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Centos7集群上搭建slurm作业管理系统

2020-11-06
cndaqiang
Linux  Slurm  Centos
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参考

Ubuntu 18.04/Mint 19 单机安装Slurm

从0搭建Centos7 计算集群

slurm安装配置

注意

  • munge完全可以使用默认的munge账户执行,不用像其他教程非要用slurm去启动munge

环境

按照从0搭建Centos7 计算集群搭建好NIS,安装EPEL仓库,关闭Selinux,NFS共享(单机时不需要)

yum -y install python
yum -y install python3
yum -y install epel-release
yum -y install gtk2
yum -y install gtk2-devel
yum -y install munge
yum -y install munge-devel
yum -y install polkit
systemctl start polkit

把/usr/local目录添加到环境变量,后期slurm安装和配置都在这里,后面如果指定slurm安装位置则更改此处

mkdir /usr/local/etc
echo "
#slurm
USRLOCAL=/usr/local
export LD_LIBRARY_PATH=\${USRLOCAL}/lib:\$LD_LIBRARY_PATH
export LIBRARY_PATH=\${USRLOCAL}/lib:\$LIBRARY_PATH
export LIBRARY_PATH=\${USRLOCAL}/lib64:\$LIBRARY_PATH
export C_INCLUDE_PATH=\${USRLOCAL}/include:\$C_INCLUDE_PATH
export PATH=\${USRLOCAL}/bin:\$PATH
export PATH=\${USRLOCAL}/sbin:\$PATH
" >> /etc/profile

安装

munge

生成密钥,并复制到所有节点

[root@master source]# /usr/sbin/create-munge-key 
Generating a pseudo-random key using /dev/urandom completed.
[root@master source]# scp /etc/munge/munge.key node8:/etc/munge

创建运行目录

chown munge:munge /etc/munge
chown munge:munge /var/run/munge
chown munge:munge /var/lib/munge
chown munge:munge /var/log/munge
chown munge:munge /etc/munge/munge.key

配置服务

vi /usr/lib/systemd/system/munge.service

内容

[Unit]
Description=MUNGE authentication service 
Documentation=man:munged(8)
After=network.target
After=syslog.target
After=time-sync.target

[Service]
Type=forking
ExecStart=/usr/sbin/munged --syslog
PIDFile=/var/run/munge/munged.pid
User=munge
Group=munge
Restart=on-abort
ExecStartPre=-/usr/bin/mkdir -m 0755 -p /var/log/munge
ExecStartPre=-/usr/bin/chown -R munge:munge /var/log/munge
ExecStartPre=-/usr/bin/mkdir -m 0755 -p /var/run/munge
ExecStartPre=-/usr/bin/chown -R munge:munge /var/run/munge

[Install]
WantedBy=multi-user.target

生效

systemctl daemon-reload

启用

[root@master ~]# systemctl start munge
[root@master ~]# systemctl status munge
[root@client01 ~]# systemctl status munge
● munge.service - MUNGE authentication service
   Loaded: loaded (/usr/lib/systemd/system/munge.service; enabled; vendor preset: disabled)
   Active: active (running) since Sat 2020-11-07 11:58:51 CST; 10min ago
     Docs: man:munged(8)
  Process: 4684 ExecStart=/usr/sbin/munged --syslog (code=exited, status=0/SUCCESS)
  Process: 4660 ExecStartPre=/usr/bin/chown -R munge:munge /var/run/munge (code=exited, status=0/SUCCESS)
  Process: 4609 ExecStartPre=/usr/bin/mkdir -m 0755 -p /var/run/munge (code=exited, status=0/SUCCESS)
  Process: 4588 ExecStartPre=/usr/bin/chown -R munge:munge /var/log/munge (code=exited, status=1/FAILURE)
  Process: 4546 ExecStartPre=/usr/bin/mkdir -m 0755 -p /var/log/munge (code=exited, status=0/SUCCESS)
 Main PID: 4724 (munged)
    Tasks: 4
   Memory: 672.0K
   CGroup: /system.slice/munge.service
           └─4724 /usr/sbin/munged --syslog

Nov 07 11:58:51 client01 munged[4724]: Found 3 users with supplementary groups in 0.003 seconds

