Re: [Denovoassembler-devel] Ray app in BaseSpace

[Boisvert, S. <boi...@an...>]

> ________________________________________
> From: Maxime Déraspe [max...@gm...]
> Sent: Wednesday, June 25, 2014 6:57 AM
> To: den...@li...
> Subject: Re: [Denovoassembler-devel] Ray app in BaseSpace
> Hi Sebastien,
> thank you for providing me this information.
> The RayCommand goes like this :
> mpiexec -n 32 Ray \
> -k \
> 31 \
> -p \
> /data/input/samples/37052/data/intensities/basecalls/s_G1_L001_R1_001.fastq.1.gz.fastq.gz \
> /data/input/samples/37052/data/intensities/basecalls/s_G1_L001_R2_001.fastq.1.gz.fastq.gz \
> -p \
> /data/input/samples/37052/data/intensities/basecalls/s_G1_L001_R1_002.fastq.1.gz.fastq.gz \
> /data/input/samples/37052/data/intensities/basecalls/s_G1_L001_R2_002.fastq.1.gz.fastq.gz \
> -o \
> /data/output/appresults/11507497/37052
> 
> I will deactivate the SM btl, would it be better to use MPICH in case
> this doesn't work ?

No. That won't change anything I think. Both are great MPI implementations.


> Maxime
> 
> On 06/25/2014 03:49 PM, Boisvert, Sebastien wrote:
> >
> > [I CC'ed devel mailing lists]
> >
> > Can you provide the full command (cat RayCommand) ?
> >
> > I have 2 ideas to troubleshoot (waiting 17 hours is not a good approach
> > to troubleshooting).
> >
> > # Idea 1
> >
> > Disabling the SM btl in Open-MPI's MCA (assuming you are using Open-MPI and not
> > MPICH).
> >
> > Before:
> > mpiexec -n <ranks> Ray -k <k> -p <file1> <file2>
> >
> > After:
> > mpiexec -n <ranks> --mca btl ^sm Ray -k <k> -p <file1> <file2>
> >
> >
> > # Idea 2
> >
> > RayPlatform has built-in debugger (it is mentioned in the doc).
> >
> > Before:
> > mpiexec -n <ranks> Ray -k <k> -p <file1> <file2>
> >
> > After:
> > mpiexec -n <ranks>  Ray -debug -k <k> -p <file1> <file2>
> >
> > This will give you plenty of information in the standard output.
> >
> >
> >
> > My bet: SM in the cloud is slow / buggy and there is a bug in the runtime there
> > (below RayPlatform).
> >
> >
> >
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> 
> ------------------------------------------------------------------------------
> Open source business process management suite built on Java and Eclipse
> Turn processes into business applications with Bonita BPM Community Edition
> Quickly connect people, data, and systems into organized workflows
> Winner of BOSSIE, CODIE, OW2 and Gartner awards
> http://p.sf.net/sfu/Bonitasoft
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