OPENHPC搭建集群

利用OpenHPC搭建CentoS7.X集群

主节点系统（CentOS-7.7）配置
管理节warewulf点配置
配置计算节点
创建计算节点启动镜像
组装Virtual Node File System (VNFS) 镜像
添加节点
计算节点完成安装后设置

目前搭建HPC的开源工具主要有RocksCluster, Xcat，Open-HPC。其中OpenHPC 是Linux基金开源的超算项目，致力于为高性能计算构建一个开源框架，适应学术研究的需求，为 HPC 环境创建一个开源框架，降低成本。

本次采用虚拟机实验，没有Infiniband,故先不介绍Infiniband的配置

主节点系统（CentOS-7.7）配置

配置参数说明

环境变量	变量名称说明	模版参数
${sms_name}	主机名	server
${sms_ip}	主节点内网地址	192.168.130.100
$sms_eth_internal	主节点内网网卡名称	ens33
${eth_provision}	主节点与计算节点通信网卡名称	ens33
${internal_netmask}	内网子网掩码	255.255.255.0
${ntp_server}	本地时间同步服务器	192.168.130.100
${c_ip[0]}, {c_ip[1]} ,…	计算节点名称	192.168.130.[1-5]
${c_name[0]}, ${c_name[1]} ,…	计算节点名称	192.168.130.[1-5]
${sms_ipoib}	主节点Inifiniband网络地址	192.168.120.100
${ipoib_netmask}	主节点Infiniband网络子网掩码	255.255.255.0
${c_ipoib[0]},&{c_ipoib[1]},…	计算节点Infiniband网络IP地址	192.168.120.[1-5]
$compute_regex	计算节点名称正则表达式	node[1-5]
${compute_prefix}	计算节点名称前缀	node
${kargs}	Linux内核启动参数	net.ifnames=1

添加hosts文件信任

 [root@server ~]#echo "192.168.130.1  node1" >> /etc/hosts[root@server ~]#echo "192.168.130.2  node2" >> /etc/hosts[root@server ~]#echo "192.168.130.3  node3" >> /etc/hosts[root@server ~]#echo "192.168.130.4  node4" >> /etc/hosts[root@server ~]#echo "192.168.130.5  node5" >> /etc/hosts

关闭防火墙

 [root@server ~]#systemctl stop firewaled.sevice[root@server ~]#systemctl disabled firewaled.sevice

关闭SELinux ；

 [root@server ~]#vi /etc/selinux/deisabled

配置NTP服务 ；

 [root@server ~]#echo "server 192.168.130.100" >> /etc/ntp.conf[root@server ~]#systemctl enable ntpd.service

配置内网网卡 ；

 [root@server ~]# vi /etc/sysconfig/network-scripts/ifcfg-ens33TYPE=EthernetPROXY_METHOD=noneBROWSER_ONLY=noBOOTPROTO=staticDEFROUTE=yesIPV4_FAILURE_FATAL=noIPV6INIT=yesIPV6_AUTOCONF=yesIPV6_DEFROUTE=yesIPV6_FAILURE_FATAL=noIPV6_ADDR_GEN_MODE=stable-privacyNAME=ens33UUID=******************************DEVICE=ens33ONBOOT=yesIPADDR=192.168.130.100PREFIX=24IPV6_PRIVACY=no

ohpc-base,warewulf,pbs ；

安装open-HPC yum源 ohpc-release；

 [root@server ~]#yum install http://build.openhpc.community/OpenHPC:/1.3/CentOS_7/x86_64/ohpc-release-1.3-1.el7.x86_64.rpm[root@server ~]#yum -y install ohpc-base[root@server ~]#yum -y install ohpc-warewulf[root@server ~]#yum -y install pbspro-server-ohpc

