在LSF作业数组中引用作业索引 [英] Referencing job index in LSF job array

问题描述

我正在尝试将作业数组中的作业索引作为参数传递给另一个bash脚本.

I'm trying to pass the index of a job in a job array as a parameter to another bash script.

numSims=3 
numTreatments=6 # uses numTreatments top rows of parameters.csv
maxFail=10
j=1
while [ $j -le $numSims ];
do
    bsub -q someQueue -J "mySim[1-$numTreatments]%2" ./another_script.sh $LSB_JOBINDEX $j $maxFail
    let j=j+1
done

这里的最终想法是为1，...，numTreatments，numSims个作业(模拟)中的每一个提交一个.我想一次运行两个作业(%2).输出格式为XX_indexNumber_simNumber，其中indexNumber从1，...，numTreatments开始，simNumber从1，...，numSims开始.

The ultimate idea here is to submit, for each of 1,...,numTreatments,numSims jobs (simulations). I'd like two jobs running at a time (%2). Outputs have the form XX_indexNumber_simNumber, where indexNumber runs from 1,...,numTreatments and simNumber from 1,...,numSims.

理想情况下，作为该脚本的一部分提交的所有内容都将具有相同的作业ID.这尚未正确设置，因为所有具有相同j的作业都被分配了不同的作业ID. 我眼前的问题是another_script.sh无法将$LSB_JOBINDEX识别为输入-它将$j和$maxFail视为第一个且只有两个传递的参数. $LSB_JOBINDEX的位置，没有问题.我在做什么错了?

Ideally, everything submitted as part of this script would have the same job ID. This isn't yet set up correctly, because all jobs with the same j are being assigned a distinct job ID. My immediate problem is that another_script.sh is not recognizing $LSB_JOBINDEX as input--it sees $j and $maxFail as the first and only two passed parameters. When I put some other variable in place of $LSB_JOBINDEX, there's no problem. What am I doing wrong?

编辑-我尝试过的一些操作:"$LSB_JOBINDEX"，${LSB_JOBINDEX}，%I和I=$LSB_JOBINDEX; bsub ... $I $j $maxFail

Edit - some things I've tried: "$LSB_JOBINDEX", ${LSB_JOBINDEX}, %I, and I=$LSB_JOBINDEX; bsub ... $I $j $maxFail

推荐答案

来自此链接:

上面的定义将不仅启动一个批处理作业，还将启动100个批处理作业，其中子作业特定的环境变量$ LSB_JOBINDEX从1到100取值.然后可以在实际的作业启动命令中利用此变量，以便每个子任务都可以已处理.

The definition above will launch not just one batch job, but 100 batch jobs where the subjob specific environment variable $LSB_JOBINDEX gets values form 1 to 100. This variable can then be utilized in the actual job launching commands so that each subtask gets processed.

在您的情况下，这意味着变量$LSB_JOBINDEX在脚本another_script.sh中可用.您无需将其作为参数传递，而只需在脚本中访问$LSB_JOBINDEX.

In your case, this means that the variable $LSB_JOBINDEX is available from inside the script another_script.sh. You do not need to pass it as a parameter, but just access $LSB_JOBINDEX in your script.

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