Queues
A queue is needed when submitting jobs, if no queue is given the SGE submits your job to your default queue. There are several queues available. Only the administrator can create others if needed. To display the available queues use the qstat or qconf command.
vill@shark:~$ qstat -g c
Prints a cluster queue summary
CLUSTER QUEUE CQLOAD USED RES AVAIL TOTAL aoACDS cdsuE
--------------------------------------------------------------------------------
12hr-KG.q 0.16 12 0 60 72 0 0
2hr-all.q 0.16 0 0 72 72 0 0
LGTC_HiSeq.q 0.64 1 0 23 24 0 0
MolEpi_HighMem.q 0.06 7 0 5 12 0 0
all.q 0.59 287 0 157 444 0 0
mpi.q 0.61 0 0 0 27 0 27
notebook.q 0.00 1 0 23 24 0 0
qlogin.q 0.00 3 0 37 40 0 0
Or
vill@shark:~$ qconf -sql
Prints only the available queues
12hr-KG.q
2hr-all.q
LGTC_HiSeq.q
MolEpi_HighMem.q
all.q
mpi.q
notebook.q
qlogin.q
Currently these queues are available for the following purposes:
queue name | Description |
---|---|
all.q | Everyone can use this queue only the basking shark cannot be used with this queue, can only be used for batch jobs |
qlogin.q | Everyone can use this queue, this queue is only for interactive jobs, and runs on koala and kiribati |
notebook.q | Everyone can use this queue for their ipython notebook IPythonNotebook |
Find the executions hosts for a queue (in this example the LGTC.q) the first command finds the hostlist for the queue.
qconf -sq all.q |grep hostlist | sed 's/[ ]\+/:/g' | cut -d : -f2
This will show : @allhosts
The second command will print all the hosts in the hostlist
qconf -shgrp @allqueue
group_name @allqueue
hostlist baskingshark.researchlumc.nl blueshark.researchlumc.nl \
camouflageshark.researchlumc.nl caribbeanshark.researchlumc.nl \
chimerashark.researchlumc.nl cowshark.researchlumc.nl \
dogfishshark.researchlumc.nl elephantshark.researchlumc.nl \
epauletteshark.researchlumc.nl frilledshark.researchlumc.nl \
goblinshark.researchlumc.nl greatwhiteshark.researchlumc.nl \
greenlandshark.researchlumc.nl kitefinshark.researchlumc.nl \
lemonshark.researchlumc.nl leopardshark.researchlumc.nl \
makoshark.researchlumc.nl megamouthshark.researchlumc.nl \
nightshark.researchlumc.nl pygmeshark.researchlumc.nl \
reefshark.researchlumc.nl sawshark.researchlumc.nl \
swellshark.researchlumc.nl threshershark.researchlumc.nl \
tigershark.researchlumc.nl whaleshark.researchlumc.nl \
whorltoothshark.researchlumc.nl wobbegongshark.researchlumc.nl \
zebrashark.researchlumc.nl
Print all hosts in every hostlist
for i in `qconf -shgrpl` ; do qconf -shgrp $i ; done
Which queue do I use?
I you don't give a queue to run on with your job the Open Grid Scheduler will use an available queue where you have access to. If you use the -q queue name option then you use a so called hard_queue list and that queue will be used.