rcannood / qsub Goto Github PK

Currently error messages are not read out of the log, and an error will be thrown because qsubapply can't find all of the output structures.

Not sure if this is unique to our cluster but I found that the error and output log paths in script.sh cause the job array to fail. When I initially ran the example in the README the individual jobs in the array didn't generate any output and the final job didn't complete, which caused my R session to hang. I got the same behavior when I submitted the script.sh job my self on the cluster. There were no logs in the log folder so I added the full path to the log paths in script.sh and it completed successfully. Here's the change I made to lines 209-210 of qsub_run.sh to get it to work:

    sprintf("#$ -e %s/log/log.$TASK_ID.e.txt\n", qs$remote_dir),
    sprintf("#$ -o %s/log/log.$TASK_ID.o.txt\n", qs$remote_dir),

Thanks for developing this package, extremely useful!

An error anywhere will cause the qsublapply function to interrupt and leave some junk in the temporary directories.

Example:

qs1 <- qsub.submit(X1, FUN1)
qs2 <- qsub.submit(X2, FUN2)
qs3 <- qsub.submit(X3, FUN3)
qsub.retrieve(qs1)
qsub.retrieve(qs2)
qsub.retrieve(qs3)

I have been unable to produce an output using qsub_lapply. I only tried to run the example of incrementing 1:3 by 1. There's an error for rsync and the log files have this message:

ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'R'
export: Command not found.
export: Command not found.
MANPATH: Undefined variable.
Rscript: Command not found.