高性能集群 并行计算 mpich hpc 及 torque作业调度系统

主机系统:rhel6.0 (数量不限)

系统环境:selinux and iptables disabled

服务节点: desktop26.example.com     192.168.0.26

计算节点: desktop80.example.com     192.168.0.80

                  desktop83.example.com     192.168.0.83

 

1. 使用SSH密钥让各个节点做到无需密码连接

 

先要在每个节点都要新建一个普通用户用作以后的集群用户

useradd yejk
passwd yejk (密码设为westos）

注意每台节点上的这个普通用户的密码和ID必须相同

 

这里要注意，无论有多少个节点，这个普通用户家目录里的数据都应该完全相同，为了达到这一点可以用一些网络存储实现，这里使用NFS实现，因为实现方法简单且工作稳定

在任意一个节点上部署NFS将yejk的家目录发布出来，其他节点直接挂载此家目录

 

yum install nfs-utils rpcbind -y
vim /etc/exports
/home/yejk      192.168.0.0/24(rw,no_root_squash)
exportfs -r     #使配置生效
exportfs -v     #查看
/etc/init.d/rpcbind start    #需要rpcbind支持
/etc/init.d/nfs start
mount 192.168.0.80:/home/yejk /home/yejk
vim /etc/fstab
192.168.0.80:/home/yejk /home/yejk              nfs     defaults        0 0

此时在任意节点上的操作就可以在每个节点上生效

su - yejk
ssh-keygen 一路回车即可
ssh-copy-id -i ~/.ssh/id_rsa.pub desktop80.example.com(与自己信任连接)
ssh-copy-id -i ~/.ssh/id_rsa.pub desktop83.example.com(与其他节点信任连接)
sh-copy-id -i ~/.ssh/id_rsa.pub desktop26.example.com(与其他节点信任连接)

 

 

2.在每个节点上安装mpich2

yum install mpich2 -y
su - yejk
cd /home/yejk

创建.mpd.conf文件 (文件前加".")

vim .mpd.conf
secretword=westos    #节点的密码，每台节点都得相同
chmod 600 .mpd.conf

创建集群节点集合文件mpd.hosts

vim mpd.hosts
desktop80.example.com
desktop83.example.com

 

 

注:如果以root用户启动mpd服务, 把mpd.conf文件创建在/etc目录中(不加"."),mpd.hosts放在root主目录中

3.1测试mpich2:

启动mpich2

mpd

观看启动机器:

 

mpdtrace
desktop80.example.com

 

退出:

 

mpdallexit

3.2运行集群系统

mpdboot -n 2 -f mpd.hosts    参数-n 2指定了要起动的机器个数,-f mpd.hosts指定了运行mpd.hosts文件中指定的节点。
mpdtrace
desktop80.example.com
desktop83.example.com
mpdallexit

 

 

3.3单机测试  

./icpi-64
Enter the number of intervals: (0 quits) 1000000000
pi is approximately 3.1415926535921401, Error is 0.0000000000023470
wall clock time = 46.571311
Enter the number of intervals: (0 quits) 10000
pi is approximately 3.1415926544231341, Error is 0.0000000008333410
wall clock time = 0.000542
Enter the number of intervals: (0 quits) 0

 

 

3.4 集群测试

mpdboot -n 2 -f mpd.hosts
mpiexec -n 2 /root/icpi-64
Enter the number of intervals: (0 quits) 1000000000
pi is approximately 3.1415926535899761, Error is 0.0000000000001830
wall clock time = 15.530082
Enter the number of intervals: (0 quits) 10000
pi is approximately 3.1415926544231323, Error is 0.0000000008333392
wall clock time = 0.006318
Enter the number of intervals: (0 quits) 0
mpdallexit

 

由上述测试的结果可以看出使用单机单进程运行,intervals设为1000000000,耗时46.571311秒,而用两台机器双进程则只有15.530082秒,明显快很多,并行运算还是

很有效果的。不过,如果我们把intervals改为10000,单机运行只用了0.000542秒,而两台机器却花了0.006318秒,这是因为并行运算过程中,参与运算的机器需要通过网

络传递一些消息,如果计算量不大的话,花在了这上面的时间影响会比较明显,因而反不如单机版的来得快

 

