Using Slurm

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The resource allocation / scheduling software on the B4F Cluster is SLURM: Simple Linux Utility for Resource Management.


Queues and defaults

Queues

Every organization has 2 queues (in slurm called partitions) : a production and a research queue. The production queue provides a higher priority to jobs (20) then the research queue (10). To find out which queues your account has been authorized for, type sinfo: <source lang='bash'> PARTITION AVAIL TIMELIMIT NODES STATE NODELIST ABGC_Production up infinite 12 down* node[043-048,055-060] ABGC_Production up infinite 6 mix fat[001-002],node[002-005] ABGC_Production up infinite 44 idle node[001,006-042,049-054] ABGC_Research up infinite 12 down* node[043-048,055-060] ABGC_Research up infinite 6 mix fat[001-002],node[002-005] ABGC_Research up infinite 44 idle node[001,006-042,049-054] ABGC_Student up infinite 12 down* node[043-048,055-060] ABGC_Student up infinite 6 mix fat[001-002],node[002-005] ABGC_Student up infinite 44 idle node[001,006-042,049-054] </source> WUR organizations also do have a Student queue. Jobs in this queue will be resubmitted if a job with higer priority needs cluster resources and those resoruces are accupied by a Student queue jobs.

Defaults

There is no default queue, so you need to specify which queue to use when submitting a job.
The default run time for a job is 1 hour!
Default memory limit is 1024MB per node!

Submitting jobs: sbatch

Example

Consider this simple python3 script that should calculate Pi to 1 million digits: <source lang='python'> from decimal import * D=Decimal getcontext().prec=10000000 p=sum(D(1)/16**k*(D(4)/(8*k+1)-D(2)/(8*k+4)-D(1)/(8*k+5)-D(1)/(8*k+6))for k in range(411)) print(str(p)[:10000002]) </source>

Loading modules

In order for this script to run, the first thing that is needed is that Python3, which is not the default Python version on the cluster, is load into your environment. Availability of (different versions of) software can be checked by the following command: 

 module avail

In the list you should note that python3 is indeed available to be loaded, which then can be loaded with the following command: 

 module load python/3.3.3

Batch script

The following shell/slurm script can then be used to schedule the job using the sbatch command: <source lang='bash'>

  1. !/bin/bash
  2. SBATCH --account=773320000
  3. SBATCH --time=1200
  4. SBATCH --mem=2048
  5. SBATCH --ntasks=1
  6. SBATCH --output=output_%j.txt
  7. SBATCH --error=error_output_%j.txt
  8. SBATCH --job-name=calc_pi.py
  9. SBATCH --partition=ABGC
  10. SBATCH --mail-type=ALL
  11. SBATCH --mail-user=email@org.nl


time python3 calc_pi.py </source> Explanation of used SBATCH parameters: <source lang='bash'>

  1. SBATCH --account=773320000

</source> Charge resources used by this job to specified account. The account is an arbitrary string. The account name may be changed after job submission using the scontrol command. For WUR users a projectnumber or KTP number would be advisable. <source lang='bash'>

  1. SBATCH --time=1200

</source> A time limit of zero requests that no time limit be imposed. Acceptable time formats include "minutes", "minutes:seconds", "hours:minutes:seconds", "days-hours", "days-hours:minutes" and "days-hours:minutes:seconds". So in this example the job will run for a maximum of 1200 minutes.

<source lang='bash'>

  1. SBATCH --mem=2048

</source> SLURM imposes a memory limit on each job. By default, it is deliberately relatively small — 1024 MB per node. If your job uses more than that, you’ll get an error that your job Exceeded job memory limit. To set a larger limit, add to your job submission: <source lang='bash'>

  1. SBATCH --mem X

</source>

where X is the maximum amount of memory your job will use per node, in MB. The larger your working data set, the larger this needs to be, but the smaller the number the easier it is for the scheduler to find a place to run your job. To determine an appropriate value, start relatively large (job slots on average have about 4000 MB per core, but that’s much larger than needed for most jobs) and then use sacct to look at how much your job is actually using or used: <source lang='bash'> $ sacct -o MaxRSS -j JOBID </source> where JOBID is the one you’re interested in. The number is in KB, so divide by 1024 to get a rough idea of what to use with –mem (set it to something a little larger than that, since you’re defining a hard upper limit). If your job completed long in the past you may have to tell sacct to look further back in time by adding a start time with -S YYYY-MM-DD. Note that for parallel jobs spanning multiple nodes, this is the maximum memory used on any one node; if you’re not setting an even distribution of tasks per node (e.g. with –ntasks-per-node), the same job could have very different values when run at different times.

<source lang='bash'>

  1. SBATCH --ntasks=1

</source> sbatch does not launch tasks, it requests an allocation of resources and submits a batch script. This option advises the SLURM controller that job steps run within the allocation will launch a maximum of number tasks and to provide for sufficient resources. The default is one task per node, but note that the --cpus-per-task option will change this default.

