish functionality of the old system Now step by step changes towards a truly homogeneous system Initially some projects were bound to subgroups of hosts
Oct 15, 2001 SGEEE Zeuthen 12
Our Queue Concept
one queue per CPU with large time limit and low priority users have to specify at least a CPU time limit (usually much smaller) Users can request other resources (memory, disk) differing from default values
optionally a second queue that gets suspended as soon as there are jobs in the first queue (idle queue)
interactive use is possible because of low batch priority relation between jobs, users and projects is respected
because of sharing policies
Oct 15, 2001 SGEEE Zeuthen 13
Complexes within SGE Complexes are containers for resource definitions Resources can be requested by a batch job
You can have hard requests that need to be fulfilled (e.g. host architecture) Soft requests are fulfilled if possible
The actual value for some resource parameters is known Amount of available main memory or disk space can be used for decisions Arbitrary "load sensors" can be written to measure resource parameters
Resources can be reserved for the current job Parameters can be made "consumable". A portion of a requested resource gets
subtracted from the value of the currently available resource parameter
The most important parameters are known to SGEEE Parameters like CPU time, virtual free memory etc. are built in already To be used some of them need to be activated in the configuration
Oct 15, 2001 SGEEE Zeuthen 14
Our Complexes Concept
Users have to specify for a job Time limit (CPU time)
Users can request for a job A certain amount of virtual and real free memory The existence of one or two scratch disks(coming soon): The available free disk space for a given scratch disk To have a guaranteed amount of disk space reserved More hardware oriented features like:
Using only machines from a subcluster (farm) Run on a specific host (not recommended)
Oct 15, 2001 SGEEE Zeuthen 15
Experiences System is easily useable from a users point of view System is highly configurable (needs some time to find the
optimum policies to implement) System is very stable
crashing jobs mostly due to failing token renewal (our plugin procedure based on arc and batchtkauth)
other failures due to missing (on purpose!) path aliases for the automounter
System adapts dynamically process priority to meet share policies or to keep up with changing policies
SGE(EE) maintainers are very active and keep implementing new ideas
quick incorporation of patches, reported bugs get fixed asap.
Oct 15, 2001 SGEEE Zeuthen 16
Advanced Use of SGEEE
Using the perl API every aspect of the batch system is accessible through the perl API the perl API is accessible after use SGE; in perl scripts there is almost no documentation but a few sample scripts in
/afs/ifh.de/user/f/friebel/public and in /afs/ifh.de/products/source/gridengine/source/experimental/perlgui
Using the load information reported by SGEEE each host reports a number of load values to the master host
(qmaster) there is a default set of load parameters that are always reported further parameters can be reported by writing load sensors qhost is a simple interface to display that information a powerful monitoring system could be built around that feature,
which is based on the "Performance Data Collection" (PDC) built in subsystem
Oct 15, 2001 SGEEE Zeuthen 17
Conclusions Ease of installation from source Access to source code Chance of integration into a monitoring system API for C and Perl Excellent load balancing mechanisms Managing the requests of concurrent groups Mechanisms for recovery from machine crashes Fallback solutions for dying daemons Weakest point is AFS integration and Token prolongation
mechanism (basically the same code as for Loadleveler and for older LSF versions)
Oct 15, 2001 SGEEE Zeuthen 18
Conclusions SGEEE has all ingredients to build a company wide batch
infrastructure Allocation of resources according to policies ranging from departmental policies
to individual user policies Dynamic adjustment of priorities for running jobs to meet policies Supports interactive jobs, array jobs, parallel jobs Can be used with Kerberos (4 and 5) and AFS
SGEEE is open source maintained by Sun Getting deeper knowledge by studying the code Can enhance the code (examples: more schedulers, tighter AFS integration,
monitoring only daemons) Code is centrally maintained by a core developer team
Could play a more important role in HEP (component of a grid environment, open industry grade batch system as recommended solution within HEPiX?)
Oct 15, 2001 SGEEE Zeuthen 19
References http://gridengine.sunsource.net/servlets/ProjectSource
Download Page for source code of SGE(EE) http://www.arl.hpc.mil/docs/grd/
lots of docs from raytheon http://supportforum.Sun.COM/gridengine/
Supportforum, Mailinglists http://hoover.hpac.tudelft.nl/cugs98cd/S98PROC/AUTHORS/
FERSTL/INDEX.HTM GRD on a Conference 1998 http://www-zeuthen.desy.de/computing/services/batch/
Zeuthen pages with URL to the reference manual http://www-zeuthen.desy.de/…/batch/sge53.pdf
The SGEEE reference manual, user and installation guide
Oct 15, 2001 SGEEE Zeuthen 20
Technical Details of SGEEE(not presented)
Submitting Jobs The graphical interface qmon Job submission and file systems Sample job script Advanced usage of qsub Abnormal job termination
Oct 15, 2001 SGEEE Zeuthen 21
Submitting Jobs Requirements for submitting jobs
have a valid token (verify with tokens), otherwise obtain a new one (klog) ensure that in your .[t]cshrc or .zshrc no commands are executed that need a
terminal (tty) (users have often a stty command in their startup scripts) you are within batch if the env variable JOB_NAME is set or if the env variable
ENVIRONMENT is set to BATCH
Submitting a job specify what resources you need (-l option) and what script should be executedqsub -l t=1:00:00 job_script in the simplest case the job script contains 1 line, the name of the executable many more options available alternatively use the graphical interface to submit jobsqmon &
Oct 15, 2001 SGEEE Zeuthen 22
The Submit Window of qmon
Oct 15, 2001 SGEEE Zeuthen 23
Job Submission and File Systems Current working directory
the directory from where the qsub command was called. STDOUT and STDERR of a job go into files that are created in $HOME. Because of quota limits and archiving policies that is not recommended.
With the -cwd option to qsub the files get created in the current working directory. For performance reasons that should be on a local file system
If cwd is in NFS space, the batch system must not use the real mount point but be translated according to /usr/SGE/default/common/sge_aliases. As every job stores the full info from sge_aliases, it is of advantage to get rid of that file and discourage the use of NFS as current working directory
If required, create your own $HOME/.sge_aliases file
Local file space (Zeuthen policies) /usr1/tmp is guaranteed to exist on all linux nodes and has typically > 10GB /data exists on some linux nodes and has typically > 15GB capacity. A job can
request the existence of /data by -l datadir $TMP[DIR] is a unique directory below /usr1/tmp, that gets erased at the end of
the job. Normal jobs should make use of that mechanism if possible
Oct 15, 2001 SGEEE Zeuthen 24
A Simple Job Script#!/bin/zsh
#$ -S /bin/zsh
#
#$ -l t=0:30:00
#$ -j y
WORKDIR=/usr1/tmp/$LOGNAME/$JOB_ID
DATADIR=/net/ilos/h1data7
echo using working directory $WORKDIR
mkdir -p $WORKDIR
cp $DATADIR/large_input $WORKDIR
cd $WORKDIR
h1_reco
cp large_out $DATADIR
if [ -s large_out = -s $DATADIR/large_out ]; then
cd; rm -r $WORKDIR
fi
otherwise the default shell would be used
the time limit for this job
Oct 15, 2001 SGEEE Zeuthen 25
Advanced Usage of qsub
Option files instead of giving qsub options on the command line, users may store those
in .sge_projects files in their $HOME or current working directories content of a sample .sge_projects file:cwd -S /usr/local/bin/perl -j y -l t=24:00:00
Array jobs SGE allows to schedule n identical jobs with one qsub call using the –t option:qsub -t 1-10 array_job_script within the script use the variable SGE_TASK_ID to select different inputs and
write to distinct output files (SGE_TASK_ID is 1...10 in the example above)
Conditional job execution jobs can be scheduled to wait for dependent jobs to successfully finish (rc=0) jobs can be submitted in hold state (needs to be released by user or operator) jobs can be told not to start before a given date start dependent jobs on the same host (using qalter -q $QUEUE ... within script)
Oct 15, 2001 SGEEE Zeuthen 26
Abnormal Job Termination Termination because of CPU limit exceeded
jobs get an XCPU signal that can be catched by the job. In that case termination procedures can be executed, before the SIGKILL signal is sent
SIGKILL will be sent a few minutes after XCPU was sent. It cannot be catched.
Restart after execution host crashes if a host crashes when a given job is running, the job will be restarted. In
that case the variable RESTARTED is set to 1 The job will be reexecuted from the beginning on any free host. If the job
can be restarted using some results achieved so far, then the variable RESTARTED can be checked. The job can be forced to be executed on the same host by inserting
qalter -q $QUEUE $JOB_ID
literally in the job script
Signaling the end of the job with the qsub option -notify a SIGUSR1 signal is sent to the job a few
minutes before the job is suspended or terminated