[Gate-users] Installing gjs
Bryan McIntosh
mcintoshster at gmail.com
Fri Oct 16 15:23:19 CEST 2015
Hi Roque,
I have not worked with gjs before, but I do know that for simulations that
don't involve optical photons GATE doesn't use a whole lot of memory. This
is perfectly normal, and you can get faster execution times if you
multi-thread your simulations.
It looks like the instructions for installing gjs haven't been updated in
several years, since they still refer to GATE 6.1. I am pretty sure that
you can still use the instructions available at
http://wiki.opengatecollaboration.org/index.php/New_Compilation_ProcedureV7.1#Installation_of_cluster_tools
and replace /opt/simulation/gate6_1 with the appropriate path for your GATE
7.1 installation.
Hope this helps!
-Bryan
On Fri, Oct 16, 2015 at 5:00 AM, <
gate-users-request at lists.opengatecollaboration.org> wrote:
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> Today's Topics:
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> 1. Re: Gate sometimes waits for nothing, why? (Simon Stute)
> 2. Re: Pixelated SPECT problem (Simon Stute)
> 3. Installing gjs (Santos, Roque)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 15 Oct 2015 16:02:21 +0200
> From: Simon Stute <gate.stute at gmail.com>
> To: Anders Garpebring <anders.garpebring at umu.se>
> Cc: "gate-users at lists.opengatecollaboration.org"
> <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] Gate sometimes waits for nothing, why?
> Message-ID:
> <CADGvxeNCEK-WTp6qVKXxk7GEvqYvAQjJNHes6-j6Emt41o=
> jxg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> Just add the command /vis/disable at the beginning to fully disable the
> visualization stuff.
>
> Cheers,
> Simon
>
> On Fri, Oct 9, 2015 at 5:22 PM, Anders Garpebring <
> anders.garpebring at umu.se>
> wrote:
>
> > Dear gate users,
> >
> >
> >
> > Im working on running a batch of Gate simulations. To test my macro I
> want
> > to run through all 28 simulation with just a single event for each
> > simulation. However, the simulation often get stuck seemingly doing
> nothing
> > for maybe 30 s. Why is this? Typically when I run just a single execution
> > of my script it just takes a second or two. If I run it again immediately
> > after it can take 30 seconds to finish.
> >
> >
> >
> > I get no errors but some warnings about the viewer (which I try to switch
> > off).
> >
> >
> >
> > WARNING: Scene "none" not found.
> >
> > /vis/scene/list to see scenes.
> >
> >
> >
> > WARNING: command "/vis/viewer/update" could not be applied: no current
> > viewer
> >
> >
> >
> > In my code there are no references to the visualization.
> >
> >
> >
> > Best,
> >
> > Anders
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
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> ------------------------------
>
> Message: 2
> Date: Thu, 15 Oct 2015 16:06:34 +0200
> From: Simon Stute <gate.stute at gmail.com>
> To: Chao Guo <chaoguomedicalphysics at gmail.com>
> Cc: "gate-users at lists.opengatecollaboration.org"
> <Gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] Pixelated SPECT problem
> Message-ID:
> <CADGvxeOp=
> eZTDVfBC_HCKU8ejQN8pySyOc57zcDsx0SscpiBaA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> The projection output is mainly designed to work on a monolithic crystal
> (without a concrete definition of geometric pixels) as you can define the
> number of pixels inside the projection output.
> The behaviour of the projection output when you are actually using pixels
> defined in the system is quite unknown to my knowledge.
> Maybe an expert in SPECT simulations could give you a more complete answer.
>
> Cheers,
> Simon
>
>
>
> On Wed, Oct 14, 2015 at 4:43 AM, Chao Guo <chaoguomedicalphysics at gmail.com
> >
> wrote:
>
> > Dear all,
> >
> >
> >
> > I?m trying to use the Pixel level under SPECT to do the pixelated crystal
> > and I met some problems. I use the crystal level and it work perfect and
> > then I add the pixel level, the projection image shows me something at
> the
> > center of the image but the actual setup is not at center. Does anyone
> have
> > any idea about this?
> >
> >
> >
> > I use the example code from the optical imaging benchmark macro:
> >
> >
> >
> > /gate/pixel/geometry/setXLength 2.0 cm
> >
> > /gate/pixel/geometry/setYLength 2.0 cm
> >
> > /gate/pixel/geometry/setZLength 1.0 cm
> >
> > /gate/pixel/setMaterial Air
> >
> > /gate/pixel/placement/setTranslation 0 0 0 cm
> >
> > /gate/pixel/vis/setColor red
> >
> > /gate/pixel/repeaters/insert cubicArray
> >
> > /gate/pixel/cubicArray/setRepeatNumberX 5
> >
> > /gate/pixel/cubicArray/setRepeatNumberY 5
> >
> > /gate/pixel/cubicArray/setRepeatNumberZ 1
> >
> > /gate/pixel/cubicArray/setRepeatVector 2.1 2.1 0 cm
> >
> > /gate/pixel/vis/forceSolid
> >
> > /gate/pixel/attachCrystalSD
> >
> > /gate/systems/OpticalSystem/pixel/attach pixel
> >
> >
> >
> > Please let me know if you guys have any suggestions, thank you
> >
> >
> >
> > Chao
> >
> >
> >
> >
> > ------------------------------
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> Message: 3
> Date: Fri, 16 Oct 2015 04:33:59 +0000
> From: "Santos, Roque" <rsantost at vols.utk.edu>
> To: "gate-users at lists.opengatecollaboration.org"
> <gate-users at lists.opengatecollaboration.org>
> Subject: [Gate-users] Installing gjs
> Message-ID: <4FDB5087-C879-47ED-B27F-5BADF04A0B14 at vols.utk.edu>
> Content-Type: text/plain; charset="us-ascii"
>
>
> Hello all,
>
> I'm trying to run gate V7.1 in Ubuntu, I've installed properly, but Gate
> is jus using 5%of the whole memory. I thought it can be solved by splitting
> the files among the cores of my computer, so I tried to install gjs. So far
> I wasn't able to install it. I think is because I cannot find the file
> env_gate.sh, so whe I try to make gjs it gives me an error.
>
> Can somebody help me. What is the procedure to install gjs.
>
> Thank you
>
>
> Sent from my iPad
>
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> End of Gate-users Digest, Vol 113, Issue 13
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