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安装前的要求如果是单机跑跑pbs, 那么什么都不要求. 如果你想在机群上pbs,那么再进行pbs安装之前你需要保证一些其他的软件都能工作.
- NFS 这个是为了在机群之间共享一个目录, 使得个个机器都能访问.
- Nis 这是是为了在机群上实现统一的用户认证.
安装pbs的安装比较简单, 应该说是一个标准的linux的tarball安装方式. 安装过程主要有如下几步:
- 下载pbs的源码包 OpenPBS-2.3.12sc2.tar。
- 解压缩软件包 $tar zxvpf OpenPBS-2.3.12sc2.tar
- 进入相应的目录, 配置,make $cd SPBS-1.0.0
$./configure --enable-docs --disable-gui
$make
注意上面的选项 --enable-docs 指定要编译文档
--disable-gui 指定去掉图形界面. 因为图形界面要求需要tck支持, 而且似乎必须是tcl-8.0的版本, 高了会出错
--enable-scp 先使用scp,再使用rcp进行数据的复制.
- 切换成root用户, 安装. $su
#make install
默认情况下, PBS会安装再/usr/spoole/PBS目录下. 该目录在./configure 的时候指定 --prefix=/you/want/dir来更改. 建议对于初次安装的人采用默认的设置.
PBS的配置一般来说, PBS系统必须有一个server和至少一个mom,
server负责作业的提交, mom接受server的控制,负责作业的执行. 假设pbs的根目录为 $PBS_HOME.
server节点为CGSP48, mom节点为CGSP48和CGSP47,也就是CGSP48既作为共享server也作为mom,
而CGSP47只作为mom.
配置server_name 编辑所有的节点的 $PBS_HOME/server_name,在里面写入选定的server的主机名. 例如 CGSP48
配置节点. 在CGSP48的 $PBS_HOME/server_priv目录下建立nodes文件. touch nodes
在nodes文件写入你所有mom节点的名称: CGSP48 np=2
CGSP47 np=3
其中的np代表的是虚拟处理器的个数. 实际上也就是该节点最多可以同时跑多少个任务.
配置mom节点,使其接受sever节点的控制. 编辑每个mom节点的 $PBS_HOME/mom_priv目录下的config文件(没有就自己建立). 写入如下信息 $logevent 0x1ff
$clienthost CGSP48
其中: $logevent 指定的日志的级别, 基本上不用修改. 默认就很好了
$clienthost 指定的server的地址
起动PBS.pbs起动最好按如下顺序. mom, sever, sched. 而且必须以root身份起动. 命令如下: # /usr/local/sbin/pbs_mom
# /usr/local/sbin/pbs_server -t create
# /usr/local/sbin/pbs_sched
其中, -t create 在第一次起动的时候要用, 用于创建一些初始化必要的环境. 以后起动就不在需要了.
创建队列.PBS中的队列分为两种类型, 执行队列和路由队列. 下面是一个创建队列的脚本.
