I seem to have found a combination of resource quotas that is preventing
the scheduler from scheduling parallel jobs across multiple queues.
I have multiple queues for jobs with different run times: veryshort.q, short.q
,
long.q, and verylong.q. Each of these queues has an increasing 'h_rt' limi
Hello,
>> {
>> name shortlimit
>> description NONE
>> enabled TRUE
>> limitqueues short.q hosts * to slots=32
> I think you can leave the "hosts *" out here and the other RQS below. It
> means "used slots across all machines" limited to 32 in this queue. The same
>
>> All the queues are on the same machines. I am not sure which "algorithm" you
>> refer to.
>
>I refer to the internal algorithm of SGE how to collect slots from various
>queues.
>
>> As mentioned, the scheduler sorts by sequence number so the queues are
>> checked in shortest to longest order.
In my experience, resource quotas that try to enforce multiple constraints are
quite buggy.
Brendan
From: users-boun...@gridengine.org [users-boun...@gridengine.org] On Behalf Of
Ray Spence [r3spe...@gmail.com]
Sent: Tuesday, June 19, 2012 4:40 PM
To: use
er-crashes-during-a-leap-second
Brendan Moloney
Senior Research Assistant / Programmer
Advanced Imaging Research Center
Oregon Health Science University
From: users-boun...@gridengine.org [users-boun...@gridengine.org] On Behalf Of
Daniel Povey [dpo...
Virtual memory includes things like shared libraries (even though these are
only loaded into memory once for all processes that use them).
-Brendan
From: users-boun...@gridengine.org [users-boun...@gridengine.org] On Behalf Of
Jérémie Dubois-Lacoste [jere
o
check whether
they exceed the memory limit for the node or not. While actually this
shared-libraries-memory will be only once in the RAM, thus SGE
overestimating their usage.
I guess I am wrong somewhere...
Jérémie
2012/9/26 Brendan Moloney :
> Virtual memory includes things like shared libr
Hello,
I have MPICH2 tightly integrated with OGS 2011.11. Everything is working great
in general. I have noticed when I submit a moderate number of small MPI jobs
(e.g. 100 jobs each using two cores) that I will get intermittent commlib
errors like:
commlib error: got select error (Broken pi
>> Hello,
>>
>> I have MPICH2 tightly
>
>Which version? It should work out-of-the-box with SGE.
Version is 1.4 and yes it does have built in integration.
>> integrated with OGS 2011.11. Everything is working great in general. I
>> have noticed when I submit a moderate number of small MPI jobs
I spent some time researching this issue in the context of OpenSSH and found
some mentions of similar problems due to the initial handshake package being
too large
(http://serverfault.com/questions/265244/ssh-client-problem-connection-reset-by-peer).
I was dubious that this was my problem but
s,
Brendan
____
From: Brendan Moloney
Sent: Friday, November 09, 2012 3:31 PM
To: Reuti
Cc: users@gridengine.org
Subject: RE: [gridengine users] Intermittent commlib errors with MPI jobs
I spent some time researching this issue in the context of OpenSSH and found
some mentions of similar probl
I suppose it could be the switch. Is the only way to test this to swap it out
for a different switch?
Thanks again,
Brendan
From: Reuti [re...@staff.uni-marburg.de]
Sent: Monday, November 12, 2012 4:17 AM
To: Brendan Moloney
Cc: users@gridengine.org
Ok I will test that out once I can schedule some down time. I might even be
able to get my hands on another switch by then.
I appreciate all the help.
From: Reuti [re...@staff.uni-marburg.de]
Sent: Tuesday, November 13, 2012 3:33 AM
To: Brendan Moloney
Sent: Wednesday, November 14, 2012 10:02 AM
To: Brendan Moloney
Cc: users@gridengine.org
Subject: Re: [gridengine users] Intermittent commlib errors with MPI jobs
Am 14.11.2012 um 00:56 schrieb Brendan Moloney:
> Ok I will test that out once I can schedule some down time. I might even be
> abl
> We've got a locally-written program that dynamically links against
> a package that's compiled with optimizations for different chipsets
> (ATLAS[2]). We've built ATLAS with multiple versions, optimized
> for each architecture in our cluster.
>
> This is fine for serial jobs--the login environme
E for small MPI
jobs. However, I would still like to know the root cause of this issue.
Thanks,
Brendan
From: users-boun...@gridengine.org [users-boun...@gridengine.org] On Behalf Of
Brendan Moloney [molo...@ohsu.edu]
Sent: Tuesday, December 11, 2012 2:08
Hello,
I use multiple queues to divide up available resources based on job run times.
Large parallel jobs will typically span multiple queues and this has generally
been working fine thus far. However I recently increased the number of queues
(from 4 to 9) so that the time limits can be more f
Hi Reuti,
>> I use multiple queues to divide up available resources based on job run
>> times.
>
> So you are requesting "-l h_rt=..."?
Yes.
> Yes, the problem is that you can't address a specific queue in `qrsh -inherit
> ...` and if you get several queues on a machine you might have used up
From: Dave Love,,, [d.l...@liverpool.ac.uk]
Sent: Monday, September 16, 2013 3:01 PM
To: Brendan Moloney
Cc: users@gridengine.org
Subject: Re: [gridengine users] Problems with multi-queue parallel jobs
Brendan Moloney writes:
> Hello,
>
> I use multiple queues to divide up available
Hi Reuti,
> Yes. But this queue can have the total slot count of the machine. Or are you
> assigning right now 4 cores to a short queue, 8 to a medium one and the
> remaining 4 cores of a 16 cores machine to a long queue?
I limit the total number of slots for each queue using an RQS. The short
ime a node is
added or removed from the cluster.
Any thoughts or suggestions?
Thanks,
Brendan
From: Brendan Moloney
Sent: Monday, September 16, 2013 5:03 PM
To: Dave Love
Cc: users@gridengine.org
Subject: RE: [gridengine users] Problems with multi-
F
jsv_sub_add_param l_hard slots_vvl 1
fi
jsv_accept "Job OK"
return
}
. ${SGE_ROOT}/util/resources/jsv/jsv_include.sh
jsv_main
I hope someone else finds this helpful.
Thanks,
Brendan
From: users-boun...@gridengine.org
away from the multiple queue
configuration, as this does not seem to be very well supported.
Thanks,
Brendan
From: Reuti [re...@staff.uni-marburg.de]
Sent: Thursday, September 26, 2013 2:39 AM
To: Brendan Moloney
Cc: users@gridengine.org
Subjec
hich each user can use at most one
slot for 12 hours.
Brendan Moloney
Research Associate
Advanced Imaging Research Center
Oregon Health Science University
From: users-boun...@gridengine.org [users-boun...@gridengine.org] on behalf of
Prentice Bisbal [prentice
No, that is not normal. I am guessing you use SSH for qlogin and don't have
tight integration setup?
From: users-boun...@gridengine.org [users-boun...@gridengine.org] on behalf of
Michael Stauffer [mgsta...@gmail.com]
Sent: Friday, April 10, 2015 12:31 PM
To: Gri
Reuti posted this link yesterday:
https://arc.liv.ac.uk/SGE/htmlman/htmlman5/remote_startup.html section "SSH
TIGHT INTEGRATION"
Brendan Moloney
Research Associate
Advanced Imaging Research Center
Oregon Health Science University
From: Michael Stauf
Hi,
I have a small cluster so exclusive node access isn't really an option. We
enforce memory constraints on jobs using h_vmem. I discovered that more recent
versions of CUDA will always allocate a huge amount of virtual memory (RAM +
SWAP + GPU_RAM) so that it can supply a "Unified Virtual Add
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