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“How to start an HPC cluster on centos 7 Linux servers”

Last modified: February 26, 2024

考虑到书写的方便性，直接在markdown里记录下来了配置的几乎全过程。 不过似乎知乎的配色方案不太好看，原本在mdnice里写的还挺漂亮。经过Grammarly查错，不知道会不会把本来的命令给改了…按说是没有的。未经许可，请勿翻译/转载。

How to start an HPC cluster on centos 7 Linux servers

Prepare several Linux servers with centos 7 installed. Make sure they are physically connected and get their IPs.

In the following, we will use these 2 machines as an example:

  • hostname: loginNode, ip: 10.66.66.88
  • hostname: bigMem0, ip: 10.66.66.100

I assume you already have a user named USERNAME with sudo privileges. If not, open /etc/sudoers and check if this line is there: %wheel ALL=(ALL) ALL. Uncomment it so that all users in the wheel group can use sudo. Use usermod to add a user to your wheel group: usermod USERNAME \-G wheel \-a(Not tested).

Allow this user to do mv, mkdir without password confirm: add to the last line of sudoers by sudo visudo: USERNAME *TAB HERE* ALL=(ALL) *TAB HERE* NOPASSWD: ALL.(possibly not safe\?)

It’s better than to disallow root to login from ssh for safety reasons. Everything following will run under USERNAME (with sudo privileges).

It is ok if you work out the following with the root user. (Not tested)

Add this username to the environment, and we will use it later: export ClusterManager=USERNAME.

Dispatch RSA keys to each slave node for ssh login

We will later use ssh to transfer scripts and make other configurations. So let’s set up public-key authentication for ssh between clusters.

Usually, you won’t want to expose your port 22 to the public. You might change the port that ssh uses by modifying its config /etc/ssh/sshd_config: Add a new line Port 10086, and remove line Port 22. Disable root login by set PermitRootLogin no. Restart sshd for rules to take effect: sudo systemctl restart sshd.

CentOs uses SELinux to enhance its safety. This change should be reported by sudo semanage port \-a \-t ssh_port_t \-p tcp 10086. If the system cannot find semanage, install it with sudo yum install policycoreutils-python.x86_64.

Now, open the manage node’s terminal and generate keys: ssh-keygen \-t rsa \-b 4096 \-N "" at the defualt position ~/.ssh/id_rsa. Copy your public key (in id_rsa.pub) and paste it to the end of all slave nodes’ file: ~/.ssh/authorized_keys.

Test if this is correctly configured. On manage node, type ssh USERNAME@SLAVE \-i ~/.ssh/id_rsa \-p 10086 to see if it requires password to login.

Add the port number to the environment, and we will use it later: export ClusterPort=10086.

Install \&\& start slurm daemon and slurm control daemon on nodes

  1. ensure that no existed munge user or slurm user in every machine. If yes, delete them directly. sudo vim /etc/passwd and find munge/slurm. To delete, use userdel.
  2. follow the link https://www.ni-sp.com/slurm-build-script-and-container-commercial-support/(copied and modified version following) to complete most of the work. These should be modified:
  • Line 90: The newest VER is now 20.11.8.
  • Line 121: Delete the HOST configuration line.

  • Line 123-186: Detailed configuration file for slurm. Edit carefully or generate it from https://slurm.schedmd.com/configurator.html

    • in case using MySQL for job completion logging. Install MySQL database to the selected position.
 #!/bin/bash

yum install mariadb-server mariadb-devel -y

export MUNGEUSER=966
sudo groupadd -g $MUNGEUSER munge
sudo useradd  -m -c "MUNGE Uid 'N' Gid Emporium" -d /var/lib/munge \
-u $MUNGEUSER -g munge  -s /sbin/nologin munge
export SLURMUSER=967
sudo groupadd -g $SLURMUSER slurm
sudo useradd  -m -c "SLURM workload manager" -d /var/lib/slurm \
-u $SLURMUSER -g slurm  -s /bin/bash slurm

sudo yum install epel-release -y
sudo yum install \
https://dl.fedoraproject.org/pub/epel/epel-release-latest-7.noarch.rpm -y

sudo yum install munge munge-libs munge-devel -y

sudo yum install rng-tools -y
sudo rngd -r /dev/urandom

sudo /usr/sbin/create-munge-key -r -f

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 systemctl enable munge
sudo systemctl start munge

sudo yum install python3 gcc openssl openssl-devel pam-devel \
numactl numactl-devel hwloc lua readline-devel ncurses-devel \
man2html libibmad libibumad rpm-build \
perl-ExtUtils-MakeMaker.noarch -y
sudo yum install rrdtool-devel lua-devel hwloc-devel -y

mkdir slurm-tmp
cd slurm-tmp
export VER=20.11.8
wget https://download.schedmd.com/slurm/slurm-$VER.tar.bz2
rpmbuild -ta slurm-$VER.tar.bz2