管理节warewulf点配置

将/etc/warewulf/provision.conf文件中的 network device = eth1 改成内网网卡ens33

 [root@server ~]# vi /etc/warewulf/provision.conf# What is the default network device that the master will use to# communicate with the nodes?network device = ens33# Which DHCP server implementation should be used?dhcp server = isc# What is the TFTP root directory that should be used to store the# network boot images? By default Warewulf will try and find the# proper directory. Just add this if it can't locate it.#tftpdir = /var/lib/tftpboot# Automatically generate and manage a dynamnic_host virtual file# object in the datastore? This is useful for provisioning this# out to nodes so they always have a current /etc/hosts file.generate dynamic_hosts = yes# Should we manage and overwrite the local hostfile file on this# system? This will cause all node entries to be added# automatically to /etc/hosts.update hostfile = yes# If no cluster/domain is set on a node, should we add 'localdomain'# as the default domainuse localdomain = yes# The default kernel arguments to pass to the nodes boot kerneldefault kargs = "net.ifnames=0 biosdevname=0 quiet"

编辑/etc/xinetd.d/tftp文件, 将disable = yes改为 disable = no

 [root@server ~]# vi /etc/xinetd.d/tftp# default: off# description: The tftp server serves files using the trivial file transfer \#       protocol.  The tftp protocol is often used to boot diskless \#       workstations, download configuration files to network-aware printers, \#       and to start the installation process for some operating systems.service tftp{socket_type             = dgramprotocol                = udpwait                    = yesuser                    = rootserver                  = /usr/sbin/in.tftpdserver_args             = -s /var/lib/tftpbootdisable                 = noper_source              = 11cps                     = 100 2flags                   = IPv4}

启动xinetd,mariadb,http服务

 [root@server ~]# systemctl restart xinetd.service[root@server ~]# systemctl enable xinetd.service[root@server ~]# systemctl restart mariadb.service[root@server ~]# systemctl enable mariadb.service[root@server ~]# systemctl enable httpd.service[root@server ~]# systemctl restart httpd.service[root@server ~]# systemctl restart dhcpd.service

重启管理节点！

配置计算节点

配置DHCP服务

 [root@server ~]# cp /etc/warewulf/dhcpd-template.conf /etc/dhcp/dhcpd.conf[root@server ~]# vi /etc/dhcp/dhcpd.conf# DHCPD Configuration written by Warewulf. Do not edit this file, rather# edit the template: /etc/warewulf/dhcpd-template.confallow booting;allow bootp;ddns-update-style interim;authoritative;option space ipxe;# Tell iPXE to not wait for ProxyDHCP requests to speed up boot.option ipxe.no-pxedhcp code 176 = unsigned integer 8;option ipxe.no-pxedhcp 1;option architecture-type   code 93  = unsigned integer 16;if exists user-class and option user-class = "iPXE" {filename "http://192.168.130.100/WW/ipxe/cfg/${mac}";} else {if option architecture-type = 00:0B {filename "/warewulf/ipxe/bin-arm64-efi/snp.efi";} elsif option architecture-type = 00:0A {filename "/warewulf/ipxe/bin-arm32-efi/placeholder.efi";} elsif option architecture-type = 00:09 {filename "/warewulf/ipxe/bin-x86_64-efi/snp.efi";} elsif option architecture-type = 00:07 {filename "/warewulf/ipxe/bin-x86_64-efi/snp.efi";} elsif option architecture-type = 00:06 {filename "/warewulf/ipxe/bin-i386-efi/snp.efi";} elsif option architecture-type = 00:00 {filename "/warewulf/ipxe/bin-i386-pcbios/undionly.kpxe";}}subnet 192.168.130.0 netmask 255.255.255.0 {not authoritative;# option interface-mtu 9000;# option subnet-mask 255.255.255.0;}# Node entries will follow below

创建BOS镜像

 [root@server ~]#export CHROOT=/opt/ohpc/admin/images/centos7.7[root@server ~]#wwmkchroot centos-7 $CHROOT[root@server ~]#yum -y --installroot=$CHROOT install ohpc-base-compute

