Did my Mox job fail...?

[yaaminiv]

I queued my bismark run on Mox and got the following emails:

Does this mean my job failed or did is it still running?

[sr320]

failed

[kubu4]

Yes, it failed.

When ExitCode is > 0 (and the word "Failed" is in the email subject), the job did not complete.

Check the slurm-jobID.out file for hints (tail slurm-381386.out).

[yaaminiv]

@kubu4 I tried that! I got the following error:

tail: cannot open ‘slurm-381386.out’ for reading: No such file or directory

How can I figure out 1) what happened to my Mox run and 2) where the output file went

[kubu4]

The output file is in your working directory (designated in the header of your SBATCH script).

[kubu4]

#!/bin/bash
## Job Name
#SBATCH --job-name=20181015_bismark
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Resources
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=10-00:00:00
## Memory per node
#SBATCH --mem=120G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=samwhite@uw.edu
## Specify the working directory for this job
#SBATCH --workdir=/gscratch/scrubbed/samwhite/20181015_oly_WGBSseq_v081

The last line of the SBATCH header specifies working directory (i.e. location of all output files).

[yaaminiv]

Turns out my job failed because my working directory path had a typo. I fixed that and now the job is running!

One last tangential question: do I have to keep the terminal window where I run my commands on Mox open during the job?

[sr320]

you are running now...

[sr320@mox1 ~]$ squeue | grep srlab
            359332     srlab  Ae_canu jldimond  R 5-03:42:20      1 n2211
            381403     srlab 20181012 yaaminiv  R       2:01      1 n2357

[sr320]

One last tangential question: do I have to keep the terminal window where I run my commands on Mox open during the job?

no

[kubu4]

No need to leave terminal window open.