bash 通过 qsub 运行 R 脚本
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Running R script through qsub
提问by user2763361
I am trying to run an Rscript called test.rthrough qsub. My Rscript is as follows:
我正在尝试运行一个R名为test.rthrough的脚本qsub。我的R脚本如下：
#!/usr/bin/Rscript
x <- 1
write.csv(x,"test.csv")
If in Ubuntu terminal I type R CMD BATCH test.r, then the script behaves as planned; test.csvgets exported in the same directory.
如果在 Ubuntu 终端中输入R CMD BATCH test.r，则脚本按计划运行；test.csv导出到同一个目录。
However if I create a bashscript called testbash.shand run it through the command qsub testbash.sh; it will run without errors but the output won't be there.
但是，如果我创建一个bash名为的脚本testbash.sh并通过命令运行它qsub testbash.sh；它将运行而不会出错，但不会有输出。
#!/usr/bin/bash
R CMD BATCH test.r
How to fix this?
如何解决这个问题？
回答by Ricardo Oliveros-Ramos
Try modifying your R script to:
尝试将 R 脚本修改为：
#!/usr/bin/Rscript
x <- 1
print(getwd())
write.csv(x,"test.csv")
When you run a script via qsub, the script is normally running in another server, and by default as in your home directory. You need to change to the original directory in your script, there is a variable PBS_O_WORKDIRfor that:
当您通过 运行脚本时qsub，该脚本通常在另一台服务器上运行，默认情况下在您的主目录中。您需要更改到脚本中的原始目录，有一个变量PBS_O_WORKDIR：
#!/usr/bin/bash
#PBS -N qsub_R_test
echo We are in the $PWD directory
cd $PBS_O_WORKDIR
echo We are now in $PBS_O_WORKDIR, running an R script.
R --vanilla < test.r > test.log 2> test.log
I normally cannot use R CMD BATCH, but redirection to R -vanillaworks. You can also specify options for the PBS in the script, starting with #PBS, like the job name in this case (qsub_R_test).
我通常不能使用R CMD BATCH，但重定向到R -vanilla工作。您还可以在脚本中为 PBS 指定选项，以 开头#PBS，例如本例中的作业名称 ( qsub_R_test)。
You can get a more detailed list of qsub parameters here: http://www.csc.fi/english/pages/louhi_guide/batch_jobs/commands/qsub
您可以在此处获得更详细的 qsub 参数列表：http: //www.csc.fi/english/pages/louhi_guide/batch_jobs/commands/qsub
And an example of a PBS script here: http://bose.utmb.edu/Compu_Center/Cluster_users/PBS%20HOWTO/PBS_HOW_TO.html
以及这里的 PBS 脚本示例：http: //bose.utmb.edu/Compu_Center/Cluster_users/PBS%20HOWTO/PBS_HOW_TO.html
回答by Dirk Eddelbuettel
You may be doing it wrong. If you have a shebang line like
你可能做错了。如果你有像这样的shebang线
#!/usr/bin/Rscript
then "simply" do chmod 0755 test.ron the file, and run it:
然后“简单地”chmod 0755 test.r对文件执行操作，然后运行它：
./test.r
That should work, and you can then have that invocation in your qsub-called script.
这应该可行，然后您可以在 qsub 调用的脚本中进行该调用。