rm slurm-$VER.tar.bz2
cd ..
rmdir slurm-tmp

cd ~/rpmbuild/RPMS/x86_64/
sudo yum --nogpgcheck localinstall slurm-[0-9]*.el*.x86_64.rpm \
slurm-contribs-*.el*.x86_64.rpm slurm-devel-*.el*.x86_64.rpm \
slurm-example-configs-*.el*.x86_64.rpm slurm-libpmi-*.el*.x86_64.rpm  \
slurm-pam_slurm-*.el*.x86_64.rpm slurm-perlapi-*.el*.x86_64.rpm \
slurm-slurmctld-*.el*.x86_64.rpm \
slurm-slurmd-*.el*.x86_64.rpm slurm-slurmdbd-*.el*.x86_64.rpm -y

sudo cat > /etc/slurm/cgroup.conf << EOF
###
#
# Slurm cgroup support configuration file
#
# See man slurm.conf and man cgroup.conf for further
# information on cgroup configuration parameters
#--
CgroupAutomount=yes

ConstrainCores=no
ConstrainRAMSpace=no

EOF

sudo mkdir /var/spool/slurm
sudo chown slurm:slurm /var/spool/slurm
sudo chmod 755 /var/spool/slurm
sudo mkdir /var/spool/slurm/slurmctld
sudo chown slurm:slurm /var/spool/slurm/slurmctld
sudo chmod 755 /var/spool/slurm/slurmctld
sudo mkdir -p /var/spool/slurm/cluster_state
sudo chown slurm:slurm /var/spool/slurm/cluster_state
sudo touch /var/log/slurmctld.log
sudo chown slurm:slurm /var/log/slurmctld.log
sudo touch /var/log/slurm_jobacct.log /var/log/slurm_jobcomp.log
sudo chown slurm: /var/log/slurm_jobacct.log /var/log/slurm_jobcomp.log

3. Go to https://slurm.schedmd.com/configurator.html and create a configuration file. Put it to /etc/slurm/slurm.conf. Following is an example:

# 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=loginNode
#
#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=pmi2
#MpiParams=ports=#-#
#PluginDir=
#PlugStackConfig=
#PrivateData=jobs
ProctrackType=proctrack/cgroup
#Prolog=
#PrologFlags=
#PrologSlurmctld=
#PropagatePrioProcess=0
#PropagateResourceLimits=
#PropagateResourceLimitsExcept=
#RebootProgram=
ReturnToService=1
SlurmctldPidFile=/var/run/slurmctld.pid
SlurmctldPort=6816
SlurmdPidFile=/var/run/slurmd.pid
SlurmdPort=6818
SlurmdSpoolDir=/var/spool/slurmd
SlurmUser=slurm
#SlurmdUser=root
#SrunEpilog=
#SrunProlog=
StateSaveLocation=/var/spool/slurm
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=loginNode
JobCompLoc=slurmLogDb
JobCompPass=slurmLog1!
JobCompPort=3306
JobCompType=jobcomp/mysql
JobCompUser=slurmLog
#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=bigMem0 State=UNKNOWN CPUs=64 Sockets=2 CoresPerSocket=16 ThreadsPerCore=2
NodeName=loginNode State=UNKNOWN CPUs=24 Sockets=2 CoresPerSocket=12
PartitionName=bigMem Nodes=bigMem0 Default=YES MaxTime=4320 State=UP

Setup lsync service to synchronize configuration files between servers

  1. Make sure rsync is installed on each node. Type rsync --version to check they have consistent protocol version numbers (31 for me).
  2. Install lsync on each node with yum -y install lsyncd.
  3. On the manage node, create a list for sync targets in /etc/cluster folder: sudo mkdir /etc/cluster. Edit file: sudo vim /etc/cluster/cluster-server.namelist loginNode 10.66.66.88 slave manager bigMem0 10.66.66.100 slave Here, slave means this will become a computation node, and manager means this node will become a manager node.
  4. Write a script to configure the hostname and open up firewalls between nodes. Centos 7 uses firewall-cmd instead of iptables to manage this. (refer: Help for firewall-cmd –zone) Say, you have saved this file to ~/set-hostname-and-firewall.sh.
 #!/bin/bash

ips=($(ifconfig -a|grep inet|grep -v 127.0.0.1|
    grep -v inet6|awk '{print $2}'|tr -d "addr:"))
while read -a namelist; do
    ip=${namelist[1]}
 if [[ ${ips/$ip/} != ${ips} ]]; then
 # this row contains the ip of this machine, set hostname
        sudo echo ${namelist[0]} > /etc/hostname
 echo "Modify hostname to: ${namelist[0]}"
 else
 # this row contains the ip of another machine, add to hosts
        flag=0
        targetHost=${namelist[1]}
 while read -a hostlist; do
 if [[ ${hostlist/$targetHost/} != ${hostlist} ]]; then
                flag=1
 break
 fi
 done < /etc/hosts
 if (( $flag == 0 )); then
 echo "add ${namelist[1]}\t${namelist[0]} to hosts"
            sudo echo -e "\n${namelist[1]}\t${namelist[0]}\n" >> /etc/hosts
 else
 echo "${namelist[1]} is already in hosts, skip"
 fi
 echo -e "add ${namelist[1]}\t${namelist[0]} to firewall trusted zone"
        sudo firewall-cmd --zone=trusted --add-source=${namelist[1]} --permanent
        sudo firewall-cmd --reload

 unset flag
 fi
done < /etc/cluster/cluster-server.namelist

5.The following script does a lot of things on all other nodes.