配置NFS服务

初始化warewulf database和ssh_keys

 [root@server ~]#wwinit database[root@server ~]#wwinit ssh_keys[root@server ~]#echo "192.168.130.100:/home /home nfs nfsvers=3,nodev,nosuid 0 0" >> $CHROOT/etc/fstab[root@server ~]#echo "192.168.130.100:/opt/ohpc/pub /opt/ohpc/pub nfs nfsvers=3,nodev 0 0" >> $CHROOT/etc/fstab[root@server ~]#echo "/home 192.168.130.0/24(rw,no_subtree_check,fsid=10,no_root_squash)" >> /etc/exports[root@server ~]#echo "/opt/ohpc/pub 192.168.130,0/24(ro,no_subtree_check,fsid=11)" >> /etc/exports[root@server ~]#exportfs -a[root@IMP-Cluster ~]# showmount -eExport list for server:/opt/ohpc/pub 192.168.130.0/24/home         192.168.130.0/24[root@server ~]#systemctl restart nfs-server.service[root@server ~]#systemctl enable nfs-server.service[root@server ~]#chroot $CHROOT systemctl enable ntpd.service[root@server ~]# echo "server 192.168.130.100" >> $CHROOT/etc/ntp.conf

配置PBSPro

 [root@server ~]# yum -y --installroot=$CHROOT install pbspro-execution-ohpc[root@server ~]# vi $CHROT/etc/pbs.confPBS_EXEC=/opt/pbsPBS_SERVER=server       !!!修改为管理节点的名称serverPBS_START_SERVER=0PBS_START_SCHED=0PBS_START_COMM=0PBS_START_MOM=1PBS_HOME=/var/spool/pbsPBS_CORE_LIMIT=unlimitedPBS_SCP=/bin/scp[root@server ~]#echo "PBS_LEAF_NAME=server" >> /etc/pbs.confPBS_EXEC=/opt/pbsPBS_SERVER=IMP-ClusterPBS_START_SERVER=1PBS_START_SCHED=1PBS_START_COMM=1PBS_START_MOM=0PBS_HOME=/var/spool/pbsPBS_CORE_LIMIT=unlimitedPBS_SCP=/bin/scpPBS_LEAF_NAME=server         !!增加这一行[root@server ~]#chroot $CHROOT opt/pbs/libexec/pbs_habitat[root@server ~]#echo "\$usecp *:/home /home" >> $CHROOT/var/spool/pbs/mom_priv/config[root@server ~]#vi $CHROOT/var/spool/pbs/mom_priv/config$clienthost server$usecp *:/home /home[root@server ~]# chroot $CHROOT systemctl enable pbs#NTP网络服务[root@server ~]# yum -y --installroot=$CHROOT install ntp#内核驱动[root@server ~]# yum -y --installroot=$CHROOT install kernel# module加载环境[root@server ~]# yum -y --installroot=$CHROOT install lmod-ohpc

取消镜像中计算节点内存资源限制

 [root@server ~]#vi $CHROOT/etc/security/limits.conf#<domain>      <type>  <item>         <value>##*               soft    core            0#*               hard    rss             10000#@student        hard    nproc           20#@faculty        soft    nproc           20#@faculty        hard    nproc           50#ftp             hard    nproc           0#@student        -       maxlogins       4* soft memlock unlimited     !!修改* hard memlock unlimited        !!修改# End of file

配置ganglia监控

 [root@server ~]# yum -y install ohpc-ganglia[root@server ~]# yum -y --installroot=$CHROOT install ganglia-gmond-ohpc[root@server ~]# cp /opt/ohpc/pub/examples/ganglia/gmond.conf /etc/ganglia/gmond.conf[root@server ~]# vi /etc/ganglia/gmond.conf/* The host section describes attributes of the host, like the location */host {location = "unspecified"}/* Feel free to specify as many udp_send_channels as you like.  Gmondused to only support having a single channel */udp_send_channel {#bind_hostname = yes # Highly recommended, soon to be default.# This option tells gmond to use a source address# that resolves to the machine's hostname.  Without# this, the metrics may appear to come from any# interface and the DNS names associated with# those IPs will be used to create the RRDs.host = server           !!!修改成当前主机名port = 8649ttl = 1}[root@server ~]# cp /etc/ganglia/gmond.conf $CHROOT/etc/ganglia/gmond.conf[root@server ~]# echo "gridname MyCluster" >> /etc/ganglia/gmetad.conf# 设置ganglia服务开机启动[root@server ~]# systemctl enable gmond.service[root@server ~]# systemctl enable gmetad.service[root@server ~]# systemctl start gmond.service[root@server ~]# systemctl start gmetad.service[root@server ~]# chroot $CHROOT systemctl enable gmond.service#重启HTTP服务[root@server ~]# systemctl try-restart httpd.service

