Output/Error log issues

[ghost]

I received errors like "ERROR: CANNOT PRINT OUT ERROR LOG" and found this was due to two issues in Qsub.java (line numbers refer to commit 88cb833):

• In my case, logHostname seems to be "localhost" and so this.errFileName becomes something like: localhost:/tmp/jenkinsPBS_8261529842131452148/erron line 129/130 which is not the same as the file path being read on line 226 (outFile = Files.newInputStream(Paths.get(this.executionDirectory, "err"))) - ie without the host. I fixed this by commenting lines 128-131 and 134.
• Errors still occurred, which I think is due to the files attempting to be read before they are actually transferred from the compute node. Adding:

try { Thread.sleep(1000); } catch (InterruptedException e) { e.printStackTrace(listener.getLogger()); }
at line 210 to delay the read for a while until the transfer is likely to have finished fixed this for me.