gridengine-goodies 1.0.2

Enhancements to the gridengine scheduler

gridengine-goodies: Enhancements to gridengine
==============================================

The `gridengine-goodies` package provides a few command line scripts that enhance the usability of the
[gridengine](https://en.wikipedia.org/wiki/Oracle_Grid_Engine) scheduling system.

### qsubx: an improved `qsub`
qsubx 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.
```bash
qsubx -n 100 job_*.sh
```
Note that N=100 is the default. `qsubx` will not return until all the jobs have been submitted.

### qdelx: delete jobs via regular expressions
To delete jobs by name
```bash
qdelx sim_T*_rho*
```
To delete all jobs waiting in the queue
```bash
qdelx qw
```
### qstatx: an improved `qstat`
It 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 cluster
Execute 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/share` folder. The behavior is similar to `qsub -b y <command>` but `qexec` is more flexible and provide persistent access to job files and logs if needed.

This job will sleep for 10 seconds
```bash
qexec -c sleep 10
```
Submit a script or a program named `code.x` and store log files in the `output_dir` folder
```bash
qexec -o output_dir -c code.x --verbose -param 1.0
```

### qbarrier: halt execution until some jobs are over
It 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.

Installation
------------
The 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 accordingly
```
git clone https://gitlab.info-ufr.univ-montp2.fr/daniele.coslovich/gridengine-goodies.git
cd gridengine-goodies
make user
```

The above procedure will put the scripts in `~/.local/bin` so make sure it is in your `PATH`
```bash
export PATH=$HOME/.local/bin:$PATH
```
Add the above line to your `.bashrc` to make it persistent across sessions.

To update to the latest version
```bash
cd gridengine-goodies
git pull
make user
```

Authors
-------
Daniele Coslovich: http://www.coulomb.univ-montp2.fr/perso/daniele.coslovich/