[Gate-users] GATE on cluster

[xcao]

hello, Fernando and Bassim

 I also have met your says problems that writing ROOT files gets slower and slower as the file increases，
and I have checked what have happed,  then I found that sometimes it have memory leak as programs 
run when your write root files. I never encounter this problems when I use Geant4 to develop my programs.
So, I have no idea with it. I don't know wheter this will give you any help.

wishes!
Shelley



xcao

From: gate-users-request
Date: 2013-10-18 21:31
To: gate-users
Subject: Gate-users Digest, Vol 89, Issue 21
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Today's Topics:

   1. Re: GATE on cluster (Fernando Rannou)


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Message: 1
Date: Fri, 18 Oct 2013 11:01:33 -0300
From: Fernando Rannou <fernando.rannou at usach.cl>
To: bassim aklan <bassim.aklan at imp.uni-erlangen.de>
Cc: "<gate-users at lists.opengatecollaboration.org>"
<Gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] GATE on cluster
Message-ID:
<CAN3A8B3Zk2WbUj6VXRtWcr9=f2R-K_ZN6MZijnHjhmsGP+E4fw at mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"

Hello Bassim

I do not know whether I understand, but we have found in very large
simulations,
that writing ROOT files gets slower and slower as the file increases.
I asked ROOT people but they told me that that should not happen... but it
happens


I attach a plot that shows how simulation grows much faster when ROOT output
is selected instead of ASCII. This is part of the paper we just published
on ParGate.



Fernando




On Fri, Oct 18, 2013 at 6:45 AM, bassim aklan <
bassim.aklan at imp.uni-erlangen.de> wrote:

>  Hello GATE users,
>
> I am simulating now a 20-cm cylindrical phantom (length: 17.8 cm ) filled
> with 18-F with an activity of 444 MBq. I installed GATE v6.1 on the cluster
> and all my simulations are running on 70 computing nodes with 8 CPUs. The
> output files of the simulation are root files with single, coincidence and
> finalCoincidence trees. My jobs on the cluster cause a very high load on
> the fileserver during GATE simulation. I attached a PNG-Image of the
> cluster's In/Output  evaluation of some of my jobs. Did anyone of GATE
> users or developer face such problem before or this issue at least is
> familiar by someone.  I would be thankful if someone can share with me his
> experience in order to solve this issue
>
> --
> Bassim Aklan, MSc.
> Institute of Medical Physics - Section for MR Imaging
> University of Erlangen-Nuremberg
> Henkestr. 91
> 91052 Erlangen, Germany
> phone: +49-(0)9131/85-25545 bassim.aklan at imp.uni-erlangen.de
>
>
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