安装SLURM

Last modified: October 08, 2024

第一步

先在loginNode上

sudo apt update
sudo apt install rng-tools
sudo rngd -r /dev/urandom

sudo mkdir -p /etc/munge
sudo sh -c  "dd if=/dev/urandom bs=1 count=1024 > /etc/munge/munge.key"
sudo chown munge: /etc/munge/munge.key
sudo chmod 400 /etc/munge/munge.key
sudo cp /etc/munge/munge.key /etc/share

sudo mkdir -p /var/spool/slurmctld/
sudo dd if=/dev/random of=/var/spool/slurmctld/jwt_hs256.key bs=32 count=1
sudo chown slurm:slurm /var/spool/slurmctld/jwt_hs256.key
sudo chmod 0600 /var/spool/slurmctld/jwt_hs256.key
sudo cp /var/spool/slurmctld/jwt_hs256.key /etc/share

# install_slurm_1.sh
# 安装slurm
sudo apt upgrade -y

# 同步时间
sudo apt install ntpdate -y
sudo timedatectl set-timezone Asia/Shanghai
sudo ntpdate -vd loginNode

# 打开防火墙
sudo apt install firewalld -y
sudo systemctl enable firewalld
sudo systemctl start firewalld
sudo firewall-cmd --zone=trusted --add-source=192.168.2.0/24 --permanent
sudo systemctl restart firewalld

# 安装munge
sudo apt install munge libmunge-dev -y
sudo systemctl start munge
sudo systemctl enable munge

# 创建munge用户和slurm用户
if id munge; then sudo userdel -r -f munge; fi
if id slurm; then sudo userdel -r -f slurm; fi
sudo groupadd -g 966 munge
sudo useradd  -m -c "MUNGE Uid and Gid Emporium" -d /var/lib/munge -u 966 -g munge -s /sbin/nologin munge
sudo groupadd -g 967 slurm
sudo useradd  -m -c "SLURM workload manager" -d /var/lib/slurm -u 967 -g slurm  -s /bin/bash slurm
id munge
id slurm

# 同步munge key
sudo mkdir -p /etc/munge
sudo cp /etc/share/munge.key /etc/munge  # assume key already exists
sudo chown -R munge: /etc/munge/ /var/log/munge/ /run/munge /var/lib/munge
sudo chmod 0700 /etc/munge/ /var/log/munge/
sudo systemctl restart munge

# 同步jwt key
sudo mkdir -p /var/spool/slurmctld/
sudo cp /etc/share/jwt_hs256.key /var/spool/slurmctld/ # assume key already exists
sudo chown slurm:slurm /var/spool/slurmctld/jwt_hs256.key
sudo chmod 0600 /var/spool/slurmctld/jwt_hs256.key

# 安装slurm prerequisites
sudo apt install bzip2 cmake libpam0g-dev libhdf5-dev hwloc libhwloc-dev libjansson4 libjansson-dev autoconf libtool g++ gfortran pkg-config libbpf-dev libdbus-1-dev libmysqlclient-dev libnuma-dev -y
mkdir -p software/slurm
cd software/slurm
git clone --depth 1 --single-branch -b json-c-0.15-20200726 https://github.com/json-c/json-c.git json-c
mkdir -p json-c-build
cd json-c-build
cmake ../json-c
make -j
sudo make install
cd ..
git clone --depth 1 --single-branch -b v2.9.4 https://github.com/nodejs/http-parser.git http_parser-c
cd http_parser-c
make -j
sudo make install
cd ..
git clone --depth 1 --single-branch -b 0.2.5 https://github.com/yaml/libyaml libyaml
cd libyaml
./bootstrap
./configure
make -j
sudo make install
cd ..
git clone --depth 1 --single-branch -b v1.12.0 https://github.com/benmcollins/libjwt.git libjwt
cd libjwt
autoreconf --force --install
./configure --prefix=/usr/local
make -j
sudo make install
sudo ldconfig -v
cd ..

第二步, 安装MySQL, 只要在ln上完成

# install_slurm_2_mysql_lnnode.sh
sudo apt install mysql-server -y
sudo mysql_secure_installation # interactive
sudo systemctl start mysql
sudo systemctl enable mysql
sudo systemctl status mysql
# sudo grep "password" /var/log/mysqld.log # 查看初始密码, 暂时没用了
sudo mysql -u root -p # 空白密码

进入MySQL.

