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 88cb83311f549bdd8684f85f46d10521866d4f3c):
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.
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 88cb83311f549bdd8684f85f46d10521866d4f3c):
this.errFileNamebecomes 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.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.