设置slurm账户权限

[root@master source]# useradd slurm
[root@master source]# passwd slurm
#NIS同步更新账户
[root@master source]# make -C /var/yp

slurm运行目录

rm -rf  /var/spool/slurm-llnl
mkdir /var/spool/slurm-llnl
chown -R slurm.slurm /var/spool/slurm-llnl
rm -rf /var/run/slurm-llnl/
mkdir /var/run/slurm-llnl/
chown -R slurm.slurm /var/run/slurm-llnl/

编译安装slurm

cd /opt/source/
#从https://download.schedmd.com/slurm/下载最新版即可
wget https://download.schedmd.com/slurm/slurm-20.11.0-0rc1.tar.bz2
tar -jxvf slurm-20.11.0-0rc1.tar.bz2 
cd slurm-20.11.0-0rc1/
./configure #默认安装到/usr/local
make -j90 #注意需要python3
make install

复制系统服务

cp etc/{slurmctld.service,slurmdbd.service,slurmd.service} /usr/lib/systemd/system

修改配置文件

根据默认设置

[root@master slurm-20.11.0-0rc1]# cat /usr/lib/systemd/system/slurmctld.service 
[Unit]
Description=Slurm controller daemon
After=network.target munge.service
ConditionPathExists=/usr/local/etc/slurm.conf

[Service]
Type=simple
EnvironmentFile=-/etc/sysconfig/slurmctld
ExecStart=/usr/local/sbin/slurmctld -D $SLURMCTLD_OPTIONS
ExecReload=/bin/kill -HUP $MAINPID
LimitNOFILE=65536


[Install]
WantedBy=multi-user.target
[root@master slurm-20.11.0-0rc1]# cat /usr/lib/systemd/system/slurmd.service 
[Unit]
Description=Slurm node daemon
After=munge.service network.target remote-fs.target
#ConditionPathExists=/usr/local/etc/slurm.conf

[Service]
Type=simple
EnvironmentFile=-/etc/sysconfig/slurmd
ExecStart=/usr/local/sbin/slurmd -D $SLURMD_OPTIONS
ExecReload=/bin/kill -HUP $MAINPID
KillMode=process
LimitNOFILE=131072
LimitMEMLOCK=infinity
LimitSTACK=infinity
Delegate=yes


[Install]
WantedBy=multi-user.target

确定配置文件是/usr/local/etc/slurm.conf 通过在线网址https://slurm.schedmd.com/configurator.html
或者sz doc/html/configurator.html本地浏览器打开配置,
将生成的配置文件填入/usr/local/etc/slurm.conf
注意事项见Ubuntu 18.04/Mint 19 单机安装Slurm,下面是示例文件