ALTER USER 'root'@'localhost' IDENTIFIED WITH mysql_native_password BY '<PASSWD>';
FLUSH PRIVILEGES;

CREATE USER 'slurm'@'%' IDENTIFIED WITH mysql_native_password BY 'da4jia1deTeXshi4ti3yu4lao3shi1jiao1de?';
GRANT ALL ON slurm_acct_db.* TO 'slurm'@'%';
CREATE DATABASE slurm_acct_db;
GRANT ALL ON job_comp_db.* TO 'slurm'@'%';
CREATE DATABASE job_comp_db;
SHOW ENGINES;

exit;

最后

sudo systemctl restart mysql

确认 MySQL 能通过 3306 端口连接:

telnet loginNode 3306

如果遇到 connection refused error, 需要修改 MySQL 的配置. 在 /etc/mysql/mysql.conf.d/mysqld.cnf, 修改 bind-address = 0.0.0.0. 最后 sudo systemctl restart mysql.

确认 MySQL 在 3306 上 listen:

sudo apt install net-tools
sudo netstat -plunt | grep mysqld

第三步

# install_slurm_2.sh
# 安装slurm
slurmversion=23.11.4
git clone -b slurm-23.11 https://github.com/ninotreve/slurm.git slurm-${slurmversion}
cd slurm-${slurmversion}
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig/:$PKG_CONFIG_PATH
sudo mkdir -p /lib/slurm/pam
sudo mkdir -p /etc/slurm/
sudo chown -R slurm: /etc/slurm/
./configure --prefix=/usr --sysconfdir=/etc/slurm --with-munge=/usr --enable-debug --enable-pam --with-pam_dir=/lib/slurm/pam --with-http-parser=/usr/local/ --with-yaml=/usr/local/  --with-jwt=/usr/local/ --enable-slurmrestd
make -j
sudo make install
slurmd -V
sudo cp /etc/share/slurm.conf /etc/slurm/
sudo cp /etc/share/cgroup.conf /etc/slurm/
sudo cp /etc/share/gres.$(hostname).conf /etc/slurm/gres.conf
for dir in /var/spool/slurm /var/spool/slurmd /var/spool/slurmctld /var/spool/slurm/slurmctld /etc/slurm # /etc/share/slurmctld
do
    sudo mkdir -p $dir
    sudo chown slurm: $dir
    sudo chmod 755 $dir
done

for file in /var/log/slurmctld.log /var/log/slurmd.log /var/log/slurmacct.log /var/log/slurmdbd.log /var/run/slurmdbd.pid /var/run/slurmctld.pid /var/run/slurmd.pid
do
    sudo touch $file
    sudo chown slurm: $file
done

sudo ldconfig -n /usr/lib/slurm
sudo cp etc/*.service /etc/systemd/system
sudo systemctl daemon-reload
# 在ln上先启动dbd和ctld
sudo systemctl enable slurmd
sudo systemctl start slurmd

第四步：用户禁止登陆

# 用户禁止登陆
slurmversion=23.11.4
cd slurm-${slurmversion}
cd ./contribs/pam_slurm_adopt/
make
sudo make install
sudo mkdir -p /lib/security
sudo rm -f /lib/security/pam_slurm_adopt.*
sudo ln -s /lib/slurm/pam/pam_slurm_adopt.so /lib/security/pam_slurm_adopt.so
sudo ln -s /lib/slurm/pam/pam_slurm_adopt.a /lib/security/pam_slurm_adopt.a
sudo ln -s /lib/slurm/pam/pam_slurm_adopt.la /lib/security/pam_slurm_adopt.la

修改 /etc/pam.d/sshd

-account    sufficient      pam_access.so
-account    required        pam_slurm_adopt.so

修改 /etc/security/access.conf :

+:root:cron crond :0 tty1 tty2 tty3 tty4 tty5 tty6
+:root:127.0.0.1
+:root:192.168.2.
+:wheel:ALL
+:admin:ALL
-:Student:ALL
-:Faculty:ALL
-:Collaborator:ALL

