0
votes
0answers
15 views

SGE to PBS/Torque qsub conversion

Hi I am setting up a software pipeline (an extensive bioinformatic annotation tool) that was originally written to submit SGE jobs but I am on a PBS/Torque cluster. Any ideas about a way to convert ...
2
votes
2answers
31 views

Gather job usage information on cluster

I am running simulations on a linux cluster shared by hundreds of other users. There is a job scheduler installed on the cluster that determines who runs where, and one of the scheduler commands ...
0
votes
1answer
66 views

Running shell script on cluster in parralel

I thought dsh(Distributed Shel) will be a good option but when i ran my shell script across my nodes, I didnt get expected output, dsh -aM -c bash /home/cloudera/bash_script.sh server2@x.x.x.110: ...
0
votes
1answer
579 views

Script for running sequential job

I started recently to learn using Linux. I want to write a script in bash shell to run a serial job on a cluster. I have been searching for hints and instructions on how to write such a script. I ...
2
votes
2answers
668 views

comm fails on bash variable input

I have a script that's supposed to get the list of files of two directories, get differences and execute some code for certain files. These are the commands to get the file lists: list_in=$(find ...
6
votes
1answer
568 views

Running parallel bash jobs on a HPC cluster using GNU parallel

On an HPC cluster I am trying to run multiple bash scripts (permute2.sh) from 1 bash script using GNU parallel, however it doesn't complete every job. It randomly completes one job, while it is stuck ...