I have a couple of jobs in the locked jobs queue with the status UserHold. Is there a way to edit the PBS file that launched them? I used qalter before to change the walltime, group or name. This time I want to change the parameters of the aprun call in the submitted PBS file.
Typically speaking you shouldn't do this. The correct procedure would be to delete your job and submit a new one with the new job script.
Related
Say I want to run a job on the cluster: job1.m
Slurm handles the batch jobs and I'm loading Mathematica to save the output file job1.csv
I submit job1.m and it is sitting in the queue. Now, I edit job1.m to have different variables and parameters, and tell it to save data to job1_edited.csv. Then I re-submit job1.m.
Now I have two batch jobs in the queue.
What will happen to my output files? Will job1.csv be data from the original job1.m file? And will job1_edited.csv be data from the edited file? Or will job1.csv and job1_edited.csv be the same output?
:(
Thanks in advance!
I am assuming job1.m is a Mathematica job, run from inside a Bash submission script. In that case, job1.m is read when the job starts so if it is modified after submission but before job start, the modified version will run. If it is modified after the job starts, the original version will run.
If job1.m is the submission script itself (so you run sbatch job1.m), that script is copied in a spool directory specific to the job so if it is modified after the job is submitted, it still will run the original version.
In any case, it is better, for reproducibility and traceability, to make use of a workflow manager such as Fireworks, or Bosco
By default, when submitting a SLURM job as an array, all jobs within the array share the same job name. In the docs (here: https://slurm.schedmd.com/job_array.html), it shows that each job in the array can have its name set separately via scontrol (described under the section "Scontrol Command Use").
Can this be done directly from an sbatch script?
I just created an account because I was trying to do this and I did find a solution.
You can use scontrol to change the name of a job, the syntax is the following:
scontrol update job=<job_id> JobName=<new_name>
You can do this manually, but you can also automatically set the name of the job from within the array job, thus automatically assigning a different name to each job in the array.
I find this useful because I'm mostly running calculations in different directories and if I have one job running much longer than the others I want to be able to quickly retrieve where it's running to see what's going on.
Of course you could set other things as your job name, as you prefer.
In my case, I add the scontrol command to the script I run through the array in order to obtain the following name for each directory: "job_name - directory". The job id and job name can be retrieved from environment variables.
scontrol update job=$SLURM_ARRAY_JOB_ID JobName="$SLURM_JOB_NAME - $folder"
Dear UNIX/PBS experts:
I am user of a UNIX HPC system (CentOS Linux 7 (Core),Linux 3.10.0-693.5.2.el7.x86_64) and I do not have any root privileges.
Various jobs have been submitted at an HPC system and almost all resources are being used.
Jobs from other users may run for weeks while my submitted job would finish in less than a day.
My goal is to run my job exactly after the first resources will be freed instead of waiting for
all other users to have their jobs finished.
My submitted job has a number qid 66005.pbs.
However the last job running at this moment has number 55004.pbs.
By checking the status of job: qstat 55005,
I obtain: qstat: Unknown Job Id 55005.pbs
Thus my question is whether it is possible to change the name of job 66005.pbs to 55005.pbs, and if this action will allow my job to run?
If yes, how can this be achieved?
If not, are there any other solutions/alternatives for making sure that my jobs run before those ones of other users in queue?
Thank you very much for your help and any suggestion.
The good thing about the computer system is that it is not human. It will be unfair to run your job (which clearly was submitted after other users) before other users and because of that "No" it is not possible to change your job-id.
You can work with your admin to move the job to a higher priority queue instead.
When we submit a job via sbatch, the pid to jobs given by incremental order. This order start from again from 1 based on my observation.
sbatch -N1 run.sh
Submitted batch job 20
//Goal is to change submitted batch job's id, if possible.
[Q1] For example there is a running job under slurm. When we reboot the node, does the job continue running? and does its pid get updated or stay as it was before?
[Q2] Is it possible to give or change pid of the submitted job with a unique id that the cluster owner want to give?
Thank you for your valuable time and help.
If the node fails, the job is requeued - if this is permitted by the JobRequeue parameter in slurm.conf. It will get the same Job ID as the previously started run since this is the only identifier in the database for managing the jobs. (Users can override requeueing with the --no-requeue sbatch parameter.)
It's not possible to change Job ID's, no.
I am looking for a way to save job information provided by sacct automatically to some file. So far I have included an sacct call in my job batch script, but then the state is always "RUNNING".
Is there a way to automatically call sacct after the job ended/died?
The only thing that came to my mind was to submit a second job that depends on the first and then calls sacct, but this is obviously not a good option.
You can set a file to store job completion data with JobCompLoc in slurm.conf. (We parse that file to send extra information in the job completion emails, and it includes (I think) everything that you get from sacct).