#
# Create and define queue verylong
#
create queue verylong
set queue verylong queue_type = Execution
set queue verylong Priority = 40
set queue verylong max_running = 10
set queue verylong resources_max.cput = 72:00:00
set queue verylong resources_min.cput = 12:00:01
set queue verylong resources_default.cput = 72:00:00
set queue verylong enabled = True
set queue verylong started = True
#
# Create and define queue long
#
create queue long
set queue long queue_type = Execution
set queue long Priority = 60
set queue long max_running = 10
set queue long resources_max.cput = 12:00:00
set queue long resources_min.cput = 02:00:01
set queue long resources_default.cput = 12:00:00
set queue long enabled = True
set queue long started = True
#
# Create and define queue medium
#
create queue medium
set queue medium queue_type = Execution
set queue medium Priority = 80
set queue medium max_running = 10
set queue medium resources_max.cput = 02:00:00
set queue medium resources_min.cput = 00:20:01
set queue medium resources_default.cput = 02:00:00
set queue medium enabled = True
set queue medium started = True
#
# Create and define queue small
#
create queue small
set queue small queue_type = Execution
set queue small Priority = 100
set queue small max_running = 10
set queue small resources_max.cput = 00:20:00
set queue small resources_default.cput = 00:20:00
set queue small enabled = True
set queue small started = True
#
# Create and define queue default
#
create queue default
set queue default queue_type = Route
set queue default max_running = 10
set queue default route_destinations = small
set queue default route_destinations += medium
set queue default route_destinations += long
set queue default route_destinations += verylong
set queue default enabled = True
set queue default started = True
#
# Set server attributes.
#
set server scheduling = True
set server max_user_run = 6
set server acl_host_enable = True
set server acl_hosts = *
set server default_queue = default
set server log_events = 63
set server mail_from = adm
set server query_other_jobs = True
set server resources_default.cput = 01:00:00
set server resources_default.neednodes = 1
set server resources_default.nodect = 1
set server resources_default.nodes = 1
set server scheduler_iteration = 60
set server default_node = 1#shared
该脚本定义了verylong long medium small 四个作业队列 和 一个default路由队列. 里面的几个比较重要的属性: enabled 指示作业队列可用. 也就是可以往里面添加新的作业了.
actived 指示作业队列处于活动状态, 可以参与调度了. 好象是这个样子的. 反正两个都设置为true就可以了.
sever的scheduling属性指示server开始调度. 这个属性非常的重要.
为了这个属性, 我浪费了一个晚上. 因为只要该属性没有设置,那么服务器中的所有的作业就一直处于Q状态.
到此为止PBS的配置基本就完成了. 当然. PBS还有很多的参数可以设置. 但那就不是这个基本配置想给大家的. 大家自己去查PBS的手册把.
PBS Script samples#LJRS -S /bin/bash
#LJRS -o script.out
#LJRS -j oe
#LJRS -q dpool
#LJRS -l nodes=8:ppn=1 (nodes:计算节点数,ppn:计算节点CPU数)
#LJRS -l walltime=48:00:00 (用户估计的最大计算时间,超时系统会自动中断作业)
limit -s unlimited
TMPFILE=`whoami`_mpich_gm.tmp
sed 's/c/g/g' $LJRS_NODEFILE > /tmp/$TMPFILE
GM_NODEFILE=/tmp/$TMPFILE
echo Working directory is $LJRS_O_WORKDIR
cd $LJRS_O_WORKDIR
echo Runing on host `hostname`
echo Starting Time is `date`
echo Directory is `pwd`
echo This jobs runs on the following processors:
echo `cat $GM_NODEFILE`
NPROCS=`wc -l out (修改为用户的并行作业执行命令)
