gt; > > -Dj
> > >
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> > > Andreas Haupt|
And do you define host groups in the PE?
On Tue, Mar 12, 2019 at 9:53 AM David Trimboli wrote:
>
> On 3/12/2019 12:05 PM, Ian Kaufman wrote:
> > Are mynode{17-24} in a queue that is configured to use your "threads" PE?
>
>
> Yes. If you disable the limit, the subm
ail:
>
> qsub -l vf=1G -l
> h="mynode17|mynode18|mynode19|mynode20|mynode21|mynode22|mynode23|mynode24"
> -pe threads 1 anyscript.sh
>
> It'll work if you remove "-pe threads 1".
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IO issues? NFS server providing data and possibly jobs running over NDS
shares as opposed to running on local disk?
On Sat, Jan 26, 2019, 11:23 AM Joseph Farran Hi Daniel.
>
> Yes I do have large job-arrays around 7k tasks BUT I have had larger job
> arrays of 500k without seeing this kind of slo
helped, you may need to
> > unload/fix the apparmor profiles already loaded in the kernel.
> >
> > I haven't worked with apparmor, so you may need to search the internet
> > for solutions.
>
>
> I'll take a look. My brief perusal suggests that it's a nontrivial task
> to do so. I'll see what I find.
>
> Thanks!
>
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and it's not really fair for other user that use qsub.
>
> Then the simpliest way avoiding this is to forbiden the connection
>
> I'm not specialist of PAM and authentication have you got a link ?
>
>
>
>
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> -- Genome Sciences Department, System Administrator
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t; weight_tickets_functional 1
> weight_tickets_share 0
>
> Perhaps these settings might be causing our issue? Seems unlikely though,
> as we're not taking project or department into account in our scheduling.
>
> Thanks,
>
> DR
>
>
> On 2017-10-
bit of googling and man page
> reading on the relevant topics and settings, but wasn't able to find a good
> explanation for the behavior we're seeing. Any help greatly appreciated!
>
> Thanks,
>
> DR
> __
ault)
>
>
> Thanks,
> Subashini.K
>
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ease
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or message ***
>
>
> /opt/gridengine/default/spool/compute-0-4/job_scripts/5020911: line 12:
> 9088 Segmentation fault (core dumped) mpirun -np 4 gmx mdrun -ntmpi 1
> -ntomp 8 -v -deffnm eql2
>
>
>
> What is the reason behind this?
>
>
> Thanks,
> Subashi
s error?
>
>
> Please help.
>
> Thanks,
> Subashini.K
>
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Executable: /usr/local/gromacs/bin/gmx
>>> Library dir: /usr/local/gromacs/share/gromacs/top
>>>
>>>
>>> Can anyone help me?
>>>
>>> Thanks,
>>> Subashini.K
>>>
>>>
>>> --
>&
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_
oups who are in child domains like
> NAFTA.COMPANY.COM and EAME.COMPANY.COM etc.
>
> -dag
>
>
>
> Ian Kaufman wrote:
>
>> If you support multiple domains, are you able to guarantee unique short
>> names? It seems to me that could be a problem. If it is a case of multiple
&
;>
>
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:50
>>> 1
>>> 1144482 0.55500 sas64 username Eqw 09/27/2016 23:30:40
>>> 1
>>> 1144484 0.55500 sas64 username Eqw 09/27/2016 23:31:30
>>>
ially if anybody is trying to do some kind of visualization
> on them, but I've never had complaints about them being under-powered yet.
>
> Any thoughts you might have are appreciated.
>
> Thanks
> Biggles
>
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>>>
>>>
>> --
>> Alex Chekholko ch...@stanford.edu
>>
>> _
h memory allocated and then use qacct
> to look at the actual max usage so they know what they should ask for next
> time. We had some teething troubles with this for a few weeks after it was
> introduced, but it's all been working smoothly for a long time now.
>
>
--
Ian Kaufman
> management behind the scenes.
>
> Chris
>
>
>
> Pat Haley wrote:
> >
> > It looks similar but one big difference is when I run "qconf -sh" I
> > see all my compute nodes listed along with my frontend. However
> > "qconf -sql"
of the sender and do not necessarily represent the views of the
>>> Babraham Institute. Full conditions at:
>>> www.babraham.ac.uk<http://www.babraham.ac.uk/terms>
>>>
>>> ___
>&g
t basis?) so jobs that don't explicitly request the resource will use
> something by default, but we've been unable to figure out how to set this
> up.
>
> We are using 6.1u3.
>
> thanks
>
> ___________
> users mailing list
> 0.0
> Host Resource(s): hl:mem_free=88.885G
>
> And everything was working until a week ago.
>
> Ilya.