在浏览器中输入http://192.168.130.100/ganglia就可以查看ganglia监控界面。

安装节点健康检查资源管理包NHC

 # 管理节点和计算节点分别安装NHC[root@server ~]# yum -y install nhc-ohpc[root@server ~]# yum -y --installroot=$CHROOT install nhc-ohpc

同步用户信息

 [root@server ~]# wwsh file import /etc/passwd[root@server ~]# wwsh file import /etc/group[root@server ~]# wwsh file import /etc/shadow

创建计算节点启动镜像

 [root@server ~]# wwbootstrap `uname -r`

组装Virtual Node File System (VNFS) 镜像

 [root@server ~]# wwvnfs --chroot $CHROOT

添加节点

设置主节点与计算节点默认网络通讯网卡

 # Set provisioning interface as the default networking device[root@server ~]# echo "GATEWAYDEV=ens33" > /tmp/network.$$[root@server ~]# wwsh -y file import /tmp/network.$$ --name network[root@server ~]# wwsh -y file set network --path /etc/sysconfig/network --mode=0644 --uid=0

设置计算节点网卡名称

 [root@server ~]# export kargs="${kargs} net.ifnames=1,biosdevname=1"[root@server ~]# wwsh provision set --postnetdown=1 "node[1-5]"

设置计算节点安装镜像，启动项与用户信息

 [root@server ~]# wwsh -y provision set "node[1-5]" --vnfs=centos7.7 --bootstrap=`uname -r` --files=dynamic_hosts,passwd,group,shadow,network

添加节点

 [root@server ~]# wwsh -y node new node1 --netdev=ens33 --ipaddr=192.168.130.1 --hwaddr=00:00:00:00:00:01 -D ens33[root@server ~]# wwsh -y node new node2 --netdev=ens33 --ipaddr=192.168.130.2 --hwaddr=00:00:00:00:00:02 -D ens33[root@server ~]# wwsh -y node new node3 --netdev=ens33 --ipaddr=192.168.130.3 --hwaddr=00:00:00:00:00:03 -D ens33[root@server ~]# wwsh -y node new node4 --netdev=ens33 --ipaddr=192.168.130.4 --hwaddr=00:00:00:00:00:04 -D ens33[root@server ~]# wwsh -y node new node5 --netdev=ens33 --ipaddr=192.168.130.5 --hwaddr=00:00:00:00:00:05 -D ens33

设置计算节点安装在本地硬盘并安装grub引导

 [root@server ~]# yum -y --installroot=$CHROOT install grub2[root@server ~]# wwvnfs --chroot $CHROOT[root@server ~]# cp /etc/warewulf/filesystem/examples/gpt_example.cmds /etc/warewulf/filesystem/gpt.cmds[root@server ~]# wwsh provision set --filesystem=gpt "node[1-5]"[root@server ~]# wwsh provision set --bootloader=sda "node[1-5]"

更新DHCP和PXE

 [root@server ~]# wwsh dhcp update[root@server ~]# wwsh pxe update

这是一个简单的脚本，可以自动完成计算节点添加与配置

#!/bin/bashNODE=node3                           !!修改为节点名
IPADDR=192.168.130.3               !!计算节点IP地址
MAC=xx:xx:xx:xx:xx:xx              !!计算节点MAC地址wwsh -y node new $NODE --netdev=enp2s0 --ipaddr=$IPADDR  --netmask=255.255.255.0 --hwaddr=$MAC -D enp2s0
sleep 1s
export kargs="enp2s0 net.ifnames=1,biosdevname=1"
wwsh -y provision set --postnetdown=1 "$NODE"
wwsh -y provision set "$NODE" --vnfs=centos7.7 --bootstrap=`uname -r` --files=dynamic_hosts,passwd,group,shadow,network
wwsh -y provision set --filesystem=gpt "$NODE"
wwsh -y provision set --bootloader=sda "$NODE"
sleep 1s
wwsh dhcp update
wwsh pxe update

