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| The resource allocation / scheduling software on the B4F Cluster is [http://en.wikipedia.org/wiki/Simple_Linux_Utility_for_Resource_Management SLURM]: '''S'''imple '''L'''inux '''U'''tility for '''R'''esource '''M'''anagement. | | The resource allocation and scheduling software on Anunna is [http://en.wikipedia.org/wiki/Simple_Linux_Utility_for_Resource_Management SLURM]: '''S'''imple '''L'''inux '''U'''tility for '''R'''esource '''M'''anagement. This page is the entry point — most topics have their own page; below is a short summary plus links. |
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| == Submitting jobs: sbatch == | | == What's on which page == |
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| === Example ===
| | * [[Partitions / Queues]] — list of partitions (<code>main</code>, <code>gpu</code>, <code>gpu_amd</code>) and how to choose one. |
| Consider this simple python3 script that should calculate Pi to 1 million digits:
| | * [[Choosing a node (constraints)]] — defaults, hardware constraints, GPU selection. |
| <source lang='python'> | | * [[Batch Jobs]] — writing sbatch scripts and submitting them, including multi-job submissions and dependencies. |
| from decimal import *
| | * [[Interactive Jobs]] — <code>sinteractive</code> and <code>salloc</code> for live shell sessions on a compute node. |
| D=Decimal
| | * [[Array jobs]] — running the same script many times with a varying parameter. |
| getcontext().prec=10000000
| | * [[Monitoring Jobs]] — <code>squeue</code>, <code>scontrol</code>, <code>sstat</code>, <code>sacct</code>, <code>node_usage_graph</code>. |
| 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))
| | * [[Cancelling Jobs]] — <code>scancel</code>. |
| print(str(p)[:10000002])
| | * [[Reservations]] — booking nodes in advance for events. |
| </source> | |
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| === Loading modules === | | == Quality of Service == |
| 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:
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| module avail
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| In the list you should note that python3 is indeed available to be loaded, which then can be loaded with the following command:
| | When submitting a job, you may optionally assign a different Quality of Service (QoS) to it: |
| module load python/3.3.3
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| === Batch script ===
| | <syntaxhighlight lang="bash"> |
| The following shell/slurm script can then be used to schedule the job using the sbatch command:
| | #SBATCH --qos=std |
| <source lang='bash'> | | </syntaxhighlight> |
| #!/bin/bash
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| #SBATCH --time=1200 | |
| #SBATCH --ntasks=1
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| #SBATCH --output=output_%j.txt
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| #SBATCH --error=error_output_%j.txt
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| #SBATCH --job-name=calc_pi.py
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| #SBATCH --partition=ABGC
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| #SBATCH --mail-type=ALL
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| #SBATCH --mail-user=email@org.nl
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| | The QoS values configured on Anunna: |
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| time python3 calc_pi.py
| | * '''std''' (priority 10) — the default. Use this unless you have a specific reason to pick another. |
| </source>
| | * '''low''' (priority 1) — reduced priority, but limited to 8 hours per job so a flood of low-priority jobs cannot lock up the cluster. |
| Explanation of used SBATCH parameters:
| | * '''high''' (priority 20) — higher priority than <code>std</code>. More expensive — see [[Tariffs]]. |
| <source lang='bash'>
| | * '''interactive''' (priority 100) — the highest priority, exclusively for immediate-running interactive jobs. You may not submit many or large jobs at this QoS. |
| #SBATCH --time=1200
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| </source>
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| 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.
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| <source lang='bash'>
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| #SBATCH --ntasks=1
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| </source>
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| 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.
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| <source lang='bash'>
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| #SBATCH --output=output_%j.txt
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| </source>
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| 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.
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| <source lang='bash'>
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| #SBATCH --error=error_output_%j.txt
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| </source>
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| 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.
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| <source lang='bash'>
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| #SBATCH --job-name=calc_pi.py
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| </source>
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| 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.
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| <source lang='bash'>
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| #SBATCH --partition=research
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| </source> | |
| Request a specific partition for the resource allocation. It is prefered to use your organizations partition.
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| <source lang='bash'>
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| #SBATCH --mail-type=ALL
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| </source>
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| 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.
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| <source lang='bash'>
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| #SBATCH --mail-user=email@org.nl
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| </source>
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| Email address to use.
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| === Submitting ===
| | Jobs can in principle be restarted and rescheduled if a higher-priority job needs cluster resources, but at the time of writing this preemption is not actually configured. |
| The script, assuming it was named 'run_calc_pi.sh', can then be posted using the following command:
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| <source lang='bash'>
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| sbatch run_calc_pi.sh
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| </source>
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| === Submitting multiple jobs === | | == Running MPI 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:
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| <source lang='bash'>for i in `seq 1 10`; do echo $i; sbatch runscript_$i.sh;done
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| </source>
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| == monitoring submitted jobs: squeue ==
| | For multi-node MPI workloads see [[MPI on B4F cluster | MPI on Anunna]]. |
| Once a job is submitted, the status can be monitored using the <code>squeue</code> command. The <code>squeue</code> command has a number of parameters for monitoring specific properties of the jobs such as time limit.
