[Camino-users] Possibility of parallelization for the datasynth command.

[Rajalekshmi Deepu]

Hi Matt,

  Thanks for the prompt response. May I ask you a reasonable value for 
the seed option?

Hope I don't have to use -separateruns option if I use single voxel 
command on several different nodes with different random seeds.

Best,

Lekshmi


On 07.06.18 15:06, Hall, Matt wrote:
>
> Hi,
>
> The simplest thing to do is to run the single voxel command on several 
> different nodes with different random seeds. You can submit each job 
> separately to your cluster’s scheduling system and process the results 
> when they’re finished. Otherwise you’ll just end up sequentially 
> running 24 voxels on a single node.
>
> Cheers,
>
> Matt.
>
> *From:*camino-users-bounces at www.nitrc.org 
> [mailto:camino-users-bounces at www.nitrc.org] *On Behalf Of *Rajalekshmi 
> Deepu
> *Sent:* 07 June 2018 14:00
> *To:* Cook, Philip <cookpa at pennmedicine.upenn.edu>
> *Cc:* camino-users at www.nitrc.org
> *Subject:* Re: [Camino-users] Possibility of parallelization for the 
> datasynth command.
>
> Hi,
>
> We have a cluster with each compute node having 24 physical and 24 
> logical cores. If I wanted to run the below command, say for 24 voxels 
> instead of 1, can I distribute it to the 24 cores? Probably with 
> -separateruns option. Will this generate different data as we use MC?
>
>  datasynth -walkers 100000 -tmax 10000 -p 0.0 -voxels 1 -initial spike 
> -voxelsizefrac 1 -diffusivity 0.6E-9 -schemefile myScheme.scheme1 
> -substrate cylinder -packing square -cylinderrad 3E-6 -cylindersep 
> 6.1E-6 -outputfile regCyl_r=3E-6_spike.Bfloat
>
> Also I am not clear with the option -seed. Here 
> <http://camino.cs.ucl.ac.uk/index.php?n=Tutorials.MCSimulator> it 
> says, "|-seed|specifies the seed for the random number generators to 
> use."
>
> On the other hand, here 
> <http://web4.cs.ucl.ac.uk/research/medic/camino/pmwiki/pmwiki.php?n=Man.Datasynth> 
> it says "Specifies the random seed to use for noise generation in 
> simulation trials."
>
> Bit confused now.
>
> Any help will be appreciated.
>
> Thanks and regards,
>
> Lekshmi
>
> On 29.05.18 16:31, Rajalekshmi Deepu wrote:
>
>     Hi,
>
>     Please find below the command:
>
>     datasynth -walkers 100000 -tmax 1000 -p 0.0 -voxels 1 -schemefile
>     59.scheme  -initial uniform
>
>     Best,
>
>     Lekshmi
>
>
>     On 29.05.18 16:19, Cook, Philip wrote:
>
>         Hi,
>
>         Can you give an example of the command you want to parallelize?
>
>
>
>             On May 29, 2018, at 9:20 AM, Rajalekshmi Deepu
>             <r.deepu at fz-juelich.de> <mailto:r.deepu at fz-juelich.de> wrote:
>
>             Dear all,
>
>               I would like to know if there is a possibility of
>             parallelization for the datasynth command?
>
>             Couldn't find any information about it.
>
>             Any help would be appreciated.
>
>             Thanks and regards,
>
>             Lekshmi
>
>
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