Questions tagged [qsub]
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20 questions
1 vote
1 answer
135 views
qsub-like behavior for a slurm cluster
I recently switched to slurm and looking for a job submission tool, that behaves similar to qsub: It takes input through a pipe It prints the output to stdout Example: for n in `seq 1 10`; do ...
- 188
0 votes
2 answers
384 views
Pass a variable that contains a comma as a -v option to qsub
After seeing the reactions on Stack Overflow on this question and an unfamiliarity with qsub, I believe thqt U&L is better suited for this question. In qsub, we can pass environment variables (a ...
- 183
1 vote
1 answer
196 views
Will `qsub` run my jobs sequentially?
Assume a script including the following content is passed to qsub as qsub myscript.sh #PBS -N Job_name #PBS -l walltime=10:30,mem=320kb #PBS -m be # step1 arg1 arg2 step2 arg3 arg4 Will step1 and ...
- 155
1 vote
1 answer
2k views
How can I submit multiple R job at once?
I have a R-script which runs multiple files say file=1 to 50. I usually submit repeated jobs say 5 times with 10 files each time by changing the number in R-script. So, how can I submit the 5-job at ...
- 21
0 votes
0 answers
3k views
How can I cancel all waiting jobs with qsub?
I am running a lot of jobs with qsub: some are running, some are waiting. Is there a way to cancel all the jobs for a given user which are queued/waiting without giving the individual job IDs?
- 133
0 votes
2 answers
2k views
Syntax for number of cores in a Sun Grid Engine job file
I want to use the HPC of my university to qsub an array job of 3 tasks. Each task runs a Matlab code which uses a solver (MOSEK) that exploits multiple threads to solve an optimization problem. A ...
- 125
0 votes
1 answer
503 views
Name is nonexistent or not a directory
I'm running an array job (400 Matlab R2018b tasks) in the HPC of my university. After having qsub the .sh file in the terminal, the 400 tasks start by they are immediately killed. In the .o file of ...
- 125
0 votes
1 answer
408 views
How to run the same command to execute a file in multiple directories?
I want to do the following, I have a set of directories: e.g) 400K 500K 600K and so on In each directory I have a "run.pbs" file, that I want to submit through batch with "qsub run.pbs". I was ...
- 125