slurm的基本使用
最后发布时间 : 2023-11-19 20:47:57
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术语
- 资源
- GRES：Generic Resource，通用资源。
- TRES：Trackable RESources，可追踪资源。
- QOS：Quality of Service，服务质量，作业优先级。
- association：关联。可利用其实现，如用户的关联不在数据库中，这将阻止用户运行作业。该选项可以阻止用户访问无效账户。
- Partition：队列、分区。用于对计算节点、作业并行规模、作业时长、用户等进行分组管理，以合理分配资源。
state解释
| idle | 节点空闲，可接受作业 |
|---|---|
| alloacted | 该节点已经分配作业且所有核心用满，在作业释放前不能再被分配作业 |
| mix | 使用部分核心，仍可以被分配作业 |
| drain | 对应节点已经下线 |
| drng | 节点已下线但仍有作业在运行 |
squeue
adev0: squeue
JOBID PARTITION NAME USER ST TIME NODES NODELIST(REASON)
65646 batch chem mike R 24:19 2 adev[7-8]
65647 batch bio joan R 0:09 1 adev14
65648 batch math phil PD 0:00 6 (Resources)
使用squeue命令确定系统上存在的jobs，ST列表示job的状态，两个job是运行的状态（运行的缩写是R）,一个job是等待的状态（PD是等待的简写）。TIME表示该job运行了多久，使用的格式是days-hours:minutes:seconds。NODELIST(REASON)字段表示job运行在哪里，或者job仍然是pending状态的原因。等待状态典型的原因是：Resources(等待资源可用)、Priority(在优先级更高的job后面)。
日常操作
sudo su - root
scontrol update NodeName=node2 State=resume
squeue | grep smk-gene | awk '{print $1}' | xargs scancel
scontrol show node node1
NodeName=node1 Arch=x86_64 CoresPerSocket=26
CPUAlloc=0 CPUEfctv=208 CPUTot=208 CPULoad=0.88
AvailableFeatures=(null)
ActiveFeatures=(null)
Gres=(null)
NodeAddr=node1 NodeHostName=node1 Version=22.05.3
OS=Linux 5.4.0-26-generic #30-Ubuntu SMP Mon Apr 20 16:58:30 UTC 2020
RealMemory=512000 AllocMem=0 FreeMem=510881 Sockets=4 Boards=1
State=IDLE ThreadsPerCore=2 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A
Partitions=ubuntu,low,med,high
BootTime=2023-03-16T10:48:53 SlurmdStartTime=2023-03-16T10:49:52
LastBusyTime=2023-03-16T10:51:36
CfgTRES=cpu=208,mem=500G,billing=208
AllocTRES=
CapWatts=n/a
CurrentWatts=0 AveWatts=0
ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s
NodeName=node1 CPUs=208 RealMemory=512000 Boards=1 SocketsPerBoard=4 CoresPerSocket=26 ThreadsPerCore=2 State=UNKNOWN
node: free -h
total used free shared buff/cache available
Mem: 503Gi 3.2Gi 498Gi 9.0Mi 1.4Gi 497Gi
Swap: 9.3Gi 0B 9.3Gi
squeue --format="%.18i %.9P %.30j %.8u %.8T %.10M %.9l %.6D %R"
full name如果要显示更多的job名称字符，只需更改％.30J的数量即可。
资源的管理
srun -w node4 --cpus-per-task=50 --mem-per-cpu=2G sleep 1000
-w(- -nodelist)表示:在计算机节点 node 上执行;- -cpus-per-task=50表示每个 task 分配50 个线程。--mem-per-cpu=2G表示每个cpu上分配2G内存
使用scontrol查看改job
scontrol show job 578444
JobId=578444 JobName=sleep
UserId=zyd(1001) GroupId=zyd(1001) MCS_label=N/A
Priority=1 Nice=0 Account=test QOS=normal
JobState=RUNNING Reason=None Dependency=(null)
Requeue=1 Restarts=0 BatchFlag=0 Reboot=0 ExitCode=0:0
RunTime=00:00:16 TimeLimit=UNLIMITED TimeMin=N/A
SubmitTime=2023-03-16T17:56:13 EligibleTime=2023-03-16T17:56:13
AccrueTime=Unknown
StartTime=2023-03-16T17:56:13 EndTime=Unknown Deadline=N/A
PreemptEligibleTime=2023-03-16T17:56:13 PreemptTime=None
SuspendTime=None SecsPreSuspend=0 LastSchedEval=2023-03-16T17:56:13 Scheduler=Main
Partition=ubuntu AllocNode:Sid=master:167597
ReqNodeList=node4 ExcNodeList=(null)
NodeList=node4
BatchHost=node4
NumNodes=1 NumCPUs=50 NumTasks=1 CPUs/Task=50 ReqB:S:C:T=0:0:*:*
TRES=cpu=50,mem=100G,node=1,billing=50
Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=*
MinCPUsNode=50 MinMemoryCPU=2G MinTmpDiskNode=0
Features=(null) DelayBoot=00:00:00
OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null)
Command=sleep
WorkDir=/data/metagenomics/pml_nextflow
Power=
可以看到
TRES=cpu=50,mem=100G表示，可追踪的CPU有50个，由于我们设置了，每个CPU 2G内存，因此mem的值为100
srun -w node4 --mem=2G --cpus-per-task=50 sleep 1000
将
--mem-per-cpu改为--mem
JobId=578445 JobName=sleep
UserId=zyd(1001) GroupId=zyd(1001) MCS_label=N/A
Priority=1 Nice=0 Account=test QOS=normal
JobState=RUNNING Reason=None Dependency=(null)
Requeue=1 Restarts=0 BatchFlag=0 Reboot=0 ExitCode=0:0
RunTime=00:01:03 TimeLimit=UNLIMITED TimeMin=N/A
SubmitTime=2023-03-16T18:11:38 EligibleTime=2023-03-16T18:11:38
AccrueTime=Unknown
StartTime=2023-03-16T18:11:38 EndTime=Unknown Deadline=N/A
PreemptEligibleTime=2023-03-16T18:11:38 PreemptTime=None
SuspendTime=None SecsPreSuspend=0 LastSchedEval=2023-03-16T18:11:38 Scheduler=Main
Partition=ubuntu AllocNode:Sid=master:167597
ReqNodeList=node4 ExcNodeList=(null)
NodeList=node4
BatchHost=node4
NumNodes=1 NumCPUs=50 NumTasks=1 CPUs/Task=50 ReqB:S:C:T=0:0:*:*
TRES=cpu=50,mem=2G,node=1,billing=50
Socks/Node=* NtasksPerN:B:S:C=0:0:*:* CoreSpec=*
MinCPUsNode=50 MinMemoryNode=2G MinTmpDiskNode=0
Features=(null) DelayBoot=00:00:00
OverSubscribe=OK Contiguous=0 Licenses=(null) Network=(null)
Command=sleep
WorkDir=/data/metagenomics/pml_nextflow
Power=
可以看到
TRES=cpu=50,mem=2G中的mem已经变成了2G
账户配置
# 增加none和test账户并赋予相应权限
sacctmgr add account none,test Cluster=MyCluster Description="My slurm cluster" Organization="USTC"
# 增加test1用户属于test账户
sacctmgr -i add user test1 account=test
QOS：Quality of Service，服务质量，作业优先级
sacctmgr show qos format=name,priority
查看账户关联的QOS
sacctmgr show assoc
sacctmgr show assoc where name=hmli
sacctmgr show assoc format=cluster,user,qos
Usage: srun [OPTIONS(0)... [executable(0) [args(0)...]]] [ : [OPTIONS(N)...]] executable(N) [args(N)...]
Parallel run options:
-A, --account=name charge job to specified account
--acctg-freq=<datatype>=<interval> accounting and profiling sampling
intervals. Supported datatypes:
task=<interval> energy=<interval>
network=<interval> filesystem=<interval>
--bb=<spec> burst buffer specifications
--bbf=<file_name> burst buffer specification file
--bcast=<dest_path> Copy executable file to compute nodes
--bcast-exclude=<paths> Shared object directory paths to exclude
-b, --begin=time defer job until HH:MM MM/DD/YY
-c, --cpus-per-task=ncpus number of cpus required per task
--comment=name arbitrary comment
--compress[=library] data compression library used with --bcast
--container Path to OCI container bundle
--cpu-freq=min[-max[:gov]] requested cpu frequency (and governor)
-d, --dependency=type:jobid[:time] defer job until condition on jobid is satisfied
--deadline=time remove the job if no ending possible before
this deadline (start > (deadline - time[-min]))
--delay-boot=mins delay boot for desired node features
-D, --chdir=path change remote current working directory
--export=env_vars|NONE environment variables passed to launcher with
optional values or NONE (pass no variables)
-e, --error=err location of stderr redirection
--epilog=program run "program" after launching job step
-E, --preserve-env env vars for node and task counts override
command-line flags
--gres=list required generic resources
--gres-flags=opts flags related to GRES management
-H, --hold submit job in held state
-i, --input=in location of stdin redirection
-I, --immediate[=secs] exit if resources not available in "secs"
--jobid=id run under already allocated job
-J, --job-name=jobname name of job
-k, --no-kill do not kill job on node failure
-K, --kill-on-bad-exit kill the job if any task terminates with a
non-zero exit code
-l, --label prepend task number to lines of stdout/err
-L, --licenses=names required license, comma separated
-M, --clusters=names Comma separated list of clusters to issue
commands to. Default is current cluster.
Name of 'all' will submit to run on all clusters.
NOTE: SlurmDBD must up.
