Ok -it's in. Thanks again! I will add a to-do item to put output-merge messages into stdout so that they're more visible.
-Scott ----- Original Message ----- > > Thanks, Peter! I'll get to it this afternoon EDT. > > -Scott > > ----- Original Message ----- > > On Thu, Oct 18, 2012 at 5:19 PM, Scott McManus > > <scottmcma...@gatech.edu> wrote: > > > > > > Hey Peter- > > > > > > Thanks - I'll look into it. If you're able to reproduce the > > > problem > > > easily > > > and wouldn't mind crafting a pull request, then it would be much > > > appreciated. Otherwise I'll put this on my to-do list to be done > > > soon. > > > I or someone else may want to revisit the exception handling to > > > prevent > > > that from happening. > > > > > > Thanks! > > > > > > -Scott > > > > OK then: > > https://bitbucket.org/galaxy/galaxy-central/pull-request/78/avoid-stall-when-merging-zero-files-fao/diff > > > > I can explain what was happening: We had a mount problem. The > > Galaxy server could talk to SGE and submit jobs, but when the > > jobs came to run the mount providing their home directory and > > the Galaxy file system was down, so they failed. Naturally this > > meant Galaxy got no output files back. > > > > Reading the code, you deliberately attempt to merge any files > > present (e.g. if 9 out of 10 come back). That does make sense > > as it could be instructive (as long as it is flagged as an error, > > which doesn't seem to be happening). > > > > I think getting zero files back from the split-jobs ought to be an > > error condition. In fact, failing to get all the expected sub-files > > back should also be an error condition (although it is still nice > > to do the merge so the user can see the partial output). > > > > I think a little re-factoring might be needed to treat these > > explicitly as errors. > > > > Regards, > > > > Peter > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
