Re: [Denovoassembler-devel] Quick update

[Sébastien B. <seb...@ul...>]

________________________________
> From: cp...@cr... 
> To: seb...@ul... 
> CC: jac...@cr... 
> Date: Fri, 16 May 2014 08:05:55 -0400 
> Subject: Quick update 
>  
> Hi Sebastien, 
>  
> OK, thanks to your help I have Ray running on the XC30 here at Cray.  
>   As I mentioned yesterday I submitted HiSeq2500 with a limit of 12 hr  
> and using slightly more than 300 cores.  This morning ran out of time.  
>   Now, while I start becoming familiar with Titan I’ll continue running  
> on the XC30 here.  Do you have any feeling for how long is going to  
> take?

What I found while experimenting on Titan was that the I/O code
that loads sequence from the file system into memory is a bottleneck.

Another bottleneck is the code the merge the assembled sequences.

> Show we try to run with the restart option?  I need to read the  
> Ray manual to see if you have any info about that option. 

The option is -read-write-checkpoints Checkpoints


It saves the progression of the calculation at key steps.

>  
> In addition, I built the code with a profiler to start familiarizing  
> myself with the code and try to identify where the bottlenecks are. 

OK

You can also send signal SIGUSR1 to a Ray process to activate RayPlatform debug
mode. This option is available by default, but I don't know if you can actually
send a signal to a running process on Cray compute nodes.

>  
> Cheers 
>  
> carlos