[Gate-users] GATE on Linux cluster

[Fernando Rannou]

Hi Simon
sorry for this misunderstanding. When I say that an output format is
supported I mean that
the tools for do the merging are explicitly provided by Gate. Clearly, the
cluster tools is capable
of writing all formats out, one for each process. And I agree with you that
most merging are
easy to do and that users should not have problem writing their own.


Fernando

On Tue, May 29, 2012 at 6:03 AM, Simon Stute <gate.stute at gmail.com> wrote:

> Hello,
>
> Just to clarify something that is often discussed and that seems unclear
> for many people.
> The cluster tools actually support all output formats, in a certain way.
>
> To be as clear as possible -- except the ROOT output, all other outputs
> only consist in files that can be either concatenated (e.g. list-mode,
> ascii), or summed (e.g. sinograms, interfile, dose maps), so it is supposed
> that you can do such simple operations by yourself. Then, the root output
> is a sophisticated output format, so to merge different root files, you
> need a specific tool: this tool is provided in the cluster tools, included
> in the Gate release (or a native root command also exists, but which won't
> preserve the eventID coherence with respect to the time).
>
> Hope I clarify something :-)
> Simon
>
> On Fri, May 25, 2012 at 4:11 PM, Fernando Rannou <fernando.rannou at usach.cl
> > wrote:
>
>> Dear Alex
>> The Gate distribution currently has a "cluster solution", which splits
>> your
>> simulation
>> in as many smaller simulations as you want. That's the standard way people
>> have been
>> using Gate on clusters, and you will find a lot of support in this list.
>>
>> However, our group has been using a different solution which does not
>> split
>> you simulation.
>> We currently support only ROOT output (just as the cluster tools (?)).
>> In the case you decide to try our MPI solution, we will be happy to help
>> you setting up your installation.
>>
>>
>> Let me know
>>
>> Fernando
>>
>> On Fri, May 25, 2012 at 9:10 AM, Alex <piratemp at gmail.com> wrote:
>>
>> > Dear Gaters,
>> >
>> > I am looking for some advice on installation of GATE on a linux cluster.
>> > My department just went through an upgrade cycle that frees up 18
>> > Intel-duo-core PCs, 4gb RAM, 320gb HD.  I have previously installed
>> GATE on
>> > a high-performance 6 CPU machine running Ubuntu.  However, I never could
>> > get GATE to run on all CPUs.  It only ran on 1.  Someone here had
>> reported
>> > that GATE is a single-thread application so that's not possible.
>>  However,
>> > I have seen a number of publications showing GATE running in parallel
>> mode
>> > on multiple CPUs?.  Some helpful links or advice to clear up my
>> confusion
>> > please!
>> >
>> > Alex
>> > UMC
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>