[gridengine users] usage of make -j

Reuti reuti at staff.uni-marburg.de
Fri Mar 15 15:23:44 UTC 2013


Am 15.03.2013 um 04:51 schrieb Vamsi Krishna:

> used the following command to submit two jobs
> 
> cwd: /test1, qsub -l exclusive -l hostname=`uname -n` -pe smp 12 batch_test.bash
> 
> cwd:/test2, qsub -l exclusive  -l hostname=`uname -n` -pe smp 12 batch_test.bash

If you specify "-exclusive" it will be "exclusive" - it's per job not to allow any other job on this machine/queue (resp. "these machines" in case of a PE request requiring several nodes). It's not per user.

If you want to reserve a node for your own use only, you can make an advance reservation first, and then submit into this advance reservation:

$ qrsub -pe smp 24 -l exclusive -d 3600
Your advance reservation 196 has been granted
$ qrstat
ar-id   name       owner        state start at             end at               duration
------------------------------------------------------------------------------------------
    196            reuti        r     03/15/2013 16:06:37  03/15/2013 17:06:37  01:00:00
$ qsub -ar 196 -pe smp 12 foobar.sh
Your job 5814 ("foobar.sh") has been submitted
$ qsub -ar 196 -pe smp 12 foobar.sh
Your job 5815 ("foobar.sh") has been submitted

resp.

$ qmake -ar 196 -pe smp 12 -- 

(It's even not necessary to specify "-l exclusive" for the advance reservation: in case you request 24 cores with "allocation_rule $pe_slots" in a node with 24 cores the advance reservation will block them already.)

-- Reuti


> only first job is running and other one is in queue wait status. but if i submit -p smp 24, successfully it is using 24slots in the host. what could be the reason in waiting for the second job when i use 12 slots.
> 
> job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID
> -----------------------------------------------------------------------------------------------------------------
> 1347219 10.35000 batch_test user1    r     03/15/2013 01:21:33                      batch.q at node1 12
> 1347220 1.60000 batch_test user1     qw    03/15/2013 01:20:36                                   12
> 
> 
> On Fri, Mar 8, 2013 at 9:29 PM, Vamsi Krishna <vkpolisetty at gmail.com> wrote:
> Thanks Reuti, Progressing well.
> 
>  - V 
> 
> 
> 
> On Wed, Mar 6, 2013 at 2:10 AM, Christopher Heiny <cheiny at synaptics.com> wrote:
> On 03/05/2013 10:35 AM, Reuti wrote:
> Hi,
> 
> Am 05.03.2013 um 18:41 schrieb Vamsi Krishna:
> 
> >is there any way to run make -j <slots in node> when we submit to batch environment to use all the slots with -pe <slots in node>
> please have a look at the `qmake` tool which is installed with SGE in case you want to start the compilation on the command line (`man qmake`).
> 
> If you are submitting the complete `make` job to a batch queue already, you could use:
> 
> make -j $NSLOTS
> 
> in your jobscript and it will be replaced at runtime with the requested number of slots as you specified it as argument to `qsub -pe smp 4` or alike. If you want to use always all cores in a machine:
> 
>   qsub -l exclusive -pe smp -999 make.sh
> 
> will always use the maximum up to 999 cores in a machine ("exclusive" is a complex being set up with "relop EXCL", "smp" a PE setup with "allocation_rule $pe_slots") and set $NSLOTS accordingly at runtime.
> 
> Hmmm.  That's an interesting trick.
> 
> Our make invocations are already embedded in lengthy Bash scripts submitted to GE.  We use on slot per machine and one slot per job to ensure exclusive access (within that queue) to a given machine.  Then we invoke make from the script like this:
> 
>     cpus=`grep processor /proc/cpuinfo | wc -l`
>     make -j ${cpus}  .......
> 
>                                                 Chris
> 
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