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

[Rajalekshmi Deepu]

Thanks Matt.

Best,

Lekshmi


On 07.06.18 15:27, Hall, Matt wrote:
>
> Hiya,
>
> Any large integer value will work, although because the value is 
> parsed as a signed 32bit int, less than about 2 billion.
>
> Cheers,
>
> Matt.
>
> *From:*Rajalekshmi Deepu [mailto:r.deepu at fz-juelich.de]
> *Sent:* 07 June 2018 14:20
> *To:* Hall, Matt <matt.hall at ucl.ac.uk>
> *Cc:* Cook, Philip <cookpa at pennmedicine.upenn.edu>; 
> camino-users at www.nitrc.org
> *Subject:* Re: [Camino-users] Possibility of parallelization for the 
> datasynth command.
>
> 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>
>     [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>
>     <mailto:cookpa at pennmedicine.upenn.edu>
>     *Cc:* camino-users at www.nitrc.org <mailto: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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>
>

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