Using Slurm: Difference between revisions

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<source lang='bash'>#!/bin/bash
<source lang='bash'>#!/bin/bash
JOB1=$(sbatch job_1.sh| rev | cut -d ' ' -f 1 | rev)
JOB1=$(sbatch job_1.sh| rev | cut -d ' ' -f 1 | rev) #Get me the last space-separated element


if ! [ "z$JOB1" == "z" ] ; then
if ! [ "z$JOB1" == "z" ] ; then
   echo "First job submitted as $JOB1"
   echo "First job submitted as jobid $JOB1"
   JOB2=$(sbatch --dependency=afterany:$JOB1 job_2.sh| rev | cut -d ' ' -f 1 | rev)
   JOB2=$(sbatch --dependency=afterany:$JOB1 job_2.sh| rev | cut -d ' ' -f 1 | rev)


   if ! [ "z$JOB2" == "z" ] ; then
   if ! [ "z$JOB2" == "z" ] ; then
   echo "Second job submitted as $JOB2, following $JOB1"
   echo "Second job submitted as jobid $JOB2, following $JOB1"
   JOB3=$(sbatch --dependency=afterany:$JOB2 job_3.sh| rev | cut -d ' ' -f 1 | rev)
   JOB3=$(sbatch --dependency=afterany:$JOB2 job_3.sh| rev | cut -d ' ' -f 1 | rev)


   if ! [ "z$JOB3" == "z" ] ; then
   if ! [ "z$JOB3" == "z" ] ; then
   echo "Third job submitted as $JOB3, following $JOB2"
   echo "Third job submitted as jobid $JOB3, following $JOB2"


   fi
   fi
Line 105: Line 105:
fi
fi
</source>
</source>


=== Submitting array jobs ===
=== Submitting array jobs ===

Revision as of 13:42, 20 July 2018

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


Queues and defaults

Queues

Every organization has 3 queues (in slurm called partitions) : a high, a standard and a low priority queue.
The High queue provides the highest priority to jobs (20) then the standard queue (10). In the low priority queue (0)
jobs will be resubmitted if a job with higer priority needs cluster resources and those resoruces are occupied by a Low queue jobs. To find out which queues your account has been authorized for, type sinfo: <source lang='bash'> PARTITION AVAIL TIMELIMIT NODES STATE NODELIST ABGC_High up infinite 12 down* node[043-048,055-060] ABGC_High up infinite 6 mix fat[001-002],node[002-005] ABGC_High up infinite 44 idle node[001,006-042,049-054] ABGC_Std up infinite 12 down* node[043-048,055-060] ABGC_Std up infinite 6 mix fat[001-002],node[002-005] ABGC_Std up infinite 44 idle node[001,006-042,049-054] ABGC_Low up infinite 12 down* node[043-048,055-060] ABGC_Low up infinite 6 mix fat[001-002],node[002-005] ABGC_Low up infinite 44 idle node[001,006-042,049-054] </source>

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 100MB 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

Main Article: Creating a sbatch 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 --comment=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_Std
  10. SBATCH --mail-type=ALL
  11. SBATCH --mail-user=email@org.nl


time python3 calc_pi.py </source>

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 (simple)

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>

Submitting multiple jobs (complex)

Lets's say you have three job scripts that depend on each other:

<source lang='bash'>job_1.sh</source> <source lang='bash'>job_2.sh</source> <source lang='bash'>job_3.sh</source>

You can create a script to simultaneously submit each job with a dependency on each other:

<source lang='bash'>#!/bin/bash JOB1=$(sbatch job_1.sh| rev | cut -d ' ' -f 1 | rev) #Get me the last space-separated element

if ! [ "z$JOB1" == "z" ] ; then 

 echo "First job submitted as jobid $JOB1"
 JOB2=$(sbatch --dependency=afterany:$JOB1 job_2.sh| rev | cut -d ' ' -f 1 | rev)

 if ! [ "z$JOB2" == "z" ] ; then
 echo "Second job submitted as jobid $JOB2, following $JOB1"
 JOB3=$(sbatch --dependency=afterany:$JOB2 job_3.sh| rev | cut -d ' ' -f 1 | rev)

 if ! [ "z$JOB3" == "z" ] ; then
 echo "Third job submitted as jobid $JOB3, following $JOB2"

 fi
fi

fi </source>

Submitting array jobs

<source lang='bash'>

  1. SBATCH --array=0-10%4

</source> SLURM allows you to submit multiple jobs using the same template. Further information about this can be found here.

Using /tmp

There is a local disk of ~300G that can be used to temporarily stage some of your workload attached to each node. This is free to use, but please remember to clean up your data after usage.

In order to be sure that you're able to use space in /tmp, you can add <source lang='bash'>

  1. SBATCH --tmp=<required size>

</source> To your sbatch script. This will prevent your job from being run on nodes where there is no free space, or it's aimed to be used by another job at the same time.

Monitoring submitted jobs

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>

Check on a pending job

A submitted job could result in a pending state when there are not enough resources available to this job. In this example I sumbit a job, check the status and after finding out is it pending I'll check when is probably will start. <source lang='bash'> [@nfs01 jobs]$ sbatch hpl_student.job 

Submitted batch job 740338

[@nfs01 jobs]$ squeue -l -j 740338 

Fri Feb 21 15:32:31 2014
 JOBID PARTITION     NAME     USER    STATE       TIME TIMELIMIT  NODES NODELIST(REASON)
740338 ABGC_Stud HPLstude bohme999  PENDING       0:00 1-00:00:00      1 (ReqNodeNotAvail)

[@nfs01 jobs]$ squeue --start -j 740338 

 JOBID PARTITION     NAME     USER  ST           START_TIME  NODES NODELIST(REASON)
740338 ABGC_Stud HPLstude bohme999  PD  2014-02-22T15:31:48      1 (ReqNodeNotAvail)

</source> So it seems this job will problably start the next day, but's thats no guarantee it will start indeed.

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: salloc

It's possible to set up an interactive session using salloc. Run salloc as follows: <source lang='bash'> salloc -p <partition, say, ABGC_Low> </source> And because of the magic of SallocDefaultCommand, you will immediately be transported to a new prompt.

Here, run 'hostname' to see which node your shell has been transported to.

If you don't want your shell to be transported but want a new remote shell, do: <source lang='bash'> salloc -p ABGC_Low $SHELL </source> Now your shell will stay on nfs01, but you can do: <source lang='bash'> srun <command> & </source> To submit tasks to this new shell!

Be aware that the time limit of salloc is default 1 hour. If you intend to run jobs for longer times than this, you need to edit the settings for it. See: https://computing.llnl.gov/linux/slurm/salloc.html

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,comment,partition,ntasks,alloccpus,elapsed,state,exitcode -j 4220 </source> This should provide information about job id 4220: 

      JobID    JobName    Comment   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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