[StarCluster] AWS instance runs out of memory and swaps

[Amirhossein Kiani]

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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