Package: gridengine-goodies
gridengine-goodies: Enhancements to gridengineThegridengine-goodiespackage provides a few command line scripts that enhance the usability of thegridenginescheduling system.qsubx: an improvedqsubqsubx allows to submit multiple jobs at a time while keeping at most N jobs in the queue.
This way you can submit tons of jobs and still be polite to your fellow users.qsubx-n100job_*.shNote that N=100 is the default.qsubxwill not return until all the jobs have been submitted.qdelx: delete jobs via regular expressionsTo delete jobs by nameqdelxsim_T*_rho*To delete all jobs waiting in the queueqdelxqwqstatx: an improvedqstatIt provides better layout and full job names (adapted from a code of Jeet Sukumaran).
The main benefit of qstatx is to provide full (or almost full) job names and better layout.------------------------------------------------------------------------------------------------
id      name      owner  submitted            state  queue  node                    slots
------------------------------------------------------------------------------------------------
124905  sleep_10  coslo  2018-10-09 15:54:42  r      all.q  varda.coulomb.univ-mon  1    
124906  sleep_10  coslo  2018-10-09 15:54:42  r      all.q  varda.coulomb.univ-mon  1    
124907  sleep_10  coslo  2018-10-09 15:54:42  r      all.q  varda.coulomb.univ-mon  1    
124908  sleep_10  coslo  2018-10-09 15:54:42  r      all.q  varda.coulomb.univ-mon  1    
124909  sleep_10  coslo  2018-10-09 15:54:44  qw                                    1    
124910  sleep_10  coslo  2018-10-09 15:54:44  qw                                    1    
124911  sleep_10  coslo  2018-10-09 15:54:44  qw                                    1    
124912  sleep_10  coslo  2018-10-09 15:54:44  qw                                    1    
------------------------------------------------------------------------------------------------
Running  :   4 (slots:    4)
Hold     :   0 (slots:    0)
Pending  :   4 (slots:    4)
Deletion :   0 (slots:    0)
Error    :   0 (slots:    0)
------------------------------------------------------------------------------------------------qexec: execute a command on the clusterExecute a command on the computing nodes directly. The job file is created on the fly and stored in a temporary directory under the user.local/sharefolder. The behavior is similar toqsub -b y <command>butqexecis more flexible and provide persistent access to job files and logs if needed.This job will sleep for 10 secondsqexec-csleep10Submit a script or a program namedcode.xand store log files in theoutput_dirfolderqexec-ooutput_dir-ccode.x--verbose-param1.0qbarrier: halt execution until some jobs are overIt provides a simple means to create command-line-level dependencies between jobs.
For finer control on job dependencies, see 'job arrays' in the gridengine documentation.qjobs: jobs' reporting toolIt provides colorized summaries and status listings of running jobs. It assumes that jobs were submitted usingqexec, but it will mostly work even if this is not the case. You can tag a list of jobs, to keep track of changes between successive calls.qjobs-tmy_jobsruns/*.jobDONE        44.26%  355 /  802  [+15.21%]
FAIL         5.11%   41 /  802  [+0.00%]
KILL         0.00%    0 /  802  [+0.00%]
OVER        49.38%  396 /  802  [+15.21%]
RUN          1.50%   12 /  802  [+0.62%]
WAIT        49.13%  394 /  802  [-15.84%]List error messages of jobs that failed, sorting by modification dateqjobs --sort --status fail $(find . -name "*.job")InstallationThe above goodies are plain python and bash scripts. You can just copy them and put them somewhere in your path.
However, to keep up with updates it is better to clone the code repository and install the scripts accordinglygit clone https://gitlab.info-ufr.univ-montp2.fr/daniele.coslovich/gridengine-goodies.git
cd gridengine-goodies
make userThe above procedure will put the scripts in~/.local/binso make sure it is in yourPATHexportPATH=$HOME/.local/bin:$PATHAdd the above line to your.bashrcto make it persistent across sessions.To update to the latest versioncdgridengine-goodies
gitpull
makeuserAuthorsDaniele Coslovich:http://www.coulomb.univ-montp2.fr/perso/daniele.coslovich/