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:
>
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> 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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Received on Tue Nov 08 2011 - 20:37:38 EST