最后

sudo systemctl stop systemd-logind
sudo systemctl mask systemd-logind

更新 SLURM 版本

cd slurm
git fetch origin
git checkout -b slurm-24.05 origin/slurm-24.05
export PKG_CONFIG_PATH=/usr/local/lib/pkgconfig/:$PKG_CONFIG_PATH
./configure --prefix=/usr --sysconfdir=/etc/slurm --with-munge=/usr --enable-debug --enable-pam --with-pam_dir=/lib/slurm/pam --with-http-parser=/usr/local/ --with-yaml=/usr/local/  --with-jwt=/usr/local/ --enable-slurmrestd
make -j
sudo make install
slurmd -V
sudo cp etc/*.service /etc/systemd/system
sudo systemctl daemon-reload
# sudo systemctl restart slurmdbd
# sudo systemctl restart slurmctld
sudo systemctl restart slurmd

cd ./contribs/pam_slurm_adopt/
make
sudo make install
sudo mkdir -p /lib/security
sudo rm -f /lib/security/pam_slurm_adopt.*
sudo ln -s /lib/slurm/pam/pam_slurm_adopt.so /lib/security/pam_slurm_adopt.so
sudo ln -s /lib/slurm/pam/pam_slurm_adopt.a /lib/security/pam_slurm_adopt.a
sudo ln -s /lib/slurm/pam/pam_slurm_adopt.la /lib/security/pam_slurm_adopt.la

SLURM 配置

`slurm.conf` (持续更新)

ClusterName=clusterHPC
SlurmctldHost=loginNode
SlurmctldHost=bigMem0
GresTypes=gpu
MpiDefault=none
ProctrackType=proctrack/cgroup
ReturnToService=1
SlurmctldPidFile=/var/run/slurmctld.pid
SlurmctldPort=6817
SlurmdPidFile=/var/run/slurmd.pid
SlurmdPort=6818
SlurmdSpoolDir=/var/spool/slurmd
SlurmUser=slurm
StateSaveLocation=/etc/share/slurmctld
SwitchType=switch/none

# TIMERS
InactiveLimit=300
KillWait=300
MinJobAge=300
SlurmctldTimeout=300
SlurmdTimeout=300
UnkillableStepTimeout=120
Waittime=300

# SCHEDULING
SchedulerType=sched/backfill
SelectType=select/cons_tres
SelectTypeParameters=CR_Core

# LOGGING AND ACCOUNTING
AccountingStorageEnforce=limits
AccountingStorageHost=loginNode
AccountingStoragePass=/var/run/munge/munge.socket.2
AccountingStoragePort=6819
AccountingStorageType=accounting_storage/slurmdbd
AccountingStorageUser=slurm
AccountingStorageTRES=gres/gpu
# AccountingStoreFlags=job_comment
JobCompHost=loginNode
JobCompLoc=job_comp_db
JobCompPass=da4jia1deTeXshi4ti3yu4lao3shi1jiao1de?
JobCompPort=3306
JobCompType=jobcomp/mysql
JobCompUser=slurm
#JobContainerType=job_container/none
JobAcctGatherFrequency=30
JobAcctGatherType=jobacct_gather/cgroup
SlurmctldDebug=debug
SlurmctldLogFile=/var/log/slurmctld.log
SlurmdDebug=debug
SlurmdLogFile=/var/log/slurmd.log

# COMPUTE NODES
NodeName=loginNode CPUs=24 RealMemory=128543 Sockets=2 CoresPerSocket=12 ThreadsPerCore=1 State=UNKNOWN Gres=gpu:nvidia_geforce_gtx_1080_ti:2
NodeName=bigMem0 CPUs=64 RealMemory=1030499 Sockets=2 CoresPerSocket=16 ThreadsPerCore=2 State=UNKNOWN Gres=gpu:tesla_t4:4
NodeName=bigMem1 CPUs=64 RealMemory=1030499 Sockets=2 CoresPerSocket=16 ThreadsPerCore=2 State=UNKNOWN Gres=gpu:nvidia_a30:4
NodeName=bigMem2 CPUs=128 RealMemory=515855 Sockets=2 CoresPerSocket=32 ThreadsPerCore=2 State=UNKNOWN
NodeName=bigMem3 CPUs=512 RealMemory=1031678 Sockets=2 CoresPerSocket=128 ThreadsPerCore=2 State=UNKNOWN
PartitionName=partition Nodes=bigMem[0-3] MaxTime=7-0 DefaultTime=06:00:00 Default=YES State=UP

`squeue` 等命令的格式

在 /home/admin/script/setvars.sh 中定义.