cat << EOF > /usr/local/etc/slurm.conf
# slurm.conf file generated by configurator.html.
# Put this file on all nodes of your cluster.
# See the slurm.conf man page for more information.
#
SlurmctldHost=master
#SlurmctldHost=
#
#DisableRootJobs=NO
#EnforcePartLimits=NO
#Epilog=
#EpilogSlurmctld=
#FirstJobId=1
#MaxJobId=999999
#GresTypes=
#GroupUpdateForce=0
#GroupUpdateTime=600
#JobFileAppend=0
#JobRequeue=1
#JobSubmitPlugins=1
#KillOnBadExit=0
#LaunchType=launch/slurm
#Licenses=foo*4,bar
#MailProg=/bin/mail
#MaxJobCount=5000
#MaxStepCount=40000
#MaxTasksPerNode=128
MpiDefault=none
#MpiParams=ports=#-#
#PluginDir=
#PlugStackConfig=
#PrivateData=jobs
ProctrackType=proctrack/pgid
#Prolog=
#PrologFlags=
#PrologSlurmctld=
#PropagatePrioProcess=0
#PropagateResourceLimits=
#PropagateResourceLimitsExcept=
#RebootProgram=
ReturnToService=1
SlurmctldPidFile=/var/spool/slurm-llnl/slurmctld.pid
SlurmctldPort=6817
SlurmdPidFile=/var/spool/slurm-llnl/slurmd.pid
SlurmdPort=6818
SlurmdSpoolDir=/var/spool/slurm-llnl
SlurmUser=slurm
#SlurmdUser=root
#SrunEpilog=
#SrunProlog=
StateSaveLocation=/var/spool/slurm-llnl
SwitchType=switch/none
#TaskEpilog=
TaskPlugin=task/affinity
#TaskProlog=
#TopologyPlugin=topology/tree
#TmpFS=/tmp
#TrackWCKey=no
#TreeWidth=
#UnkillableStepProgram=
#UsePAM=0
#
#
# TIMERS
#BatchStartTimeout=10
#CompleteWait=0
#EpilogMsgTime=2000
#GetEnvTimeout=2
#HealthCheckInterval=0
#HealthCheckProgram=
InactiveLimit=0
KillWait=30
#MessageTimeout=10
#ResvOverRun=0
MinJobAge=300
#OverTimeLimit=0
SlurmctldTimeout=120
SlurmdTimeout=300
#UnkillableStepTimeout=60
#VSizeFactor=0
Waittime=0
#
#
# SCHEDULING
#DefMemPerCPU=0
#MaxMemPerCPU=0
#SchedulerTimeSlice=30
SchedulerType=sched/backfill
SelectType=select/cons_tres
SelectTypeParameters=CR_Core
#
#
# JOB PRIORITY
#PriorityFlags=
#PriorityType=priority/basic
#PriorityDecayHalfLife=
#PriorityCalcPeriod=
#PriorityFavorSmall=
#PriorityMaxAge=
#PriorityUsageResetPeriod=
#PriorityWeightAge=
#PriorityWeightFairshare=
#PriorityWeightJobSize=
#PriorityWeightPartition=
#PriorityWeightQOS=
#
#
# LOGGING AND ACCOUNTING
#AccountingStorageEnforce=0
#AccountingStorageHost=
#AccountingStoragePass=
#AccountingStoragePort=
AccountingStorageType=accounting_storage/none
#AccountingStorageUser=
AccountingStoreJobComment=YES
ClusterName=cluster
#DebugFlags=
#JobCompHost=
#JobCompLoc=
#JobCompPass=
#JobCompPort=
JobCompType=jobcomp/none
#JobCompUser=
#JobContainerType=job_container/none
JobAcctGatherFrequency=30
JobAcctGatherType=jobacct_gather/none
SlurmctldDebug=info
#SlurmctldLogFile=
SlurmdDebug=info
#SlurmdLogFile=
#SlurmSchedLogFile=
#SlurmSchedLogLevel=
#
#
# POWER SAVE SUPPORT FOR IDLE NODES (optional)
#SuspendProgram=
#ResumeProgram=
#SuspendTimeout=
#ResumeTimeout=
#ResumeRate=
#SuspendExcNodes=
#SuspendExcParts=
#SuspendRate=
#SuspendTime=
#
#
# COMPUTE NODES
NodeName=master,client01 CPUs=96 State=UNKNOWN
PartitionName=long Nodes=master,client01 Default=YES MaxTime=INFINITE State=UP
EOF

设置权限

chown slurm:slurm /usr/local/etc/slurm.conf

启动

systemctl start slurmd
systemctl enable slurmd
systemctl start slurmctld
systemctl enable slurmctld

查看状态正常

[root@master slurm-20.11.0-0rc1]# systemctl status slurmctld
● slurmctld.service - Slurm controller daemon
   Loaded: loaded (/usr/lib/systemd/system/slurmctld.service; enabled; vendor preset: disabled)
   Active: active (running) since Fri 2020-11-06 22:41:46 CST; 8s ago
 Main PID: 101889 (slurmctld)
   CGroup: /system.slice/slurmctld.service
           └─101889 /usr/local/sbin/slurmctld -D

Nov 06 22:41:46 master systemd[1]: Started Slurm controller daemon.
[root@master slurm-20.11.0-0rc1]# systemctl status slurmd
● slurmd.service - Slurm node daemon
   Loaded: loaded (/usr/lib/systemd/system/slurmd.service; enabled; vendor preset: disabled)
   Active: active (running) since Fri 2020-11-06 22:41:36 CST; 20s ago
 Main PID: 101848 (slurmd)
   CGroup: /system.slice/slurmd.service
           └─101848 /usr/local/sbin/slurmd -D

Nov 06 22:41:36 master systemd[1]: Started Slurm node daemon.

