Re: [Denovoassembler-devel] Ray app in BaseSpace

[Maxime D. <max...@gm...>]

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 ?

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).
> 
> 
> 
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> Denovoassembler-devel mailing list
> Den...@li...
> https://lists.sourceforge.net/lists/listinfo/denovoassembler-devel
>