-m, --distribution=type distribution method for processes to nodes
(type = block|cyclic|arbitrary)
--mail-type=type notify on state change: BEGIN, END, FAIL or ALL
--mail-user=user who to send email notification for job state
changes
--mcs-label=mcs mcs label if mcs plugin mcs/group is used
--mpi=type type of MPI being used
--multi-prog if set the program name specified is the
configuration specification for multiple programs
-n, --ntasks=ntasks number of tasks to run
--nice[=value] decrease scheduling priority by value
--ntasks-per-node=n number of tasks to invoke on each node
-N, --nodes=N number of nodes on which to run (N = min[-max])
-o, --output=out location of stdout redirection
-O, --overcommit overcommit resources
--overlap Allow other steps to overlap this step
--het-group=value hetjob component allocation(s) in which to launch
application
-p, --partition=partition partition requested
--power=flags power management options
--priority=value set the priority of the job to value
--prolog=program run "program" before launching job step
--profile=value enable acct_gather_profile for detailed data
value is all or none or any combination of
energy, lustre, network or task
--propagate[=rlimits] propagate all [or specific list of] rlimits
--pty run task zero in pseudo terminal
--quit-on-interrupt quit on single Ctrl-C
-q, --qos=qos quality of service
-Q, --quiet quiet mode (suppress informational messages)
--reboot reboot block before starting job
-r, --relative=n run job step relative to node n of allocation
-s, --oversubscribe over-subscribe resources with other jobs
-S, --core-spec=cores count of reserved cores
--send-libs[=yes|no] autodetect and broadcast shared objects
--signal=[R:]num[@time] send signal when time limit within time seconds
--slurmd-debug=level slurmd debug level
--spread-job spread job across as many nodes as possible
--switches=max-switches{@max-time-to-wait}
Optimum switches and max time to wait for optimum
--task-epilog=program run "program" after launching task
--task-prolog=program run "program" before launching task
--thread-spec=threads count of reserved threads
-T, --threads=threads set srun launch fanout
-t, --time=minutes time limit
--time-min=minutes minimum time limit (if distinct)
-u, --unbuffered do not line-buffer stdout/err
--use-min-nodes if a range of node counts is given, prefer the
smaller count
-v, --verbose verbose mode (multiple -v's increase verbosity)
-W, --wait=sec seconds to wait after first task exits
before killing job
--wckey=wckey wckey to run job under
-X, --disable-status Disable Ctrl-C status feature
Constraint options:
--cluster-constraint=list specify a list of cluster-constraints
--contiguous demand a contiguous range of nodes
-C, --constraint=list specify a list of constraints
--mem=MB minimum amount of real memory
--mincpus=n minimum number of logical processors (threads)
per node
--reservation=name allocate resources from named reservation
--tmp=MB minimum amount of temporary disk
-w, --nodelist=hosts... request a specific list of hosts
-x, --exclude=hosts... exclude a specific list of hosts
-Z, --no-allocate don't allocate nodes (must supply -w)
Consumable resources related options:
--exact use only the resources requested for the step
(by default, all non-gres resources on each node
in the allocation will be used in the step)
--exclusive[=user] for job allocation, this allocates nodes in
in exclusive mode
for job steps, this is equivalent to --exact
--exclusive[=mcs] allocate nodes in exclusive mode when
cpu consumable resource is enabled
and mcs plugin is enabled (--exact implied)
or don't share CPUs for job steps
--mem-per-cpu=MB maximum amount of real memory per allocated
cpu required by the job.
--mem >= --mem-per-cpu if --mem is specified.
--resv-ports reserve communication ports
Affinity/Multi-core options: (when the task/affinity plugin is enabled)
For the following 4 options, you are
specifying the minimum resources available for
the node(s) allocated to the job.
--sockets-per-node=S number of sockets per node to allocate
--cores-per-socket=C number of cores per socket to allocate
--threads-per-core=T number of threads per core to allocate
-B --extra-node-info=S[:C[:T]] combine request of sockets per node,
cores per socket and threads per core.
Specify an asterisk (*) as a placeholder,
a minimum value, or a min-max range.
--ntasks-per-core=n number of tasks to invoke on each core
--ntasks-per-socket=n number of tasks to invoke on each socket
--cpu-bind= Bind tasks to CPUs
(see "--cpu-bind=help" for options)
--hint= Bind tasks according to application hints
(see "--hint=help" for options)
--mem-bind= Bind memory to locality domains (ldom)
(see "--mem-bind=help" for options)
GPU scheduling options:
--cpus-per-gpu=n number of CPUs required per allocated GPU
-G, --gpus=n count of GPUs required for the job
--gpu-bind=... task to gpu binding options
--gpu-freq=... frequency and voltage of GPUs
--gpus-per-node=n number of GPUs required per allocated node
--gpus-per-socket=n number of GPUs required per allocated socket
--gpus-per-task=n number of GPUs required per spawned task
--mem-per-gpu=n real memory required per allocated GPU
Help options:
-h, --help show this help message
--usage display brief usage message
Other options:
-V, --version output version information and exit