Am 06.06.2014 um 02:42 schrieb Ron Palmer:

I have a small cluster of computers with uneven clock speed CPUs and currently I am running with "-np" == total number of cores. However, it appears as if the fastest computer has to wait for the slower ones to finish at the end (at least I believe so). The most recent process took 65 hours so I am interested in finding ways to optimise the process.

Is it possible to, say, use a larger "-np" and then increase the thread number for the faster CPUs in the machine file to make the faster computers do more work so, ideally, they all finish about the same time? Will it finish off the first batch then start on the next batch? Or, will the faster computers just get more concurrent jobs, possibly slowing down the processing?

eg, if the single CPU of PC_A has twice the clock rating to that of single CPU PC_B, and both has quad cores, then use -np=12 and then have the following in the machinefile: PC_A:8 PC_B:4

Perhaps this is something better addressed with job scheduling software like GridEngine? Reuti?

You could define more slots than cores are available in the queue definition for (a) particular node(s), but this would enable the workaround you outlined already in SGE's way only. The way MPI was designed was having equal computing power per rank in mind I think (and often clusters are designed this way nowadays, even after an upgrade of a cluster buy adding newer/faster nodes you could route the jobs to use only machines of the same kind in SGE). In PVM there was even an entry for the relative speed of a machine in the hostfile (as a collection of different machines was often seen that days), but there is nothing similar in MPI AFAIK. -- Reuti

Thanks, Ron

-- Ron Palmer MSc MBA. Principal Geophysicist [email protected] 0413 579 099 07 3103 4963

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