Hi Dan: qsub -cwd -b y 'metal < input.file > log.file'
Might work, if users/you still want to work without script files. Default queue -- to $SGE_ROOT/default/common/sge_request add: -q all.q (or whatever your default queue is) That sets a hard queue, which can be overridden with '-q someotherqueue'. Not sure about the last ... generally nodes will only error out if the error is a GE error, not a job error, so maybe they're just job errors? Do simple jobs work? -Hugh -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Dan Hyatt Sent: Tuesday, June 09, 2015 9:02 AM To: [email protected] Subject: Re: [gridengine users] command runs in grid engine but does not complete. As my grid engine was stable and working...and that was more important than anything else. I left it mostly running minimally administered for a year. When I went to add 6 more nodes to the grid, I inadvertently and stupidly reconfigured the grid breaking it. So I am trying to get the grid back to where my users expect it. I found what my problem was and a work around... the command was qsub -cwd -b y metal < input.file > log.file and it was choking when I put metal < input.file > log.file into a script file, and ran qsub -cwd script.bash it works fine The next two issues that I have been googling and pouring over the documentation.... When I send a job to a queue, if the queue is busy it sends it to the next queue (defeating the purpose of separate queues in my env). How do I set the queues to run jobs ONLY in the appointed queue? The execute nodes were updated, and some are not playing well in the sandbox. When the grid sends a job there, it hangs, sends an error but does not remove that blade from the execute node list like it did before. Is there an easy way to manually test the execute nodes (there are 180), and why is it not removing bad nodes from the available nodes as it did before? Before it would mark it unusable so when I list the execute nodes I would see that the node was bad and it would not accept jobs. On 06/08/2015 02:10 PM, Alex Chekholko wrote: > What was the "grid reconfiguration"? > > On 06/08/2015 11:42 AM, Dan Hyatt wrote: >> >> We are running a binary program called metaanalysis, which the user says >> was working prior to a grid reconfiguration. >> >> >> qsub -cwd -b y /dsg_cent/bin/metal < c22srcfile.txt > c22SBP.log >> >> This starts, runs, creates the logs, and then fails to create the data >> files >> qsub -cwd -b y /dsg_cent/bin/metal < c22srcfile.txt > c22SBP.log >> >> -rw-rw-r-- 1 aldi genetics 8523209 Jun 8 09:53 c22GENOA.SBP.EA.M1.csv >> -rw-rw-r-- 1 aldi genetics 8660667 Jun 8 09:53 c22FamHS.SBP.ea.M1.csv >> -rw-rw-r-- 1 aldi genetics 6025412 Jun 8 09:53 >> c22HYPERGEN.SBP.EA.M1.csv >> -rw-rw-r-- 1 aldi genetics 2061 Jun 8 09:53 c22srcfile.txt >> -rw-rw-r-- 1 dhyatt genetics 43 Jun 8 13:40 c22SBP.log >> -rw-r--r-- 1 dhyatt genetics 0 Jun 8 13:40 metal.e1043 >> -rw-r--r-- 1 dhyatt genetics 2743 Jun 8 13:40 metal.o1043 >> [dhyatt@blade5-2-1 c22 >> >> the control/output file indicates everything runs there are .o and .e >> files, but no data >> >> >> The command line works fine, and creates the data files. But I need to >> run large jobs on the queue >> >> -rw-rw-r-- 1 aldi genetics 8523209 Jun 8 09:53 >> c22GENOA.SBP.EA.M1.csv >> -rw-rw-r-- 1 aldi genetics 8660667 Jun 8 09:53 >> c22FamHS.SBP.ea.M1.csv >> -rw-rw-r-- 1 aldi genetics 6025412 Jun 8 09:53 >> c22HYPERGEN.SBP.EA.M1.csv >> -rw-rw-r-- 1 aldi genetics 2061 Jun 8 09:53 c22srcfile.txt >> -rw-rw-r-- 1 dhyatt genetics 8177082 Jun 8 13:39 METAANALYSIS1.TBL >> -rw-rw-r-- 1 dhyatt genetics 1054 Jun 8 13:39 >> METAANALYSIS1.TBL.info >> -rw-rw-r-- 1 dhyatt genetics 10487038 Jun 8 13:39 METAANALYSIS2.TBL >> -rw-rw-r-- 1 dhyatt genetics 1316 Jun 8 13:39 >> METAANALYSIS2.TBL.info >> -rw-rw-r-- 1 dhyatt genetics 5030 Jun 8 13:39 c22SBP.log >> >> any thoughts? >> >> Dan >> _______________________________________________ >> users mailing list >> [email protected] >> https://gridengine.org/mailman/listinfo/users > _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