查看上线信息,因为当前只配置了master节点，仅有一个上线

[root@master ~]# sinfo
PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
long*        up   infinite      1   idle master

提交作业

[cndaqiang@master NVE-TDDFT-4000K_156_78x2_input]$ sbatch slurm.sh 
Submitted batch job 4
[cndaqiang@master NVE-TDDFT-4000K_156_78x2_input]$ squeue
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON) 
                 4      long      ECD cndaqian  R       0:04      1 master

开始多节点配置

登陆计算节点client01

[cndaqiang@master ~]$ ssh root@node8
root@node8's password: 
Last login: Fri Nov  6 15:26:55 2020
[root@client01 ~]#

配置和前面的管理节点完全相同，只需启用slurmd服务

[root@client01 slurm-20.11.0-0rc1]# systemctl start slurmd
[root@client01 slurm-20.11.0-0rc1]# systemctl status slurmd
● slurmd.service - Slurm node daemon
   Loaded: loaded (/usr/lib/systemd/system/slurmd.service; disabled; vendor preset: disabled)
   Active: active (running) since Fri 2020-11-06 22:58:01 CST; 3s ago
 Main PID: 19608 (slurmd)
    Tasks: 1
   Memory: 1.1M
   CGroup: /system.slice/slurmd.service
           └─19608 /usr/local/sbin/slurmd -D

Nov 06 22:58:01 client01 systemd[1]: Started Slurm node daemon.
[root@client01 slurm-20.11.0-0rc1]# sinfo
PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
long*        up   infinite      1  drain master
long*        up   infinite      1   idle client01

测试

提交双节点作业

[cndaqiang@master NVE-TDDFT-4000K_156_78x2_input]$ sbatch slurm.sh 
Submitted batch job 11
[cndaqiang@master NVE-TDDFT-4000K_156_78x2_input]$ squeue
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON) 
                11      long      ECD cndaqian  R       0:39      2 client01,master

错误处理

状态为drain

[root@master ~]# sinfo
PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
long*        up   infinite      1  drain master
long*        up   infinite      1   idle client01

解决

scontrol update NodeName=master State=RESUME

如果还报错，安装参考资料SLURM 节点状态总是drained问题方案

[root@master ~]# scontrol update NodeName=master State=DOWN Reason=cndaqiang
[root@master ~]# systemctl restart slurmd
[root@master ~]# scontrol update NodeName=master State=RESUME
[root@master ~]# sinfo
PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
long*        up   infinite      2   idle client01,master

重启后节点都是down，添加到/etc/rc.local,暂时原因未知

#scontrol update NodeName=master State=RESUME
#scontrol update NodeName=client01 State=RESUME

状态为down,计算节点的slurmd服务正常

计算节点刚开机，还没连上管理节点(等待即可)或者其他原因，均可以

scontrol update NodeName=client01 State=RESUME

状态为unk*

[cndaqiang@master ~]$ sinfo
PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
long*        up   infinite      1   unk* client01
long*        up   infinite      1   idle master

登陆计算节点查看

[root@client01 cndaqiang]# systemctl status slurmd
● slurmd.service - Slurm node daemon
   Loaded: loaded (/usr/lib/systemd/system/slurmd.service; disabled; vendor preset: disabled)
   Active: inactive (dead)

因为默认没有启动slurmd服务

[root@client01 cndaqiang]# systemctl enable  slurmd
Created symlink from /etc/systemd/system/multi-user.target.wants/slurmd.service to /usr/lib/systemd/system/slurmd.service.
[root@client01 cndaqiang]# systemctl start  slurmd

再查看

[cndaqiang@master ~]$ sinfo
PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
long*        up   infinite      2   idle client01,master

状态idle*

[cndaqiang@client01 ~]$ sinfo
PARTITION AVAIL  TIMELIMIT  NODES  STATE NODELIST
long*        up   infinite      1  idle* client01
long*        up   infinite      1   idle master

登陆计算节点，重启slurm服务

slurm_update error: Invalid user id

使用root或slurm执行slurm管理命令

slurm不自动启动

干脆使用开机脚本

systemctl disable slurmd
echo 'systemctl restart slurmd' >> /etc/rc.local
echo 'sleep 5' >> /etc/rc.local
echo 'scontrol update NodeName=client01 State=RESUME' >> /etc/rc.local