export SQUEUE_FORMAT2="JobID:5 ,UserName:7 ,Name:11 ,StateCompact:2 ,NumCPUs:4 ,tres-per-node:4 ,EndTime:16 ,NodeList:11 ,ReqNodes:11"
export SQUEUE_SORT="N,n,-e"
export SINFO_SORT="P"
alias sinfo="sinfo -O NodeHost:11,Available:7,StateCompact:7,CPUsState:19,GresUsed:30 -S P"

`sacctmgr` 相关命令

要限制用户, 参考: https://slurm.schedmd.com/sacctmgr.html#SECTION_GENERAL-SPECIFICATIONS-FOR-ASSOCIATION-BASED-ENTITIES

要修改qos, 参考: https://slurm.schedmd.com/sacctmgr.html#SECTION_SPECIFICATIONS-FOR-QOS

新增账户和用户:

# 获取系统用户列表
USER_LIST=$(cat /etc/passwd | grep '/home' | cut -d: -f1)

# 为每个用户添加到 SLURM
for user in $USER_LIST; do
    USER_EXISTS=$(sacctmgr show user $user format=User%30 -n)

    if [ -z "$USER_EXISTS" ]; then
        echo "Adding user $user to SLURM and associating with account $ACCOUNT"

        sudo sacctmgr add account $user
        sudo sacctmgr add user $user account=$user
    else
        echo "User $user already exists in SLURM, skipping."
    fi
done

修改用户的核时限制:

sudo sacctmgr modify user yjzhang set GrpTRESRunMins=cpu=64
sudo sacctmgr modify user yjzhang set MaxTRESMinsPerJob=cpu=64
sudo sacctmgr modify user yjzhang set GrpTRESRunMins=cpu=-1 # 恢复到不受限制
sudo sacctmgr modify user yjzhang set MaxTRESMinsPerJob=cpu=-1

查看用户的核时限制:

sacctmgr show assoc where user=yjzhang format=User,Account,GrpTRESRunMins,MaxTRESMinsPerJob

修改 QOS 的核时限制:

sudo sacctmgr modify qos normal set MaxTRESRunMinsPerUser=cpu=69120
sudo sacctmgr modify qos normal set MaxTRESMinsPerJob=cpu=69120

查看 QOS 的核时限制:

sacctmgr show qos normal format=Name,MaxTRESRunMinsPerUser,MaxTRESMinsPerJob

添加新的 QOS

有时候, 用户需要的核时可能更多, 这个时候我们要对用户创建新的 QOS. 步骤如下:

检查用户要使用的 node 有没有一个单独的 partition, 如果没有, 使用 scontrol create PartitionName=<partition_name> Nodes=<node_list> MaxTime=<time_limit> DefaultTime=<default_time> Default=<YES> State=<UP> 新建一个 partition. 具体配置可以参考 /etc/slurm/slurm.conf 文件.
用 sacctmgr show qos format=name,priority,MaxTRESRunMinsPerUser,MaxTRESMinsPerJob 查看已有的 QOS 和配置.
用 sudo sacctmgr add qos <qos_name> 创建新的 QOS.
用 sudo scontrol update partition=<partition_name> qos=<qos_name> 把这个 QOS 分配给对应的分区, 可以用 scontrol show partition <partition_name> 查看. 如果要移除这个, 可以用 sudo scontrol update partition=<partition_name> qos=.
用 sudo sacctmgr modify qos <qos_name> set priority=<num> 配置优先级.
用 sudo sacctmgr modify qos <qos_name> set MaxTRESRunMinsPerUser=cpu=<time> 和 sudo sacctmgr modify qos <qos_name> set MaxTRESMinsPerJob=cpu=<time> 设置新 QOS 的核时限制.
用 sudo sacctmgr modify user <user_name> set qos+=<qos_name> 给用户添加新的 QOS. 现在, 用户可以在提交任务时用 --qos=<qos_name> 使用不用的 QOS.
用 sacctmgr show assoc where user=<user_name> format=User,Account,QOS%50 查看某一用户有的 QOS, 这里 %50 是为了防止长度不够.
用户使用完成后, 用 sudo sacctmgr modify user <user_name> set qos-=<qos_name> 和 sudo sacctmgr delete qos <qos_name> 删除对应的 QOS.

预约资源

sudo scontrol create reservation starttime=2024-02-01T00:00:00 duration=1-00:00:00 user=yqliu nodes=bigMem1 flags=ignore_jobs
sudo scontrol create reservation starttime=2024-03-03T00:00:00 duration=06:00:00 user=root flags=maint,ignore_jobs nodes=ALL