计算节点完成安装后设置

计算节点安装成功后设置从本地硬盘启动

 [root@server ~]# wwsh provision set --bootlocal=normal "node[1-5]"

查看安装节点

 #### node1 ####################################################################node1: BOOTSTRAP        = 3.10.0-1062.el7.x86_64node1: VNFS             = centos7.7node1: FILES            = dynamic_hosts,group,network,passwd,shadownode1: PRESHELL         = FALSEnode1: POSTSHELL        = FALSEnode1: CONSOLE          = UNDEFnode1: PXELINUX         = UNDEFnode1: SELINUX          = DISABLEDnode1: KARGS            = "net.ifnames=1,biosdevname=1"node1: FS               = "select /dev/sda,mklabel gpt,mkpart primary 1MiB 3MiB,mkpart primary ext4 3MiB 513MiB,mkpart primary linux-swap 513MiB 50%,mkpart primary ext4 50% 100%,name 1 grub,name 2 boot,name 3 swap,name 4 root,set 1 bios_grub on,set 2 boot on,mkfs 2 ext4 -L boot,mkfs 3 swap,mkfs 4 ext4 -L root,fstab 4 / ext4 defaults 0 0,fstab 2 /boot ext4 defaults 0 0,fstab 3 swap swap defaults 0 0"node1: BOOTLOADER       = sdanode1: BOOTLOCAL        = NORMAL#### node2 ####################################################################node2: BOOTSTRAP        = 3.10.0-1062.el7.x86_64node2: VNFS             = centos7.7node2: FILES            = dynamic_hosts,group,network,passwd,shadownode2: PRESHELL         = FALSEnode2: POSTSHELL        = FALSEnode2: CONSOLE          = UNDEFnode2: PXELINUX         = UNDEFnode2: SELINUX          = DISABLEDnode2: KARGS            = "net.ifnames=1,biosdevname=1"node2: FS               = "select /dev/sda,mklabel gpt,mkpart primary 1MiB 3MiB,mkpart primary ext4 3MiB 513MiB,mkpart primary linux-swap 513MiB 50%,mkpart primary ext4 50% 100%,name 1 grub,name 2 boot,name 3 swap,name 4 root,set 1 bios_grub on,set 2 boot on,mkfs 2 ext4 -L boot,mkfs 3 swap,mkfs 4 ext4 -L root,fstab 4 / ext4 defaults 0 0,fstab 2 /boot ext4 defaults 0 0,fstab 3 swap swap defaults 0 0"node2: BOOTLOADER       = sdanode2: BOOTLOCAL        = NORMAL#### node3 ####################################################################node3: BOOTSTRAP        = 3.10.0-1062.el7.x86_64node3: VNFS             = centos7.7node3: FILES            = dynamic_hosts,group,network,passwd,shadownode3: PRESHELL         = FALSEnode3: POSTSHELL        = FALSEnode3: CONSOLE          = UNDEFnode3: PXELINUX         = UNDEFnode3: SELINUX          = DISABLEDnode3: KARGS            = "net.ifnames=1,biosdevname=1"node3: FS               = "select /dev/sda,mklabel gpt,mkpart primary 1MiB 3MiB,mkpart primary ext4 3MiB 513MiB,mkpart primary linux-swap 513MiB 50%,mkpart primary ext4 50% 100%,name 1 grub,name 2 boot,name 3 swap,name 4 root,set 1 bios_grub on,set 2 boot on,mkfs 2 ext4 -L boot,mkfs 3 swap,mkfs 4 ext4 -L root,fstab 4 / ext4 defaults 0 0,fstab 2 /boot ext4 defaults 0 0,fstab 3 swap swap defaults 0 0"node3: BOOTLOADER       = sdanode3: BOOTLOCAL        = NORMAL#### node4 ####################################################################node4: BOOTSTRAP        = 3.10.0-1062.el7.x86_64node4: VNFS             = centos7.7node4: FILES            = dynamic_hosts,group,network,passwd,shadownode4: PRESHELL         = FALSEnode4: POSTSHELL        = FALSEnode4: CONSOLE          = UNDEFnode4: PXELINUX         = UNDEFnode4: SELINUX          = DISABLEDnode4: KARGS            = "net.ifnames=1,biosdevname=1"node4: FS               = "select /dev/sda,mklabel gpt,mkpart primary 1MiB 3MiB,mkpart primary ext4 3MiB 513MiB,mkpart primary linux-swap 513MiB 50%,mkpart primary ext4 50% 100%,name 1 grub,name 2 boot,name 3 swap,name 4 root,set 1 bios_grub on,set 2 boot on,mkfs 2 ext4 -L boot,mkfs 3 swap,mkfs 4 ext4 -L root,fstab 4 / ext4 defaults 0 0,fstab 2 /boot ext4 defaults 0 0,fstab 3 swap swap defaults 0 0"node4: BOOTLOADER       = sdanode4: BOOTLOCAL        = NORMAL#### node5 ####################################################################node5: BOOTSTRAP        = 3.10.0-1062.el7.x86_64node5: VNFS             = centos7.7node5: FILES            = dynamic_hosts,group,network,passwd,shadownode5: PRESHELL         = FALSEnode5: POSTSHELL        = FALSEnode5: CONSOLE          = UNDEFnode5: PXELINUX         = UNDEFnode5: SELINUX          = DISABLEDnode5: KARGS            = "net.ifnames=1,biosdevname=1"node5: FS               = "select /dev/sda,mklabel gpt,mkpart primary 1MiB 3MiB,mkpart primary ext4 3MiB 513MiB,mkpart primary linux-swap 513MiB 50%,mkpart primary ext4 50% 100%,name 1 grub,name 2 boot,name 3 swap,name 4 root,set 1 bios_grub on,set 2 boot on,mkfs 2 ext4 -L boot,mkfs 3 swap,mkfs 4 ext4 -L root,fstab 4 / ext4 defaults 0 0,fstab 2 /boot ext4 defaults 0 0,fstab 3 swap swap defaults 0 0"node5: BOOTLOADER       = sdanode5: BOOTLOCAL        = NORMAL

