Issue with modellauncher

[serbinsh]

2019-01-21 23:32:33 INFO   [PEcAn.workflow::run.write.configs] :
   parameter values for runs in
   /data/sserbin/Modeling/sipnet/US-WCr/ILAMB_CRUNCEP.TempBDF.2//samples.RData
2019-01-21 23:32:34 INFO   [start.model.runs] :
   -------------------------------------------------------------------
2019-01-21 23:32:34 INFO   [start.model.runs] :
   Starting model runs SIPNET
2019-01-21 23:32:34 INFO   [start.model.runs] :
   -------------------------------------------------------------------
  |                                                                      |   0%Warning in file.remove(file.path(run_id_dir, "joblist.txt")) :
  cannot remove file '/data/sserbin/Modeling/sipnet/US-WCr/ILAMB_CRUNCEP.TempBDF.2//run/2000098933/joblist.txt', reason 'No such file or directory'
Error in writeLines(c(file.path(settings$host$rundir, run_id_string)),  :
  'con' is not a connection
Calls: <Anonymous> -> start.model.runs -> writeLines

seems it is looking for a "joblist.txt" file to remove it and also hits a complaint about a database connection. I built the model launcher exe and setup my xml like this

    <qsub>qsub -l walltime=36:00:00,nodes=2:ppn=10 -V -N @NAME@ -o @STDOUT@ -e @STDERR@ -S /bin/bash</qsub>
    <qsub.jobid>([[:digit:]]+)\.modex\.bnl\.gov</qsub.jobid>
    <qstat>qstat @JOBID@ || echo DONE</qstat>
    <modellauncher>
        <binary>/data/sserbin/Modeling/pecan/contrib/modellauncher/modellauncher</binary>
        <qsub.extra>-l ncpus=10</qsub.extra>
    </modellauncher>
  </host>

[serbinsh]

Are there any folks in PEcAn-land successfully using model launcher in pecan develop?

[tonygardella]

@femeunier

[robkooper]

problem looks to be in https://github.com/PecanProject/pecan/blob/develop/base/remote/R/start.model.runs.R#L90 the jobfile used to be opened for writing here.

[serbinsh]

Ahhh....ok. that makes sense I think....so does it need to be open for writing again?

[serbinsh]

Blame is pointing to these changes: d66e5a3 . but I am not sure yet if that is it. @ashiklom any thoughts on this PR causing issues with ML? Do you use ML?

[serbinsh]

LOL. OK @robkooper is already on it

[serbinsh]

Fixed