[Gate-users] Gate-users Digest, Vol 68, Issue 11

Tue Jan 17 13:03:02 CET 2012

Dear Saeed,

Thank you for your response.  I am splitting my simulation by time slices;

/gate/application/setTimeSlice      0.004  s
/gate/application/setTimeStart      0.    s
/gate/application/setTimeStop       0.500  s

becomes 125 instances of the model in gjs 
(first being 0->0.004s, the second 0.004->0.008s and so on up to half a second)
which are queued and managed by a small PBS server.

within each set of time slices returned there are a number (usually about half a douzen) which contain only about half as many detected events as the other files.  The simulated time slices with reduced statistics appear to be complete, have taken the same number of CPU hours to run as the other time slices, and events are detected evenly across the whole 4ms time window.  The amount of fluorescence in eDep seems to be much greater in the reduced "detected events" runs.

Kind Regards,

Nick

-----Original Message-----
From: gate-users-bounces at lists.opengatecollaboration.org [mailto:gate-users-bounces at lists.opengatecollaboration.org] On Behalf Of Saeed Heidary
Sent: 17 January 2012 10:57
To: gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] Gate-users Digest, Vol 68, Issue 11

Dear Nick
I did not understand ur problem exactly.
Just I have an experience in gjs time slicing as follow;

when there is some kind of rotation during simulation, for example
16 run 37.5 sec in benchSPECT, your time slicing must be a coefficient
of each run time
I mean some things like 8 runs in 75 sec. and I encountered errors if
did anythings else!

On 1/17/12, gate-users-request at lists.opengatecollaboration.org
<gate-users-request at lists.opengatecollaboration.org> wrote:
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> Today's Topics:
>
>    1. about VGATE (?mit Kara)
>    2. loss of intensity at irregular time intervals gjs (Nick Laver)
>    3. Geant4 versions to be avoided when working with	Optical
>       Photons (Vesna Cuplov)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 16 Jan 2012 15:57:48 +0200
> From: ?mit Kara <umitkara1983 at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] about VGATE
> Message-ID:
> 	<CAO7_u7O+k3fj1XvgnHX34EKXrqR8BaiipONYp6QeXCB0WA6QXQ at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Hi
> Recently we  installed vGATE on visual machine, right now we have on
> desktop Imagej terminal so.on.. but 1 problem is i don't know that "how o
> run a simple example" how to get results and anaylize ... when we open a
> new terminal we wrote "Gate" and then we don't know what to do next..  can
> you inform me about to details of steps on using vGATE... we urgently need
> help on using vGATE.. would you mind, can you inform me about this topic..
>
> Best Regards
>
> Umit KARA
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 16 Jan 2012 17:23:10 +0000
> From: Nick Laver <Nick.Laver at kromek.com>
> To: "gate-users at lists.opengatecollaboration.org"
> 	<gate-users at lists.opengatecollaboration.org>
> Subject: [Gate-users] loss of intensity at irregular time intervals
> 	gjs
> Message-ID:
> 	<F8CD54188923C649BF1327859AF2BA9E5173A132 at K-MAIL1-V.kromek.local>
> Content-Type: text/plain; charset="us-ascii"
>
> Good evening Gaters,
>
> I am seeing a loss of intensity in a number of "time slices" when running my
> model using the gjs (gate job splitter), I was wondering if anybody had
> experienced anything similar?
> I am unable to run my model without the gjs to compare as 500+ CPU hours are
> required in each run to achieve a significant number of detected counts.
>
> I am splitting my simulation into 125 4ms slices (0.5 seconds in total)
> across as 9 node simulation farm (on which 67 "cores" are avaliable with 5
> remaining spare to allow access via a single node for code development and
> adding more runs to the pbs queue whilst simulations are running).
>
> My data output is into a ROOT format only and I have run my model with both
> moving and stationary samples and for an open beam measurement, and repeated
> identical runs with a different seed (autoseed is always used)
>
> My model is a (slightly modified in source code to allow > 3 clusters)
> version of the CTScanner scanner with 9 clusters and pixellated detectors.
>
> The loss of intensity does not seem to occur in regular time slices in each
> run nor are they a result of incomplete runs or my code crashing (verified
> from the log and err files produced at the end of each run and the
> completeness of the output root files)
>
> In the root files of reduced detected intensity, there are approximately
> half the expected counts (compared to the 4ms before and 4ms after for an
> open beam run) detected and an unusual amount of fluorescence in the output
> spectum.  The distribution of x-rays (singles) interacting with the crystal
> is also unusual in distribution between the front and back rows of pixels.
>
> Apologies for the poor description of my problem.
>
> Any advice/ideas are much appreciated.
>
> Kind regards,
>
> Nick
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 17 Jan 2012 11:17:24 +0100
> From: Vesna Cuplov <vesna.cuplov at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Geant4 versions to be avoided when working with
> 	Optical Photons
> Message-ID:
> 	<CAOibXMGB9zgGK44SVRS2OLDkhyP+HmJ1xGvEKLywJnHSSM1J8g at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Dear Gate users,
>
> For those of you using the Optical Photons with Gate, I would like to warn
> you about Geant4 versions to be avoided
> when working with optical photons.
>
> see:
> http://hypernews.slac.stanford.edu/HyperNews/geant4/get/opticalphotons/420/1.html
>
> Two recent versions of Geant4 simulate the timing of optical photons
> incorrectly: G4.9.4p02 and G4.9.5.
>
> It was suggested to use G4.9.4p03 for the simple reason that p03 collects
> all real bug-fixes to the original version 9.4
> in all domains of the Geant4 software.
>
> You can check the release information for each of the patches to learn what
> has been fixed.
>
> http://geant4.cern.ch/support/Patch4.9.4-1.txt
> http://geant4.cern.ch/support/Patch4.9.4-2.txt
> http://geant4.cern.ch/support/Patch4.9.4-3.txt
>
> vesna
>
>
> ------------------------------
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