newbler cpu core usage

[malatorr]

Hi, I'm trying to run newbler in ubuntu server (8 cores, 8G ram) and can make it use more than one core.

I have mpich installed. And I've tried with:

export GS_LAUNCH_MODE=MULTI
export GS_CACHEDIR=/data

and:

export GS_LAUNCH_MODE=GSRPM
export GS_CACHEDIR=/data

I also tried run it using mpirun newbler project. It runs but only using one core...

I set 4 cores in the assembly XML file. So frustrating because I can not find good documentation about this issue.

[kmcarr]

The environment variables you are playing with are for the gsRunProcesser, they have nothing to do with newbler (now officially called gsAssembler). Only the latest version of gsAssembler (2.3) is able to utilize multiple CPUs. While earlier versions of the assembler wrote a <numCPU> tag to the 454AssemblyProject.xml file, I suspect it was just anticipating future functionality. gsAssembler can use multiple cpus/cores on a single machine, not across a cluster so MPI is irrelevant.

[malatorr]

Thanks, now I see. I will get gsAssembler 2.3

PS: They were anticipating the new functionallity too early...Documantation shows that cpu number parameter is working.