When requesting multiple tasks, you may or may not want the job to be partitioned among multiple nodes. You can specify the minimum number of nodes using the -N or --node flag. If you provide only one number, this will be minimum and maximum at the same time. For instance: <source lang='bash'>

  1. SBATCH --nodes=1

</source> This should force your job to be scheduled to a single node.

Because the cluster has a hybrid configuration, i.e. normal and fat nodes, it may be prudent to schedule your job specifically for one or the other node type, depending for instance on memory requirements. This can be done by using the -C or --constraints flag. <source lang='bash'>

  1. SBATCH --constraint=normalmem

</source> The example above will result in jobs being scheduled to the regular compute nodes. By using largemem as option the job will specifically be scheduled to one of the fat nodes.

<source lang='bash'>

  1. SBATCH --output=output_%j.txt

</source> Instruct SLURM to connect the batch script's standard output directly to the file name specified in the "filename pattern". By default both standard output and standard error are directed to a file of the name "slurm-%j.out", where the "%j" is replaced with the job allocation number. See the --input option for filename specification options. <source lang='bash'>

  1. SBATCH --error=error_output_%j.txt

</source> Instruct SLURM to connect the batch script's standard error directly to the file name specified in the "filename pattern". By default both standard output and standard error are directed to a file of the name "slurm-%j.out", where the "%j" is replaced with the job allocation number. See the --input option for filename specification options. <source lang='bash'>

  1. SBATCH --job-name=calc_pi.py

</source> Specify a name for the job allocation. The specified name will appear along with the job id number when querying running jobs on the system. The default is the name of the batch script, or just "sbatch" if the script is read on sbatch's standard input. <source lang='bash'>

  1. SBATCH --partition=research

</source> Request a specific partition for the resource allocation. It is prefered to use your organizations partition. <source lang='bash'>

  1. SBATCH --mail-type=ALL

</source> Notify user by email when certain event types occur. Valid type values are BEGIN, END, FAIL, REQUEUE, and ALL (any state change). The user to be notified is indicated with --mail-user. <source lang='bash'>

  1. SBATCH --mail-user=email@org.nl

</source> Email address to use.

Submitting

The script, assuming it was named 'run_calc_pi.sh', can then be posted using the following command: <source lang='bash'> sbatch run_calc_pi.sh </source>

Submitting multiple jobs

Assuming there are 10 job scripts, name runscript_1.sh through runscript_10.sh, all these scripts can be submitted using the following line of shell code: <source lang='bash'>for i in `seq 1 10`; do echo $i; sbatch runscript_$i.sh;done </source>

monitoring submitted jobs: squeue

Once a job is submitted, the status can be monitored using the squeue command. The squeue command has a number of parameters for monitoring specific properties of the jobs such as time limit.

Generic monitoring of all running jobs

<source lang='bash'> 

 squeue

</source>

You should then get a list of jobs that are running at that time on the cluster, for the example on how to submit using the 'sbatch' command, it may look like so: 

   JOBID PARTITION     NAME     USER  ST       TIME  NODES NODELIST(REASON)
  3396      ABGC BOV-WUR- megen002   R      27:26      1 node004
  3397      ABGC BOV-WUR- megen002   R      27:26      1 node005
  3398      ABGC BOV-WUR- megen002   R      27:26      1 node006
  3399      ABGC BOV-WUR- megen002   R      27:26      1 node007
  3400      ABGC BOV-WUR- megen002   R      27:26      1 node008
  3401      ABGC BOV-WUR- megen002   R      27:26      1 node009
  3385  research BOV-WUR- megen002   R      44:38      1 node049
  3386  research BOV-WUR- megen002   R      44:38      1 node050
  3387  research BOV-WUR- megen002   R      44:38      1 node051
  3388  research BOV-WUR- megen002   R      44:38      1 node052
  3389  research BOV-WUR- megen002   R      44:38      1 node053
  3390  research BOV-WUR- megen002   R      44:38      1 node054
  3391  research BOV-WUR- megen002   R      44:38      3 node[049-051]
  3392  research BOV-WUR- megen002   R      44:38      3 node[052-054]
  3393  research BOV-WUR- megen002   R      44:38      1 node001
  3394  research BOV-WUR- megen002   R      44:38      1 node002
  3395  research BOV-WUR- megen002   R      44:38      1 node003

Monitoring time limit set for a specific job

The default time limit is set at one hour. Estimated run times need to be specified when running jobs. To see what the time limit is that is set for a certain job, this can be done using the squeue command. <source lang='bash'> squeue -l -j 3532 </source> Information similar to the following should appear: 

 Fri Nov 29 15:41:00 2013
  JOBID PARTITION     NAME     USER    STATE       TIME TIMELIMIT  NODES NODELIST(REASON)
  3532      ABGC BOV-WUR- megen002  RUNNING    2:47:03 3-08:00:00      1 node054

Query a specific active job: scontrol

Show all the details of a currently active job, so not a completed job. <source lang='bash'> nfs01 ~]$ scontrol show jobid 4241 JobId=4241 Name=WB20F06 