 [root@server ~]# wwsh node listNAME                GROUPS              IPADDR              HWADDR
================================================================================
node1               UNDEF               192.168.130.1       xx:xx:xx:xx:xx:01
node2               UNDEF               192.168.130.2       xx:xx:xx:xx:xx:02
node3               UNDEF               192.168.130.3       xx:xx:xx:xx:xx:03
node4               UNDEF               192.168.130.4       xx:xx:xx:xx:xx:04
node5               UNDEF               192.168.130.5       xx:xx:xx:xx:xx:05

可查看/etc/hosts文件，通过warewulf添加成功的hosts

 ### ALL ENTRIES BELOW THIS LINE WILL BE OVERWRITTEN BY WAREWULF ##### See provision.conf for configuration paramaters# Node Entry for node: node1 (ID=1)192.168.130.1           node1.localdomain node1 node1-ens33.localdomain node1-ens33# Node Entry for node: node2 (ID=2)192.168.130.2           node2.localdomain node2 node2-ens33.localdomain node2-ens33# Node Entry for node: node3 (ID=3)192.168.130.3           node3.localdomain node3 node3-ens33.localdomain node3-ens33# Node Entry for node: node4 (ID=4)192.168.130.4           node4.localdomain node4 node4-ens33.localdomain node4-ens33# Node Entry for node: node5 (ID=5)192.168.130.5           node5.localdomain node5 node5-ens33.localdomain node5-ens33

至此，整个集群搭建完成，可以部署相关计算应用环境。

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