4. 排错

 

mpdcheck获得帮助信息
mpdcheck -pc
mpdcheck -l
通过mpd.hosts文件查错
mpdcheck -f mpd.hosts
mpdcheck -f mpd.hosts -ssh
对任意两台机器进行查错
Station11上:
mpdcheck -s
返回主机名host和端口port
server listening at INADDR_ANY on: station11 52576
station12上:
mpdcheck -c 192.168.0.1 40782
client successfully recvd ack from server: ack_from_server _to_client
station11 上返回消息传递结果
server has conn on from ('192.168.0.12', 54438)
server successfully recvd msg from client: hello_from_client_to_server
station1上:
mpd -e &
返回使用的端口
[1]12703
mpd_port=42498
station12上:
mpd -h station11 -p 41563 &
[1]5122

 torque作业调度系统

 

yum install gcc gcc-c++ make -y
tar zxf torque-3.0.0.tar.gz
cd torque-3.0.0
./configure --with-rcp=scp --with-default-server=desktop26.example.com (--with-rcp=scp用于ssh key方式)
make
make install (torque的配置目录: /var/spool/torque)
make packages (生成计算节点安装包,即在station11和station12上安装的包,确保所有计算节点和服务节点的架构是相同的)
cp contrib/init.d/pbs_server /etc/init.d/
cp contrib/init.d/pbs_sched /etc/init.d/
scp contrib/init.d/pbs_mom desktop80.example.com:/etc/init.d
scp contrib/init.d/pbs_mom desktop83.example.com:/etc/init.d
vi /var/spool/torque/server_priv/nodes (设定计算节点,服务节点也可做计算)
desktop80.example.com
desktop83.example.com
./torque.setup root (设置torque的管理帐户)
qterm -t quick (停止torque)
service pbs_server start (启动torque)
service pbs_sched start  (启动调度程序）
scp torque-package-clients-linux-x86_64.sh torque-package-mom-linux-x86_64.sh desktop80.example.com:~
scp torque-package-clients-linux-x86_64.sh torque-package-mom-linux-x86_64.sh desktop83.example.com:~

 在所有计算节点安装torque,在所有计算节点执行如下命令:

 

./torque-package-clients-linux-x86_64.sh --install
./torque-package-mom-linux-x86_64.sh --install

注:如果计算节点的架构和服务节点不同,安装方法如下:

 

tar zxf torque-3.0.0.tar.gz
./configure --with-rcp=scp --with-default-server=server1.example.com
make
make install_mom install_clients

 

vi /var/spool/torque/mom_priv/config (所有计算节点执行此配置)
$pbsserver server1.example.com
$logevent 255
service pbs_mom start (所有计算节点执行此命令,启动计算节点守护进程)

测试

torque的调度需要使用非root用户

 

su - yejk
cd /home/yejk
vim job1.pbs (串行作业)
#!/bin/bash
#PBS -N job1
#PBS -o job1.log
#PBS -e job1.err
#PBS -q batch
cd /home/yejk
echo Running on hosts `hostname`
echo Time is `date`
echo Directory is $PWD
echo This job runs on the following nodes:
cat $PBS_NODEFILE
echo This job has allocated 1 node
./prog

vi job2.pbs (并行作业)
#!/bin/bash
#PBS -N job2
#PBS -o job2.log
#PBS -e job2.err
#PBS -q batch
#PBS -l nodes=2
cd /home/yejk
echo Time is `date`
echo Directory is $PWD
echo This job runs on the following nodes:
cat $PBS_NODEFILE
NPROCS=`wc -l < $PBS_NODEFILE`
echo This job has allocated $NPROCS nodes
mpiexec -machinefile $PBS_NODEFILE -np $NPROCS ./prog

vi prog
#!/bin/bash
echo 1000000000 | ./icpi-64 (icpi程序是mpi自带的,拷贝过来即可)
chmod +x prog

 

qsub jobx.pbs(提交作业)
qstat (查看作业)
pbsnodes (查看节点)

使用单节点计算,串行计算截图：

 

 

查看结果

[yejk@desktop26 ~]$ cat job1.log
Running on hosts desktop80.example.com
Time is Sat Jun 2 05:33:32 CST 2012
Directory is /home/yejk
This job runs on the following nodes:
desktop80.example.com
This job has allocated 1 node
Enter the number of intervals: (0 quits) pi is approximately 3.1415926535899708, Error is 0.0000000000001776
wall clock time = 43.059767
Enter the number of intervals: (0 quits) No number entered; quitting

使用集群并行计算截图：

 

 

[yejk@desktop26 ~]$ cat job2.log
Time is Sat Jun 2 05:49:29 CST 2012
Directory is /home/yejk
This job runs on the following nodes:
desktop83.example.com
desktop80.example.com
This job has allocated 2 nodes
Enter the number of intervals: (0 quits) pi is approximately 3.1415926535900072, Error is 0.0000000000002141
wall clock time = 23.318623
Enter the number of intervals: (0 quits) No number entered; quitting
You have mail in /var/spool/mail/yejk
[yejk@desktop26 ~]$

可以看到同样的任务并行的时间用的短

注:1. 以上测试我是以yejk用户测试,确保所有节点上有此用户,并且在计算节点上的yejk用户目录中有 prog 和 icpi 两个可执行程序

2. 启动mpd程序时要使用yejk用户 因为在调度时会连接计算节点上/tmp/

mpd2.console_yejk