Re: AWS instance runs out of memory and swaps

From: Amirhossein Kiani <no email>
Date: Fri, 2 Dec 2011 15:36:18 -0800

Dear Rayson,

Did you have a chance to test your solution on this? Basically, all I want is to prevent a job from running on an instance if it does not have the memory required for the job.

I would very much appreciate your help!

Many thanks,
Amir


On Nov 21, 2011, at 10:29 AM, Rayson Ho wrote:

> Amir,
>
> You can use qhost to list all the node and resources that each node has.
>
> I have an answer to the memory issue, but I have not have time to properly type up a response and test it.
>
> Rayson
>
>
>
> From: Amirhossein Kiani <amirhkiani_at_gmail.com>
> To: Justin Riley <justin.t.riley_at_gmail.com>
> Cc: Rayson Ho <rayrayson_at_gmail.com>; "starcluster_at_mit.edu" <starcluster_at_mit.edu>
> Sent: Monday, November 21, 2011 1:26 PM
> Subject: Re: [StarCluster] AWS instance runs out of memory and swaps
>
> Hi Justin,
>
> Many thanks for your reply.
> I don't have any issue with multiple jobs running per node if there is enough memory for them. But since I know about the nature of my jobs, I can predict that only one per node should be running.
> How can I see how much memory does SGE think each node have? Is there a way to list that?
>
> Regards,
> Amir
>
>
> On Nov 21, 2011, at 8:18 AM, Justin Riley wrote:
>
> > Hi Amir,
> >
> > Sorry to hear you're still having issues. This is really more of an SGE
> > issue more than anything but perhaps Rayson can give a better insight as
> > to what's going on. It seems you're using 23G nodes and 12GB jobs. Just
> > for drill does 'qhost' show each node having 23GB? Definitely seems like
> > there's a boundary issue here given that two of your jobs together
> > approaches the total memory of the machine (23GB). Is it your goal only
> > to have one job per node?
> >
> > ~Justin
> >
> > On 11/16/2011 09:00 PM, Amirhossein Kiani wrote:
> >> Dear all,
> >>
> >> I even wrote the queue submission script myself, adding
> >> the mem_free=MEM_NEEDED,h_vmem=MEM_MAX parameter but sometimes two jobs
> >> are randomly sent to one node that does not have enough memory for two
> >> jobs and they start running. I think the SGE should check on the
> >> instance memory and not run multiple jobs on a machine when the memory
> >> requirement for the jobs in total is above the memory available in the
> >> node (or maybe there is a bug in the current check)
> >>
> >> Amir
> >>
> >> On Nov 8, 2011, at 5:37 PM, Amirhossein Kiani wrote:
> >>
> >>> Hi Justin,
> >>>
> >>> I'm using a third-party tool to submit the jobs but I am setting the
> >>> hard limit.
> >>> For all my jobs I have something like this for the job description:
> >>>
> >>> [root_at_master test]# qstat -j 1
> >>> ==============================================================
> >>> job_number: 1
> >>> exec_file: job_scripts/1
> >>> submission_time: Tue Nov 8 17:31:39 2011
> >>> owner: root
> >>> uid: 0
> >>> group: root
> >>> gid: 0
> >>> sge_o_home: /root
> >>> sge_o_log_name: root
> >>> sge_o_path:
> >>> /home/apps/bin:/home/apps/vcftools_0.1.7/bin:/home/apps/tabix-0.2.5:/home/apps/BEDTools-Version-2.14.2/bin:/home/apps/samtools/bcftools:/home/apps/samtools:/home/apps/bwa-0.5.9:/home/apps/Python-2.7.2:/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/bin:/home/apps/sjm-1.0/bin:/home/apps/hugeseq/bin:/usr/lib64/openmpi/1.4-gcc/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/cuda/bin:/usr/local/cuda/computeprof/bin:/usr/local/cuda/open64/bin:/opt/sge6/bin/lx24-amd64:/root/bin
> >>> sge_o_shell: /bin/bash
> >>> sge_o_workdir: /data/test
> >>> sge_o_host: master
> >>> account: sge
> >>> stderr_path_list:
> >>> NONE:master:/data/log/SAMPLE.bin_aln-chr1_e111108173139.txt
> >>> *hard resource_list: h_vmem=12000M*
> >>> mail_list: root_at_master
> >>> notify: FALSE
> >>> job_name: SAMPLE.bin_aln-chr1
> >>> stdout_path_list:
> >>> NONE:master:/data/log/SAMPLE.bin_aln-chr1_o111108173139.txt
> >>> jobshare: 0
> >>> hard_queue_list: all.q
> >>> env_list:
> >>> job_args: -c,/home/apps/hugeseq/bin/hugeseq_mod.sh
> >>> bin_sam.sh chr1 /data/chr1.bam /data/bwa_small.bam &&
> >>> /home/apps/hugeseq/bin/hugeseq_mod.sh sam_index.sh /data/chr1.bam
> >>> script_file: /bin/sh
> >>> verify_suitable_queues: 2
> >>> scheduling info: (Collecting of scheduler job information
> >>> is turned off)
> >>>
> >>> And I'm using the Cluster GPU Quadruple Extra Large instances which I
> >>> think has about 23G memory. The issue that I see is too many of the
> >>> jobs are submitted. I guess I need to set the mem_free too? (the
> >>> problem is the tool im using does not seem to have a way tot set that...)
> >>>
> >>> Many thanks,
> >>> Amir
> >>>
> >>> On Nov 8, 2011, at 5:47 AM, Justin Riley wrote:
> >>>
> >>>>
> >> Hi Amirhossein,
> >>
> >> Did you specify the memory usage in your job script or at command
> >> line and what parameters did you use exactly?
> >>
> >> Doing a quick search I believe that the following will solve the
> >> problem although I haven't tested myself:
> >>
> >> $ qsub -l mem_free=MEM_NEEDED,h_vmem=MEM_MAX yourjob.sh
> >>
> >> Here, MEM_NEEDED and MEM_MAX are the lower and upper bounds for your
> >> job's memory requirements.
> >>
> >> HTH,
> >>
> >> ~Justin
> >>
> >> On 7/22/64 2:59 PM, Amirhossein Kiani wrote:
> >>> Dear Star Cluster users,
> >>
> >>> I'm using Star Cluster to set up an SGE and when I ran my job list,
> >> although I had specified the memory usage for each job, it submitted
> >> too many jobs on my instance and my instance started going out of
> >> memory and swapping.
> >>> I wonder if anyone knows how I could tell the SGE the max memory to
> >> consider when submitting jobs to each node so that it doesn't run the
> >> jobs if there is not enough memory available on a node.
> >>
> >>> I'm using the Cluster GPU Quadruple Extra Large instances.
> >>
> >>> Many thanks,
> >>> Amirhossein Kiani
> >>
> >>>>
> >>>
> >>
> >>
> >>
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> >
>
>
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Received on Fri Dec 02 2011 - 18:36:20 EST