Sequential Jobs: Followup Part 2

Followup on hold jobs

In this post I have found a way to hold a pipeline from excecuting if any of the preceding jobs have errored.
I created a quick R file, named it test.R. Contents of test.R:

print(x)

 

Error: object 'x' not found

Most of you can see that this is destined to fail since x can’t be found, which is the point. I want it to fail. Now I created my bash file, named it test.sh, with contents below:

#!/bin/bash
R --no-save < test.R
if [ "$?" -gt "0" ]
then
  exit 100
fi

This program simply says run this R file, then check the last exit status in bash saved as $?, see if its greater than 0. If this is greater than 0, then R file failed. Then just exit bash with exit code 100. Now, why use exit code 100? If you do

man qsub

you’ll notice that under -hold_jid they have noted:

If any array task of the referenced jobs exits with exit code 100, the dependent tasks of the submitted job will remain ineligible for execution.

so we need to tell the Sun Grid Engine (SGE) that there is an exit code of 100 if we want it to hold up our jobs.

What happens with held jobs?

What happens when we try something like

#!/bin/bash
qsub -cwd -N test1 test.sh
qsub -cwd -hold_jid test1 -N test2 test.sh

and then things fail? We get the following output:

job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID
-----------------------------------------------------------------------------------------------------------------
 990025 0.58333 test1      XXXXXXXX     Eqw   11/19/2013 16:54:56                                    1
 990026 0.00000 test2      XXXXXXXX     hqw   11/19/2013 16:54:56                                    1

the E denotes tthere was an error. The test2 job will not run and will stay held (unless you delete the test1 job using qdel).

Now, the big problem with this is that it tells our cluster administrator that your job has failed, which is not really the best option. We may work out a system where we can put a special naming convention so that the failure can be filtered out compared to true failures (such as node crashes).

Alternative option not using exit code 100

But for now, you could do something simple like at the beginning of pipline/series of sh scripts:

echo 0 > check.txt

then in each sh script you can do:

while read line
do
  if [ "$line" -gt "0" ]
  then
      exit 1
    fi
done < check.txt
R --no-save < test.R
echo $? >> check.txt

so that any time you get an exit status > 0, then you can stop everything down stream. This works and is considered somewhat of a “blackboard” approach in that jobs check a blackboard before continue running.

Potential problems:

  • Needing to cleanup the check.txt file
  • Multiple jobs reading the file at the same time (race condition). This may be mitigated if you have a pause command after the last echo.
  • You don’t have a record of what file actually failed (or which array index) – you can cat/echo more to the file and then use awk or something else to just take the first column (exit code).

But for now, I’ll just try to make sure things run smoothly interactively for a bit, maybe doing some of this.

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