重启脚本

#下面仅在管理节点
/bin/systemctl restart slurmctld
scontrol update NodeName=master State=RESUME
scontrol update NodeName=client01 State=RESUME

drain,drng的另一个原因

发现node02无法正常交作业

[root@mgmt CELL_Z]# sinfo
PARTITION  AVAIL  TIMELIMIT  NODES  STATE NODELIST
debug         up      30:00      1  drain node02
debug         up      30:00      8  alloc node[01,03-09]
regular       up 7-00:00:00      1  drain node02
regular       up 7-00:00:00      8  alloc node[01,03-09]
long          up 30-00:00:0      4  alloc node[06-09]
intel_long    up 30-00:00:0      2  alloc node[11-12]
[root@mgmt CELL_Z]# scontrol update NodeName=node02 State=RESUME
[root@mgmt CELL_Z]# sinfo
PARTITION  AVAIL  TIMELIMIT  NODES  STATE NODELIST
debug         up      30:00      1   drng node02
debug         up      30:00      8  alloc node[01,03-09]
regular       up 7-00:00:00      1   drng node02
regular       up 7-00:00:00      8  alloc node[01,03-09]
long          up 30-00:00:0      4  alloc node[06-09]
intel_long    up 30-00:00:0      2  alloc node[11-12]

查看节点现状,看起来是内存过低Low RealMemory

[root@mgmt CELL_Z]# scontrol show node 
NodeName=node01 Arch=x86_64 CoresPerSocket=24 
   CPUAlloc=48 CPUTot=48 CPULoad=49.05
   AvailableFeatures=(null)
   ActiveFeatures=(null)
   Gres=(null)
   NodeAddr=node01 NodeHostName=node01 Version=19.05.8
   OS=Linux 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 
   RealMemory=190000 AllocMem=96000 FreeMem=140680 Sockets=2 Boards=1
   State=ALLOCATED ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A
   Partitions=debug,regular 
   BootTime=2021-08-04T08:14:34 SlurmdStartTime=2021-08-04T08:28:58
   CfgTRES=cpu=48,mem=190000M,billing=48
   AllocTRES=cpu=48,mem=96000M
   CapWatts=n/a
   CurrentWatts=0 AveWatts=0
   ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s
   

NodeName=node02 Arch=x86_64 CoresPerSocket=24 
   CPUAlloc=0 CPUTot=48 CPULoad=0.01
   AvailableFeatures=(null)
   ActiveFeatures=(null)
   Gres=(null)
   NodeAddr=node02 NodeHostName=node02 Version=19.05.8
   OS=Linux 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 
   RealMemory=190000 AllocMem=0 FreeMem=178416 Sockets=2 Boards=1
   State=IDLE+DRAIN ThreadsPerCore=1 TmpDisk=0 Weight=1 Owner=N/A MCS_label=N/A
   Partitions=debug,regular 
   BootTime=2021-12-10T17:18:42 SlurmdStartTime=2021-12-14T16:05:17
   CfgTRES=cpu=48,mem=190000M,billing=48
   AllocTRES=
   CapWatts=n/a
   CurrentWatts=0 AveWatts=0
   ExtSensorsJoules=n/s ExtSensorsWatts=0 ExtSensorsTemp=n/s
   Reason=Low RealMemory [slurm@2021-12-14T16:02:18]

登录各个节点，查看, 确实是node02的内存变少了，应该对应物理问题

[root@mgmt CELL_Z]# ssh node01
Last login: Tue Dec 14 16:05:37 2021 from 11.11.11.101
[root@node01 ~]# free -m
              total        used        free      shared  buff/cache   available
Mem:         191907       25383      140673         346       25850      165465
Swap:         32767           0       32767
[root@node01 ~]# exit
logout
Connection to node01 closed.
[root@mgmt CELL_Z]# ssh node02
Last login: Tue Dec 14 16:03:24 2021 from 11.11.11.101
[root@node02 ~]# free -m
              total        used        free      shared  buff/cache   available
Mem:         184599        6004      178413          10         181      178014
Swap:         32767           0       32767

在售后来换内存之前，先改配置运行

NodeName=node02 CPUs=48 Boards=1 SocketsPerBoard=2 CoresPerSocket=24 ThreadsPerCore=1 RealMemory=160000

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