  UserId=megen002(16795409) GroupId=domain users(16777729)
  Priority=1 Account=(null) QOS=normal
  JobState=RUNNING Reason=None Dependency=(null)
  Requeue=1 Restarts=0 BatchFlag=1 ExitCode=0:0
  RunTime=02:55:25 TimeLimit=3-08:00:00 TimeMin=N/A
  SubmitTime=2013-12-09T13:37:29 EligibleTime=2013-12-09T13:37:29
  StartTime=2013-12-09T13:37:29 EndTime=2013-12-12T21:37:29
  PreemptTime=None SuspendTime=None SecsPreSuspend=0
  Partition=research AllocNode:Sid=nfs01:21799
  ReqNodeList=(null) ExcNodeList=(null)
  NodeList=node023
  BatchHost=node023
  NumNodes=1 NumCPUs=4 CPUs/Task=1 ReqS:C:T=*:*:*
  MinCPUsNode=1 MinMemoryNode=0 MinTmpDiskNode=0
  Features=(null) Gres=(null) Reservation=(null)
  Shared=OK Contiguous=0 Licenses=(null) Network=(null)
  Command=/lustre/scratch/WUR/ABGC/...
  WorkDir=/lustre/scratch/WUR/ABGC/...

</source>

Removing jobs from a list: scancel

If for some reason you want to delete a job that is either in the queue or already running, you can remove it using the 'scancel' command. The 'scancel' command takes the jobid as a parameter. For the example above, this would be done using the following code: <source lang='bash'> scancel 3401 </source>

Allocating resources interactively: sallocate

< text here>

Get overview of past and current jobs: sacct

To do some accounting on past and present jobs, and to see whether they ran to completion, you can do: <source lang='bash'> sacct </source> This should provide information similar to the following: 

        JobID    JobName  Partition    Account  AllocCPUS      State ExitCode 
 ------------ ---------- ---------- ---------- ---------- ---------- -------- 
 3385         BOV-WUR-58   research                    12  COMPLETED      0:0 
 3385.batch        batch                                1  COMPLETED      0:0 
 3386         BOV-WUR-59   research                    12 CANCELLED+      0:0 
 3386.batch        batch                                1  CANCELLED     0:15 
 3528         BOV-WUR-59       ABGC                    16    RUNNING      0:0 
 3529         BOV-WUR-60       ABGC                    16    RUNNING      0:0

Or in more detail for a specific job: <source lang='bash'> sacct --format=jobid,jobname,account,partition,ntasks,alloccpus,elapsed,state,exitcode -j 4220 </source> This should provide information about job id 4220: 

      JobID    JobName    Account  Partition   NTasks  AllocCPUS    Elapsed      State ExitCode 
 ------------ ---------- ---------- ---------- -------- ---------- ---------- ---------- -------- 
 4220         PreProces+              research                   3   00:30:52  COMPLETED      0:0 
 4220.batch        batch                              1          1   00:30:52  COMPLETED      0:0

Job Status Codes

Typically your job will be either in the Running state of PenDing state. However here is a breakdown of all the states that your job could be in.

Code State Description
CA CANCELLED Job was explicitly cancelled by the user or system administrator. The job may or may not have been initiated.
CD COMPLETED Job has terminated all processes on all nodes.
CF CONFIGURING Job has been allocated resources, but are waiting for them to become ready for use (e.g. booting).
CG COMPLETING Job is in the process of completing. Some processes on some nodes may still be active.
F FAILED Job terminated with non-zero exit code or other failure condition.
NF NODE_FAIL Job terminated due to failure of one or more allocated nodes.
PD PENDING Job is awaiting resource allocation.
R RUNNING Job currently has an allocation.
S SUSPENDED Job has an allocation, but execution has been suspended.
TO TIMEOUT Job terminated upon reaching its time limit.

Running MPI jobs on B4F cluster

Main article: MPI on B4F Cluster < text here >

Understanding which resources are available to you: sinfo

By using the 'sinfo' command you can retrieve information on which 'Partitions' are available to you. A 'Partition' using SLURM is similar to the 'queue' when submitting using the Sun Grid Engine ('qsub'). The different Partitions grant different levels of resource allocation. Not all defined Partitions will be available to any given person. E.g., Master students will only have the Student Partition available, researchers at the ABGC will have 'student', 'research', and 'ABGC' partitions available. The higher the level of resource allocation, though, the higher the cost per compute-hour. The default Partition is the 'student' partition. A full list of Partitions can be found from the Bright Cluster Manager webpage.

<source lang='bash'> sinfo </source> 

 PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
 student*     up   infinite     12  down* node[043-048,055-060]
 student*     up   infinite     50   idle fat[001-002],node[001-042,049-054]
 research     up   infinite     12  down* node[043-048,055-060]
 research     up   infinite     50   idle fat[001-002],node[001-042,049-054]
 ABGC         up   infinite     12  down* node[043-048,055-060]
 ABGC         up   infinite     50   idle fat[001-002],node[001-042,049-054]

See also

External links

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