  • Copy the namelist file to them.
  • Run the script ~/set-hostname-and-firewall.sh.
  • Create a new user with uid 968 and gid 968 for lsyncd service, and use /opt/lsync as its home directory.
  • generate an ssh key pair for lsync and change the owner of several directories
  • share this key pair to all nodes for user lsync

You can either copy it to your bash shell or save it as a script file to run.

#!/bin/bash

echo "Add user lsync and set home directory..."
sudo mkdir /opt/lsync
sudo groupadd -g 968 lsync
sudo useradd -m -c "lsync writer" -d /opt/lsync \
-u 968 -g 968 -s /bin/bash lsync/bin/bash

echo -e "generate 4096 bit RSA ssh key pair at /opt/lsync/.ssh/id_rsa"
sudo mkdir /opt/lsync/.ssh
ssh-keygen -t rsa -b 4096 -C "lsync" -f ~/tmp_id_rsa -N "" -q
SECRET_FILE=~/tmp_id_rsa
PUBLIC_FILE=~/tmp_id_rsa.pub
sudo cp $SECRET_FILE /opt/lsync/.ssh/id_rsa
sudo cat $PUBLIC_FILE > /opt/lsync/.ssh/authorized_keys

ips=($(ifconfig -a|grep inet|grep -v 127.0.0.1|
    grep -v inet6|awk '{print $2}'|tr -d "addr:"))
while read -a namelist; do
    ip=${namelist[1]}
 if [[ ${ips/$ip/} == ${ips} ]]; then

        Remote=${ClusterManager}@${ip}
 echo -e "\n======Communicating with $ip======"
 # this row contains the ip of other nodes
        scp -P $ClusterPort /etc/cluster/cluster-server.namelist \
 $Remote:~/cluster-server.namelist
        ssh -p $ClusterPort $Remote \
 'sudo mkdir /etc/cluster && '\
 'sudo mv ~/cluster-server.namelist '\
 '/etc/cluster/cluster-server.namelist && '\
 'rm -f ~/cluster-server.namelist'
 echo -e "\n"

        scp -P $ClusterPort ~/set-hostname-and-firewall.sh \
 $Remote:~/set-hostname-and-firewall.sh
        ssh -p $ClusterPort $Remote 'sudo bash ~/set-hostname-and-firewall.sh'

 echo "Add user lsync and set home directory..."
        ssh -p $ClusterPort $Remote \
 'sudo mkdir /opt/lsync && sudo groupadd -g 968 lsync && '\
 'sudo useradd -m -c "lsync writer" -d /opt/lsync '\
 '-u 968 -g 968 -s /bin/bash lsync/bin/bash'
 echo -e "\nsuccess"

 echo -e "\ncopy ssh key files..."
        scp -P $ClusterPort $SECRET_FILE $Remote:/opt/lsync/.ssh/id_rsa
        scp -P $ClusterPort $PUBLIC_FILE $Remote:/opt/lsync/.ssh/authorized_keys

 echo -e "\nChange owner of /etc/slurm, /opt/lsync"
        ssh -p $ClusterPort $Remote 'sudo chown -R lsync /opt/lsync/'
        ssh -p $ClusterPort $Remote 'sudo chown -R lsync /etc/slurm/'

 fi
done < /etc/cluster/cluster-server.namelist

sudo chown -R lsync /etc/slurm/
sudo chown -R lsync /opt/lsync/
rm -f $SECRET_FILE
rm -f $PUBLIC_FILE
sudo runuser -l lsync -c "lsyncd -rsyncssh /etc/slurm bigMem0 /etc/slurm"

How to mount a disk from another Linux machine

For slurm to share data between nodes, each node should mount the same disk to all nodes at the same directory

  1. yum install nfs-utils on both client and server
  2. edit server-side: /etc/exports like /home 10.66.66.100(rw)
  3. run systemctl start nfs on both client and server
  4. call mount 10.66.66.88:/home /home (use showmount -e server_ip to see what is available / use telnet to ensure firewall is configured) Files in original HOME directory WILL be unable to access until you umount it.

Other references

To view the current default target, run: systemctl get-default

To set a default target, run: systemctl set-default TARGET.target

installing modules yum install environment-modules

In case nodes are restarted manually, scontrol will set the node to DOWN state. You should run scontrol update NodeName=nodename State=RESUME to reset.

In case you mount something wrongly, for me it was mount \-o loop /mnt/xx/xx /mnt, try to umount with -f(force) and -l (lazy) options.

slurm报错: Job credential expired证书过期

可能的问题: 机器时间不同步，误差超过30s；机器之间munge的uid不一致；munge.key不一致

时间同步可以使用ntpdate, 一起向loginNode同步时间.

参考: https://www.cnblogs.com/williamjie/p/10768657.html

Useful links

=== not done yet ====

install MATLAB

install open-mpi

correct gcc/g++/gfrotran version

correct python/anaconda version

manage python packages

install docker

use pam_slurmd

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