Questions tagged [platform-lsf]
Platform LSF is a job scheduler for high-performance computing environments
16
questions
0
votes
0
answers
34
views
How to use ${LSB_JOB_INDEX} to run a for loop in LSF platform
I have a for loop that looks like this, and I want to convert it to an array job.
I want to run 100 jobs in parallel, but I am not entirely sure where I can add
the ${LSB_JOB_INDEX} parameter.
Any ...
- 101
0
votes
0
answers
21
views
Which is correct format for memory allocation in LSF bsub
which is correct format for memory allocation in LSF bsub?
a) bsub -K -R mem=100000
b) bsub -K -R "rusage[mem=256GB]"
and what's the difference between them?
1
vote
0
answers
501
views
Parallel job submission of for loop
I have written for loop and parallelized it with & and limited the threshold to running 3 jobs at one time. Below is my script. I am reserving 32 cores and 256 GB memory through BSUB command. The ...
- 137
1
vote
1
answer
42
views
Tools for batching N commands over L scripts (for N≫L)?
Let's say that I have access to a high-performance Linux cluster equipped with a scheduler (e.g. LSF, Slurm, etc.) that will allow me to have up to M jobs either running or pending at any one time, of ...
- 14.2k
1
vote
1
answer
802
views
What is "Platform LSF"?
Every day, I encounter at least one Wikipedia article about something computer-related, which should logically make sense to me if I've spent my entire life growing up with and dealing with computers ...
- 11
0
votes
1
answer
2k
views
Python script runs manually but not in cronjob
So this is a super weird issue. I have a python script that calls many bash commands via subprocess.call based on certain criteria. Now, the script runs just fine manually but when thrown into a ...
- 39
1
vote
1
answer
279
views
Live changing bjobs output
When using LSF command bjobs, I would like to get instantly changing output if I submit another job, because I feel stressful to run the same command again and again. I would like something like top ...
- 385
1
vote
1
answer
298
views
Getting wall time limit in bjobs
I'm writing a script that collect job information. I would like to get the wall time limit for each pending job (as specified with bsub -W) using bjobs. I can get information such as the number of ...
- 11
1
vote
1
answer
89
views
Is LSF queue allowed to preempt itself?
I have an LSF queue, say it's queue A. I only want higher priority jobs in queue A to preempt lower priority jobs in queue A, but not jobs in any other queues. If I set queue A to be preemptable, ...
- 11
1
vote
1
answer
355
views
Running lsf jobs in personal ubuntu pc
I have somewhat maybe little bit strange question running my jobs in my ubuntu laptop instead of running them hpc clusters.
The reason I want to to that is now I have 6 core 12 threads. I used to run ...
- 113
2
votes
2
answers
825
views
Pipe (pass the output of previous command to the next command) with "|" when using "bsub"
Hi I guess this is a very basic question:
Is there any specific syntax to do the "piping" when using "bsub"?
I am asking that because when I had an issue like this:
# try to run the same command ...
- 511
2
votes
1
answer
358
views
How can a script tell if Platform LSF is available in an environment?
We have some shell scripts that presently utilize Platform LSF to manage job execution.
These scripts will eventually be migrated to an environment that uses a different job scheduler.
During the ...
- 10.2k
5
votes
2
answers
15k
views
lsf bkill all PEND jobs without killing RUN jobs
I'v lots bjobs running on lsf, jobs have two status, RUN and PEND. And I want to kill all bjobs with PEND status, how to do that use script? A hard-coded way I think is saving them in a file then ...
- 253
0
votes
1
answer
261
views
What's the correct job time limit specification for jobs to LSF
What is the correct way to specify how long a job can run on a computer cluster using LSF as the resource manager/ job scheduler?
LSF is a job scheduler that computing clusters use to allocate ...
- 103
1
vote
0
answers
153
views
how to make your tcsh command promt show LSF job count?
I want to monitor LSF job count through command prompt. %j will not give me the LSF job count. Can anyone tell how to configure command prompt to show the LSF job count?
- 61
5
votes
2
answers
9k
views
Pass argument to script, then redirect script as input to bsub
I am currently working with the bsub job submission system from Platform LSF. I need to submit job scripts, but I am running into a problem with passing arguments to the job script.
What I need is as ...
- 71