sge conf should be pbs? about flowr HOT 3 CLOSED

This is an interesting point. Torque, SLURM, SGE and MOAB all accept PBS directives. There is major overlap between all these configuration files. I have files named after scheduler, so we may not need a file called pbs.sh

https://www.glue.umd.edu/hpcc/help/slurm-vs-moab.html

The nice aspect of these configuration files is that you can place them in ~/flowr/conf and customize to glory. Additionally, I am open to pull requests with more customized examples of SGExxx directives. I do not have easy access to an SGE cluster, so may not be able to test it readily.

from flowr.

SGE accepts similar directives to PBS, but not identical. Here are two semantically identical directives for joining input/output files that differ syntactically:

PBS:
#PBS -j oe

SGE:
#$ -j y

The directive will be ignored silently by the other submission manager, depending on which you use.

I have ready access to an SGE cluster that can be used for testing, but we'd have to jump through a couple hoops to get you direct access

[edit]: I believe SLURM, MOAB, et. al. do actually accept PBS directives

from flowr.

Great!

@studentism Do you have more such examples; potential issues with this file?
https://github.com/sahilseth/flowr/blob/devel/inst/conf/sge.sh

An option is that you could make such changes in a sge.sh file in your home, test them and let us know what works best.

I usually test the simple sleep workflow (http://docs.flowr.space/install.html#test).

from flowr.