Extra options on SGE

[nantonel]

In our cluster in order to run a job on SGE we need to specify an additional option which indicates our group.

I manage to add this by modifying qsub.jl adding the kwarg opt:

addprocs_sge(np::Integer; queue::AbstractString="", qsub_env::AbstractString="", res_list::AbstractString="", opt::Cmd=``) =
        addprocs(SGEManager(np, queue),qsub_env=qsub_env,res_list=res_list,opt=opt)

which should be a Cmd and can interpolate correctly in qsub_cmd:

`qsub -N $jobname -terse -j y -R y -t 1-$np -V $res_list $queue $qsub_env $opt`

Do you think it makes sense? In case I could prepare a PR. Thanks!

[bjarthur]

why not just use qsub_env?

[nantonel]

We could use that argument, but it still need more modifications:

        if params[:qsub_env] == ""
            qsub_env = ``
        else
            evar = params[:qsub_env]
            qsub_env = `-v $evar`
        end

since the option I need doesn't belong to the -v arguments.

[bjarthur]

oh, right. and queue and res_list also are suffixed to hard-coded flags. maybe it would be simpler to replace all of them with a single options argument that is appended to the bsub and have the user specify the fixed flags explicitly?

[nantonel]

yes I think that solution would be much cleaner!

[bjarthur]

closed by #153