>
> Original Message
> Subject: Re: [gridengine users] Cannot request resource if it is a load
> value of memory type: SGE reports it as unk
-
>>>>>>> -
>>>>>>> gpu038 lx24-amd64 16 2.11 126.1G 15.7G
>>>>>>> 4.0G 0.0
>>>>>>> Host Resource(s): hl:mem_free=110.416G
>>>>>>>
>>>>>>>
g list
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>
>
>
> --
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> Lead Bioinformatician
> Bioinformatics Support Service
> Imperial College, London
>
>
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a user to use more than 3 entire nodes.
>
> Maybe there is some sorts of resource equivalency between slot and memory can
> achieve that?
>
> Thanks
> D
>
> Sent from my iPad
>
>> On 1 Jul 2014, at 5:57 am, Ian Kaufman wrote:
>>
>> I don't get th
ive or take. So it makes it really impracticle actually.
> However so far I've just set the default h_vmem and s_vmem values high
> enough to accomadate jvm apps, and increased the per-host consumable
> appropriately. We don't get fine-grained memory control, but it definitely
>
If not, you may want to limit the number of jobs to the
number of cores/slots you have, otherwise you will run into a backlog
of jobs, and if an array job, this can even be more serious.
Ian
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L
> parser, or is there a more convenient way to get the host?
>
> Tim
>
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; Yes and no. This is clearly a client-side configuration error that is
> impacting GE, but if GE is the only application/service that can't get user
> information correctly, maybe there is a problem with GE. Ultimately, I was
> just asking for help in figuring out what is misconfigu
gives the signal.
>> > is there something I'm missing as to how maxvmem is calculated?
>>
>> SGE will not look at one process only, but at the complete process tree.
>> Is PhythonRender the one and only child of `sge_shepherd`?
>>
>> -- Reuti
>
>
>
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Nyhuis
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> 2211 Elliott Avenue
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And here is some more info:
http://serverfault.com/questions/322073/howto-set-up-sge-for-cuda-devices
On Mon, Apr 14, 2014 at 1:39 PM, Ian Kaufman wrote:
> If everything is configured correctly, GridEngine will be aware that
> the GPU in node1 is in use, and schedule around it, ensurin
If everything is configured correctly, GridEngine will be aware that
the GPU in node1 is in use, and schedule around it, ensuring that the
8 GPU job will get unused GPUs.
Ian
On Mon, Apr 14, 2014 at 1:38 PM, Ian Kaufman wrote:
> Look at the info presented here:
>
> http://stackove
s are still free for jobs.
>
> I submit one job with PE=8. SGE allocate all the 3 nodes to me with 8
> GPU slots. The problem is now: how my job knows what GPUs it can get
> on node1?
>
> Best
>
>
>
>
> On Mon, Apr 14, 2014 at 4:13 PM, Ian Kaufman wrote:
>>
t;
>> Like the option to request sockets instead of cores which I posted in the
>> last couple of days, you can use a similar approach to get the number of the
>> granted GPU out of the queue name.
>>
>> -- Reuti
>>
>>
>>> On Mon, Apr 14, 2014 at
olution, since some jobs may still happen to collide to each
> other on the same GPU on a multiple GPU node. If GE can have the
> memory to record the GPUs allocated to a job, then this can be
> perfect.
>
>
> On Mon, Apr 14, 2014 at 1:46 PM, Ian Kaufman wrote:
>> I belie
and manage GPU(and Phi). Not need to be complicated and
> powerful, just do basic work.
>
> Thanks,
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2.118G
>
> and I requesting the wrong resource? how gridengine measured it's 2.118G is
> unclear to me.
>
>
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; Regards
>>
>> Lionel
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in this case it is neither. The host
> only has this one queue instance, and the job only requests this one
> complex.
>
> Suggestions?
>
> Regards,
> --
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> ** **
>
> *From:* Ian Kaufman [ma
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s comments - there would be no "$" preceding the "\r" since the very
next character after the newline gets interpreted is the "\r".
Ian
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h
>>>
>>> #$-N SAFKTAT1
>>> #$-t 6970-10230:1
>>>
>>>
>>>
>>> /var/software/packages/Mathematica/7.0/Executables/math -run
>>> "teller=$SGE_TASK_ID;<< ModelFotokatalyseTAT.m"
>>>
>>>
>>
>
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RAM consumed at any one point in time up until the
moment you ran the qstat command.
Ian
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s of production and just recently over 100K jobs in two
months).
Ian
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ithout mucking with any flags. Additionally,
the crew I work with use a workflow/job management tool that isn't
thread aware, so every child Java app that gets launched gets its own
JVM. That is high on the list of things to fix!
Ian
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ws me to ensure that on a 12 core box
and 48GB of RAM, I can run nearly 12 jobs keeping the desired 1 per
core.
Ian
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ault, Grid Engine uses one slot per
core, and one job fits in each slot.
Ian
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rectly limits user alpha to 320 jobs, user beta to 128 jobs,
and all others to 32 jobs. In your rqs, you are limiting users to 16
jobs, not 2.
Ian
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