####################################
rm -f /tmp/$TMPFILE
echo Ending Time is `date`
##########################################################################
#
# Script for submitting parallel Gaussian 03 jobs to the cluster.
#
###########################################################################
# To use this script, first make the following changes:
#
# 1. Add the G03 .com filename to "jobname=", but leave out the suffix .com.
# Example: jobname=input
# 2. Add the same filename to #LJRS -o with the suffix .err.
# Example: #LJRS -o water03.err
# 3. Specify the number of nodes(nodes = x) and processors per node
# (ppn = y) needed for the job. Note that each job should typically use
# both processors on each node(i.e., ppn = 2). Therefore, set nodes equal
# to the total number of processors divided by 2.
# Example: If the job needs 16 processors total, then:
# #LJRS -l nodes=8:ppn=2
# Note that the appropriate number of processors must be requested in
# the .com file. In the above example, %nprocl=16 must be specified
# before the job command line(i.e., the line beginning with "#").
# (Note: Either the command nprocl or nproclinda can be used.)
# If only one processor is required, then %nprocl does not need to be
# specified. In the .g03 file, one processor is specified as:
# #LJRS -l nodes=4:ppn=2
# 4. Set the maximum length of time the job will use.
# Example: #LJRS -l walltime=24:00:00
# 5. Make sure the input (.com) and submitting script (.g03) files are in
# the same directory.
#
# Submit the script using "qsub input.g03".
###########################################################################
# Lines that begin with #LJRS are PBS directives (not comments).
# True comments begin with "# " (i,e., # followed by a space).
###########################################################################
#LJRS -S /bin/bash
#LJRS -o water333.err
#LJRS -j oe
#LJRS -q dpool
#LJRS -l nodes=4:ppn=2 (与input.com文件保持一致)
#LJRS -l walltime=860:00:00 (用户估计的最大计算时间,超时系统会自动中断作业)
#LJRS -V
cat "$LJRS_NODEFILE"
#############################################################################
# -S: shell the job will run under
# -o: name of the queue error filename
# -j: merges stdout and stderr to the same file
# -l: resources required by the job: number of nodes and processors per node
# -l: resources required by the job: maximun job time length
#############################################################################
# Define variable "jobname".
jobname=input (g03输入文件名,不包括.com扩展名)
username=`whoami`
ulimit -s unlimited
# Make a directory in scr and copy .com and .g03 file to there.
GAUSS_RUNDIR=/scratch/${username}
if [ ! -a $GAUSS_RUNDIR ]; then
echo "Scratch directory $GAUSS_RUNDIR created."
mkdir -p $GAUSS_RUNDIR
fi
cp $LJRS_O_WORKDIR/${jobname}.* $GAUSS_RUNDIR
ORIG_LJRS_O_WORKDIR=${LJRS_O_WORKDIR}
LJRS_O_WORKDIR=${GAUSS_RUNDIR}
cd $LJRS_O_WORKDIR
# Setup for Gaussian 03:
# =======================
# Make a scratch directory if it doesn't already exist.
GAUSS_SCRDIR=/scratch/${username}/${jobname}
if [ ! -a $GAUSS_SCRDIR ]; then
echo "Scratch directory $GAUSS_SCRDIR created."
mkdir -p $GAUSS_SCRDIR
fi
export GAUSS_SCRDIR
echo "Using $GAUSS_SCRDIR for temporary Gaussian 03 files."
# Define the location where Gaussian was installed and run
# a setup script, g03.profile.
g03root=/export/local/g03
source $g03root/g03/bsd/g03.profile
#source /export/local/g03/g03/bsd/g03.profile
# Define PATH to include location of LINDA
PATH=$PATH:/export/local/g03/g03/linda7.1/intel-linux2.4/bin
# Define node list
#echo $LJRS_NODEFILE $LJRS_JOBID > /tmp/g03log
sed 's/c/g/g' $LJRS_NODEFILE > $GAUSS_SCRDIR/tsnet.nodes
#cat /tmp/$2 > $LJRS_NODEFILE
G03_NODEFILE="$GAUSS_SCRDIR/tsnet.nodes"
GAUSS_LFLAGS="-mp 2 -nodefile $G03_NODEFILE"
# Export variable list
export PATH g03root GAUSS_LFLAGS
echo pbs nodefile:
cat $G03_NODEFILE
#Run a Gaussian command file, water03.com, redirecting output
#to a file, water03.log
echo "Starting Gaussian run at" `date`
time g03l $GAUSS_RUNDIR/${jobname}.log
echo "Finished Gaussian run at" `date`
LJRS_O_WORKDIR=${ORIG_LJRS_O_WORKDIR}
echo $LJRS_O_WORKDIR
mv $GAUSS_RUNDIR/${jobname}.* $LJRS_O_WORKDIR
mv $GAUSS_RUNDIR/*.chk $LJRS_O_WORKDIR
echo "$GAUSS_SCRDIR"
rm -Rf $GAUSS_SCRDIR
[color="#000099"]原文地址
http://grid.tsinghua.edu.cn/home/liulk/publish/computer/pbsconfig.html
本文来自ChinaUnix博客,如果查看原文请点:http://blog.chinaunix.net/u3/96497/showart_2052538.html |
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