[GE users] Short medium and long queue setup

Reuti reuti at staff.uni-marburg.de
Thu Oct 19 18:15:35 BST 2006


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Am 19.10.2006 um 17:05 schrieb Jerome:

> Reuti wrote:
>>> Hi Reuti.
>>> Yes, i compiled (or i think so) the mpi as it is indicated in  
>>> the  Howto on SGE website. I use the third solution, compilation  
>>> of the  sources.
>>> If all the process in the paster node of the mpi group are with  
>>> a  nice value of 19, as i show you in teh folowing (command: "ps  
>>> f -eo  nice,user,pgrp,command --cols=70")
>>>
>>>   0 sge       3387 /opt/gridengine/bin/lx26-x86/sge_execd
>>>   0 sge      16942  \_ sge_shepherd-35 -bg
>>> -19 lorenzo  17017      \_ /bin/tcsh /opt/gridengine/default/ 
>>> spool/c-1
>>> -19 lorenzo  17017          \_ /bin/sh /opt/mpich/gnu/bin/mpirun - 
>>> np 8
>>> -19 lorenzo  17017              \_ /home/lorenzo/mrbayes-3.1.2/mb  
>>> -p4p
>>> -19 lorenzo  17017                  \_ /home/lorenzo/ 
>>> mrbayes-3.1.2/mb
>>> -19 lorenzo  17017                  \_ /opt/gridengine/bin/lx26- 
>>> x86/qr
>>> -19 lorenzo  17017                  |   \_ /usr/bin/ssh -n -p  
>>> 33984 c-
>>> -19 lorenzo  17017                  \_ /opt/gridengine/bin/lx26- 
>>> x86/qr
>>> -19 lorenzo  17017                  |   \_ /usr/bin/ssh -n -p  
>>> 33985 c-
>>> -19 lorenzo  17017                  \_ /opt/gridengine/bin/lx26- 
>>> x86/qr
>>> -19 lorenzo  17017                  |   \_ /usr/bin/ssh -n -p  
>>> 34035 c-
>>> -19 lorenzo  17017                  \_ /opt/gridengine/bin/lx26- 
>>> x86/qr
>>> -19 lorenzo  17017                  |   \_ /usr/bin/ssh -n -p  
>>> 33959 c-
>>> -19 lorenzo  17017                  \_ /opt/gridengine/bin/lx26- 
>>> x86/qr
>>> -19 lorenzo  17017                  |   \_ /usr/bin/ssh -n -p  
>>> 33947 c-
>>> -19 lorenzo  17017                  \_ /opt/gridengine/bin/lx26- 
>>> x86/qr
>>> -19 lorenzo  17017                  |   \_ /usr/bin/ssh -n -p  
>>> 33980 c-
>>> -19 lorenzo  17017                  \_ /opt/gridengine/bin/lx26- 
>>> x86/qr
>>> -19 lorenzo  17017                      \_ /usr/bin/ssh -n -p  
>>> 33891 c-
>>>
>>> In one of the slave node, i notice that uniquely the sshd to   
>>> connect this node from the master one have a nice value of 19:
>>>
>>>   0 sge       3364 /opt/gridengine/bin/lx26-x86/sge_execd
>>>   0 sge      16975  \_ sge_shepherd-35 -bg
>>> -19 root     16976      \_ sshd: lorenzo [priv]
>>>   0 lorenzo  16976          \_ sshd: lorenzo at notty
>> Aha, are you using Debian? Otherwise it might be a problem of the   
>> sshd by default that the nice value is lost. AFAIK this should be  
>> the  same for all child processes of a niced process. - Reuti
>

We are using the SGE supplied rshd and with this it's definitely  
working. In the OpenSSH source I can't find a renice, neither in 3.9  
nor in 4.4.1. The bash startup doesn't seem to set the nice, as a  
"qrsh bash" also retains the set nice values from SGE. Maybe it's in  
your pam? This was the issue with Debian, where the pam was patched  
to remove any set limits from SGE. After unpatching pam it worked fine.

-- Reuti

PS: is the -19 just because of copy and past? The -20 is the highest  
prority, 19 the lowest. Nice below 0 should only be used by system  
processes.


> Hi Reuti.
> I'm using Rocks version 4.2.1 , with openssh-3.9. How can i  
> investigate to solve this problem?
> Thank's.
> Best Regards.
>
> -- 
> -- Jérôme
> "Geoffroy, je lui ai dit, les copains, on t'a mis en quarantaine."
> "Je croyais qu'on allait plus lui parler" a dit Clotaire.
> "Il faut bien que je lui parle pour lui dire qu'on ne lui parle plus",
> j'ai dit.
> 	(Histoires inédites du Petit Nicolas, Goscinny & Sempé)
>
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