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| === Generic monitoring of all running jobs === | | == See also == |
| <source lang='bash'>
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| squeue
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| </source>
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| 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:
| | * [[Partitions / Queues]] |
| JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
| | * [[Choosing a node (constraints)]] |
| 3396 ABGC BOV-WUR- megen002 R 27:26 1 node004
| | * [[Batch Jobs]] |
| 3397 ABGC BOV-WUR- megen002 R 27:26 1 node005
| | * [[Interactive Jobs]] |
| 3398 ABGC BOV-WUR- megen002 R 27:26 1 node006
| | * [[Array jobs]] |
| 3399 ABGC BOV-WUR- megen002 R 27:26 1 node007
| | * [[Monitoring Jobs]] |
| 3400 ABGC BOV-WUR- megen002 R 27:26 1 node008
| | * [[Cancelling Jobs]] |
| 3401 ABGC BOV-WUR- megen002 R 27:26 1 node009
| | * [[Reservations]] |
| 3385 research BOV-WUR- megen002 R 44:38 1 node049
| | * [[Tariffs | Costs associated with resource usage]] |
| 3386 research BOV-WUR- megen002 R 44:38 1 node050
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| 3387 research BOV-WUR- megen002 R 44:38 1 node051
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| 3388 research BOV-WUR- megen002 R 44:38 1 node052
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| 3389 research BOV-WUR- megen002 R 44:38 1 node053
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| 3390 research BOV-WUR- megen002 R 44:38 1 node054
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| 3391 research BOV-WUR- megen002 R 44:38 3 node[049-051]
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| 3392 research BOV-WUR- megen002 R 44:38 3 node[052-054]
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| 3393 research BOV-WUR- megen002 R 44:38 1 node001
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| 3394 research BOV-WUR- megen002 R 44:38 1 node002
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| 3395 research BOV-WUR- megen002 R 44:38 1 node003
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| === Monitoring time limit set for a specific job === | | == External links == |
| 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 <code>squeue</code> command.
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| <source lang='bash'>
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| squeue -l -j 3532
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| </source>
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| Information similar to the following should appear:
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| Fri Nov 29 15:41:00 2013
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| JOBID PARTITION NAME USER STATE TIME TIMELIMIT NODES NODELIST(REASON)
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| 3532 ABGC BOV-WUR- megen002 RUNNING 2:47:03 3-08:00:00 1 node054
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| === Query a specific active job: scontrol ===
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| Show all the details of a currently active job, so not a completed job.
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| <source lang='bash'>
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| nfs01 ~]$ scontrol show jobid 4241
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| JobId=4241 Name=WB20F06
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| UserId=megen002(16795409) GroupId=domain users(16777729)
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| Priority=1 Account=(null) QOS=normal
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| JobState=RUNNING Reason=None Dependency=(null)
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| Requeue=1 Restarts=0 BatchFlag=1 ExitCode=0:0
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| RunTime=02:55:25 TimeLimit=3-08:00:00 TimeMin=N/A
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| SubmitTime=2013-12-09T13:37:29 EligibleTime=2013-12-09T13:37:29
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| StartTime=2013-12-09T13:37:29 EndTime=2013-12-12T21:37:29
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| PreemptTime=None SuspendTime=None SecsPreSuspend=0
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| Partition=research AllocNode:Sid=nfs01:21799
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| ReqNodeList=(null) ExcNodeList=(null)
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| NodeList=node023
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| BatchHost=node023
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| NumNodes=1 NumCPUs=4 CPUs/Task=1 ReqS:C:T=*:*:*
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| MinCPUsNode=1 MinMemoryNode=0 MinTmpDiskNode=0
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| Features=(null) Gres=(null) Reservation=(null)
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| Shared=OK Contiguous=0 Licenses=(null) Network=(null)
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| Command=/lustre/scratch/WUR/ABGC/...
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| WorkDir=/lustre/scratch/WUR/ABGC/...
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| </source>
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| == Removing jobs from a list: scancel ==
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| 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:
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| <source lang='bash'>
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| scancel 3401
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| </source>
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| == Allocating resources interactively: sallocate ==
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| < text here>
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| == Get overview of past and current jobs: sacct ==
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| To do some accounting on past and present jobs, and to see whether they ran to completion, you can do:
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| <source lang='bash'>
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| sacct
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| </source>
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| This should provide information similar to the following:
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| JobID JobName Partition Account AllocCPUS State ExitCode
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| ------------ ---------- ---------- ---------- ---------- ---------- --------
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| 3385 BOV-WUR-58 research 12 COMPLETED 0:0
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| 3385.batch batch 1 COMPLETED 0:0
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| 3386 BOV-WUR-59 research 12 CANCELLED+ 0:0
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| 3386.batch batch 1 CANCELLED 0:15
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| 3528 BOV-WUR-59 ABGC 16 RUNNING 0:0
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| 3529 BOV-WUR-60 ABGC 16 RUNNING 0:0
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| == Running MPI jobs on B4F cluster ==
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| < text here >
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| == Understanding which resources are available to you: sinfo ==
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| 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.
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| <source lang='bash'>
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| sinfo
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| </source>
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| PARTITION AVAIL TIMELIMIT NODES STATE NODELIST
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| student* up infinite 12 down* node[043-048,055-060]
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| student* up infinite 50 idle fat[001-002],node[001-042,049-054]
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| research up infinite 12 down* node[043-048,055-060]
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| research up infinite 50 idle fat[001-002],node[001-042,049-054]
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| ABGC up infinite 12 down* node[043-048,055-060]
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| ABGC up infinite 50 idle fat[001-002],node[001-042,049-054]
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| == See also ==
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| * [[B4F_cluster | B4F Cluster]]
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| * [[BCM_on_B4F_cluster | BCM on B4F cluster]]
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| * [[Setting_up_Python_virtualenv | Setting up and using a virtual environment for Python3 ]]
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| == External links ==
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| * [http://slurm.schedmd.com Slurm official documentation] | | * [http://slurm.schedmd.com Slurm official documentation] |
| * [http://en.wikipedia.org/wiki/Simple_Linux_Utility_for_Resource_Management Slurm on Wikipedia] | | * [http://en.wikipedia.org/wiki/Simple_Linux_Utility_for_Resource_Management Slurm on Wikipedia] |
| * [http://www.youtube.com/watch?v=axWffyrk3aY Slurm Tutorial on Youtube]
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