我想向我的群集上的几个队列提交模拟 . 只要一个队列启动它,它就会被其他队列取消 . 我知道它可能是不明确的,因为几个工作可能会在几个队列上同时开始 .
监视队列的bash脚本可能会这样做 . 提交作业时是否可以直接使用qsub?
编辑:下面是一个使用bash脚本的工作示例 . 这可能不是最佳的,因为它需要(慢)磁盘访问 .
#!/bin/bash -
#
# Exit in case of error
set -e
#
# Command-line argument is the name of the shared file
fid=$*
if [ -f ${HOME}/.dep_jobs/${fid} ]; then
echo "Given name already used, abort."
exit 1
else
echo "Initialize case."
touch ${HOME}/.dep_jobs/${fid}
fi
#
# Submit master job and retrieve the ID
echo "Submitting master job"
MID=$(qsub -l select=1:ncpus=1:mpiprocs=1 -q queue1 run.pbs)
echo ${MID##* }
#
# Add the ID to the shared file
ln -s ${HOME}/.dep_jobs/${fid} ${HOME}/.dep_jobs/${MID##* }
echo "M ${MID##* }" >> ${HOME}/.dep_jobs/${fid}
#
# Submit slave job and retrieve the ID
echo "Submitting slave job"
SID=$(qsub -l select=1:ncpus=1:mpiprocs=1 -q queue2 run.pbs)
echo ${SID##* }
#
# Add the ID to the shared file
ln -s ${HOME}/.dep_jobs/${fid} ${HOME}/.dep_jobs/${SID##* }
echo "S ${SID##* }" >> ${HOME}/.dep_jobs/${fid}
#
# Terminus, finalize case
echo "Finalize case"
echo "OK" >> ${HOME}/.dep_jobs/${fid}
提交的PBS脚本应该如下所示
#!/bin/bash
#PBS -S /bin/bash
#PBS -N Parallel
#
# Define shared file
shared_file=${HOME}/.dep_jobs/${PBS_JOBID}
#
# Read it until it finishes with "OK"
while [[ "$(more ${shared_file} | tail -n1)" != "OK" ]]; do
sleep 1
done
#
# Read master and slave job id
while read -r line
do
key=$(echo ${line} | awk '{print $1}')
if [ "$key" = "M" ]; then
MID=$(echo ${line} | awk '{print $2}')
elif [ "$key" = "S" ]; then
SID=$(echo ${line} | awk '{print $2}')
fi
done < ${shared_file}
#
# Current job is master or slave?
if [ ${PBS_JOBID} = ${MID} ]; then
key="M"
other="${SID}"
else
key="S"
other="${MID}"
fi
#
# Check the status of the other job
status="$(qstat ${other} | tail -n1 | awk '{print $5}')"
#
# I am running, if the other is in queue, qdel it
if [ "${status}" = "Q" ]; then
$(qdel ${other})
# If the other is running, we have race and only master survives
elif [ "${status}" = "R" ]; then
if [ "${key}" = "M" ]; then
$(qdel ${other})
else
exit
fi
else
echo "We should not be here"
exit
fi
#
# The simulation goes here
1 回答
这是一个使用SGE调度程序运行的脚本 . 对于PBS调度程序,您需要进行一些最小的更改,例如使用
#PBS
而不是#$
并将$JOB_ID
更改为$PBS_JOBID
. 同样对于SGE调度程序,更好的方法是运行qstat -u user_name -s p
命令,该命令仅列出挂起的作业,但我找不到PBS调度程序的类似选项,因此假设它不存在,一种方法可能是使用以下脚本您的模拟作业(您不需要任何主脚本):您需要在用户名的qstat命令中更改上述脚本的用户名 . 我还建议一次检查一个命令,以确保它们在您的环境中正确运行 .
以下是我在脚本中使用的命令的一些简要说明: