Tahereh Niknejad | 24 Jun 20:40 2014
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Merged root file size

Dear Gate users,
 
I used file splitter and merger. The final merged file should have been of the size equal to about 25 GB. But, instead of having one output of this size, the file merger gave me two outputs, one 16 Gb and one 9 GB. Is there any limitation on the root file size?
 
Cheers,
Tahereh

--
Tahereh Niknejad

PhD Candidate
LIP - Laboratory of Instrumentation and Experimental Particle Physics
<div><div dir="ltr">
<div>Dear Gate users,</div>
<div>&nbsp;</div>
<div>I used file&nbsp;splitter and merger. The final merged file should have been of the size equal to about 25 GB. But, instead of having one output of this size, the file merger gave me two outputs, one 16 Gb and one 9 GB. Is there any limitation&nbsp;on the root file size?</div>

<div>&nbsp;</div>
<div>Cheers,</div>
<div>Tahereh</div>
<div>
<br>-- <br>
</div>
<div dir="ltr">Tahereh Niknejad<br><br>PhD Candidate<br>LIP - Laboratory of Instrumentation and Experimental Particle Physics<br>
</div>
</div></div>
Amy Meldrum | 24 Jun 15:30 2014

Optical photons now absorbed, not transported

Hello GATE users,

I have been running simple scintillation simulations with a scintillator sheet and a PMT. My simulations work just fine on the VGate computers I have. Recently I have tried loading Gate onto my university's cluster, and transferred the surfaces and materials files from my VGate computer to my space on the cluster. However, now when I run my simulations, all of my optical photons end up as "OpticalAbsorption," when running the same simulation on my VGate computer gives the normal output with plenty of photons being marked as "Transportation."

What could cause this difference? I am having difficulties troubleshooting this problem. Any advice is appreciated.


-Amy
<div><div dir="ltr">Hello GATE users,<div><br></div>
<div>I have been running simple scintillation simulations with a scintillator sheet and a PMT. My simulations work just fine on the VGate computers I have. Recently I have tried loading Gate onto my university's cluster, and transferred the surfaces and materials files from my VGate computer to my space on the cluster. However, now when I run my simulations, all of my optical photons end up as "OpticalAbsorption," when running the same simulation on my VGate computer gives the normal output with plenty of photons being marked as "Transportation."</div>
<div><br></div>
<div>What could cause this difference? I am having difficulties troubleshooting this problem. Any advice is appreciated.</div>
<div><br></div>
<div><br></div>
<div>-Amy</div>
</div></div>
Qide Xiao | 24 Jun 04:44 2014
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create a phase space using a GPU architecture

the phase space used in the simulation for radiotherapy ,Is it able to
speed up the process using the GPU ?
Dong Joo Rhee | 24 Jun 01:48 2014
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Job submission in cluster

Dear all

We have 3 computers with 24 cores each and try to use them as a cluster for Gate running. I have tried the jobsplitter + openPBS for submitting the jobs and it only submits the job to the one computer (24 cores). This seems to make sense since I didn't install Gate to the other computers but the host computer.

I'd like to know if there is a way to submit the job to the computer where Gate is not installed.

Thanks in advance 

Dong Joo

-- 

Dong Joo RHEE
Researcher
Medical Radiation Physics Laboratory,
Research center, Dongnam Institute of Radiological & Medical Sciences
40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 619-953, KOREA
Tel. 82-51-720-5852, Fax. 82-51-720-5826
<div><div dir="ltr">Dear all<div><br></div>
<div>We have 3 computers with 24 cores each and try to use them as a cluster for Gate running. I have tried the jobsplitter + openPBS for submitting the jobs and it only submits the job to the one computer (24 cores). This seems to make sense since I didn't install Gate to the other computers but the host computer.</div>

<div><br></div>
<div>I'd like to know if there is a way to submit the job to the computer where Gate is not installed.</div>
<div><br></div>
<div>Thanks in advance&nbsp;</div>
<div><br></div>
<div>Dong Joo</div>
<div>
<br>--&nbsp;<div dir="ltr">

<div>
<br><span>Dong Joo RHEE</span><br><span>Researcher</span><br><span>Medical Radiation Physics Laboratory,</span><br><span>Research center, Dongnam Institute of Radiological &amp; Medical Sciences</span><br><span>40 Jwadong-gil, Jangan-eup, Gijang-gun, Busan, 619-953, KOREA</span><br><span>Tel. 82-51-720-5852, Fax. 82-51-720-5826</span><br>
</div>
</div>
</div>
</div></div>
Debendranath Sahoo | 22 Jun 12:33 2014
Picon

optical-photon-simulation-result-interpretation

June 22

Dear Gate-users,

I am simulating optical photons in a 5cmX5cm LaBr(Ce) crystal in GATE 7.0. I have chosen a Beam type gps source of gamma ray (140 keV) 1 Bq for 1 sec which means only one incident gamma photon on the crystal. The 64X64 anodes on the PSPMT detect the scintillation photons generated. However, I also get a lot of trajectories passing through the system. What do these trajectories correspond to? Are these gamma rays from Compton events? But I started with just one gamma photon incident on the crystal! What does one make out of this? I am enclosing the macro files along with a jpg file showing the view I get in display. My main file to run is named "newcam.mac".

Any interpretation will be appreciated.

deba999  

--
Dr Debendranath Sahoo
Honorary Professor
Physics Department
Sri Sathya Sai Institute of Higher Learning
Prashanthi Nilayam
Puttaparthy
A.P. 515 134
e-mail: deba999-Re5JQEeQqe8AvxtiuMwx3w@public.gmane.org
Mobile: 094945-43026

Attachment (smallCam.tar.gz): application/x-gzip, 1008 KiB
<div><div dir="ltr">
<div>
<div>
<div>
<div>June 22<br><br>
</div>Dear Gate-users,<br><br>
</div>I am simulating optical photons in a 5cmX5cm LaBr(Ce) crystal in GATE 7.0. I have chosen a Beam type gps source of gamma ray (140 keV) 1 Bq for 1 sec which means only one incident gamma photon on the crystal. The 64X64 anodes on the PSPMT detect the scintillation photons generated. However, I also get a lot of trajectories passing through the system. What do these trajectories correspond to? Are these gamma rays from Compton events? But I started with just one gamma photon incident on the crystal! What does one make out of this? I am enclosing the macro files along with a jpg file showing the view I get in display. My main file to run is named "newcam.mac".<br><br>
</div>Any interpretation will be appreciated.<br><br>
</div>deba999 &nbsp; <br clear="all"><div><div><div><div><div>
<br>-- <br>Dr Debendranath Sahoo<br>Honorary Professor<br>Physics Department<br>Sri Sathya Sai Institute of Higher Learning<br>

Prashanthi Nilayam<br>Puttaparthy<br>A.P. 515 134<br>e-mail: <a href="mailto:deba999@..." target="_blank">deba999@...</a><br>Mobile: 094945-43026<br><br>
</div></div></div></div></div>
</div></div>
Picon

GPU

Hi:

Has anyone successfully run simulations on the GPU that is available with GATE v7.0 ?

Thanks,

-Shanta
Hyeok-jun Choe | 20 Jun 11:09 2014
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Noise module problem on GATE Cluster

Dear Gate users,
 
(1) Noise module problem on GATE Cluster
 
I am using a Gate_v7.0 Cluster (HTCondor). The cluster consisted of 24 nodes (i7-4770k (8 nodes) × 3).
 
I noticed that a node in a CPU (8 nodes) was consuming most CPU resource when noise module was described in mac file.
 
If the noise module is removed, all nodes are executing all splitted jobs, simultaneously.
 
Does any one know why it happens and solution?

 
(2) (Again) The root output size of benchPET on Gate_v7.0 and Gate_v6.2
 
I noticed that the root output size of benchPET simulated by Gate_v7.0 was different that of Gate_v6.2.
 
It was about ~500 MB on Gate_v7.0  and ~75 MB on Gate_v6.2. 
 
I'm wondering whether it is just OK or not.
 
 
Thanks in advance !!
 
 
Hyeok-jun Choe, Ph.D student
MiRe (Molecular Imaging Research & Education) Lab. 
Department of Electronic Engineering,
Sogang University
1, Shinsu-Dong, Mapo-Gu, Seoul, South Korea 121-742 
Tel : +82-2-713-2652
Mobile : +82-10-2794-0520
<div><div dir="ltr">
<div>Dear Gate users,</div>
<div>&nbsp;</div>
<div>(1) Noise module problem on GATE Cluster</div>
<div>&nbsp;</div>
<div>I am using a Gate_v7.0 Cluster (HTCondor). The cluster&nbsp;consisted of&nbsp;24 nodes (i7-4770k (8 nodes)&nbsp;&times; 3). </div>
<div>&nbsp;</div>
<div>I&nbsp;noticed that&nbsp;a node in&nbsp;a CPU (8 nodes)&nbsp;was&nbsp;consuming&nbsp;most CPU resource when noise module was described in mac file. </div>
<div>&nbsp;</div>
<div>If the noise module&nbsp;is removed, all nodes are executing all splitted jobs, simultaneously.</div>
<div>&nbsp;</div>
<div>Does any one know why it happens and solution?</div>
<div>
<br clear="all">&nbsp;</div>
<div>(2) (Again) The root output size of benchPET on Gate_v7.0 and Gate_v6.2</div>
<div>&nbsp;</div>
<div>
<div>I noticed that the root output&nbsp;size&nbsp;of benchPET&nbsp;simulated by&nbsp;Gate_v7.0 was different that of Gate_v6.2. </div>
<div>&nbsp;</div>
<div>It was about ~500 MB on Gate_v7.0&nbsp; and ~75 MB on Gate_v6.2.&nbsp;</div>
<div>&nbsp;</div>
<div>I'm wondering whether it is just OK or not.</div>
<div>&nbsp;</div>
<div>&nbsp;</div>
<div>Thanks in advance !!</div>
<div>&nbsp;</div>&nbsp;</div>
<div><div dir="ltr">
<div>
<span>Hyeok-jun Choe, Ph.D student</span><br>
</div>
<div><div><div>
<div>MiRe (Molecular Imaging Research &amp; Education)&nbsp;Lab.&nbsp;</div>
<div>Department of&nbsp;Electronic Engineering,<br><div>Sogang University<br>1, Shinsu-Dong, Mapo-Gu, Seoul, South Korea 121-742&nbsp;<br>Tel : +82-2-713-2652<br>Mobile : +82-10-2794-0520</div>
<div>e-mail : <a href="mailto:issue87@..." target="_blank">issue87@...</a><br>
</div>
</div>
</div></div></div>
</div></div>
</div></div>
Miran Park | 20 Jun 08:21 2014
Picon

X-ray simulation in GATE

Dear gaters,


I am trying to simulate a x-ray tube using GATE to get x-ray energy spectrum. For the tube design, there is a hole from which photons come out.


I'm wondering there is a priority of objects in GATE, so that put a object with hole prior to the cylinder chamber to make a hole.


Or is there any other way to make a large hole on the cylinder surface? 


Sincerely,

Miran Park.


--

Miran Park, Doctoral Candidate

Dept. Nucl. & Quant. Engr.

, KAIST

Office: +82-42-350-5868

Cell: +82-10-9437-4037

 

<div>
<div>
<p><span>Dear gaters,</span></p>
<p><span><br></span></p>
<p><span>I am trying to simulate a x-ray tube using GATE to get&nbsp;x-ray energy spectrum. For the tube design, there is a hole from which photons come out.</span></p>
<p><span><br></span></p>
<p><span>I'm wondering there is a priority of&nbsp;objects in GATE, so that put a object with hole prior to the cylinder chamber to make a hole.</span></p>
<p><span><br></span></p>
<p><span>Or is there any other way to make&nbsp;a large hole on the cylinder surface?&nbsp;</span></p>
<p><span><br></span></p>
<p><span>Sincerely,</span></p>
<p><span>Miran Park.</span></p>
<br><table width="99%" align="center"><tr valign="top"><td>
<p class="MsoNormal"><span lang="EN-US"><span>--</span></span></p>
<p class="MsoNormal"><span lang="EN-US"><span>Miran P</span><span>ark, </span></span><span lang="EN-US"><span>Doctoral&nbsp;Candidate</span></span></p>
<p class="MsoNormal"><span lang="EN-US"><span>Dept. Nucl. &amp; Quant. Engr.</span><p></p></span><span>, </span><span lang="EN-US"><span><span>KAI</span><span>S</span><span>T</span></span><p></p></span><span lang="EN-US"><p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">Office: +82-42-350-5868</span></p>
<p class="MsoNormal"><span lang="EN-US">Cell: +82-10-9437-4037</span></p>
<p class="MsoNormal">&nbsp;</p>
</td></tr></table>
</div>
</div>
LARS.EWELL | 19 Jun 14:24 2014

Bremsstrahlung Data File

To Whom it May Concern,

 

  We are using Gate 6.2 on our linux cluster running Scientific Linux release 6.5 (Carbon). 

 

  We have been attempting to run the ‘main’ macro under the examples/example_Radiotherapy/example6.

 

  It starts out OK, but then the program crashes with the error

 

Bremsstrahlung data file <:/extra/apps/GEANT4/data/data_4.9.5.p01/G4EMLOW6.23/brem_SB/br7> is not opened!

G4LEDATA version should be G4EMLOW6.23 or later.

 

  However, as you can see from the path, we are, as far as I can tell, using G4LEDATA version G4EMLOW6.23 or later.

 

  Any ideas?

 

  Thanks in advance.

 

  Regards,

 

  Lars Ewell

 

The information contained in this message is intended only for the recipient, and may otherwise be privileged and confidential. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, please be aware that any dissemination or copying of this communication is strictly prohibited. If you have received this communication in error, please immediately notify us by replying to the message and deleting it from your computer. This footnote also confirms that this email has been scanned for all viruses by the Hampton University Center for Information Technology Enterprise Systems service.
<div>
<div class="WordSection1">
<p class="MsoNormal">To Whom it May Concern,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; We are using Gate 6.2 on our linux cluster running Scientific Linux release 6.5 (Carbon).&nbsp;
<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; We have been attempting to run the &lsquo;main&rsquo; macro under the examples/example_Radiotherapy/example6.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; It starts out OK, but then the program crashes with the error
<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">Bremsstrahlung data file &lt;:/extra/apps/GEANT4/data/data_4.9.5.p01/G4EMLOW6.23/brem_SB/br7&gt; is not opened!<p></p></p>
<p class="MsoNormal">G4LEDATA version should be G4EMLOW6.23 or later.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; However, as you can see from the path, we are, as far as I can tell, using G4LEDATA version G4EMLOW6.23 or later.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; Any ideas?<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; Thanks in advance.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; Regards,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">&nbsp; Lars Ewell<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div>

<div>
The information contained in this message is intended only for the recipient, and may otherwise be privileged and confidential. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, please be aware that any dissemination or copying of this communication is strictly prohibited. If you have received this communication in error, please immediately notify us by replying to the message and deleting it from your computer. This footnote also confirms that this email has been scanned for all viruses by the Hampton University Center for Information Technology Enterprise Systems service.<br>
</div>
</div>
Patay Gergely | 18 Jun 10:54 2014
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geant4 solids, interfile reader

Dear Gaters,

here are a few patches against the upstream (ie. master branch) Gate source 
code. Since I am not a member of the collaboration, I cannot directly commit 
them into the git repository.

The first patch was written by Dávid Völgyes (formerly at Mediso and at COMPET). 
These are C++ bugfixes (unchecked ranges, memory corruptions).
[1] https://dl.dropboxusercontent.com/u/43097994/gate7/cppfix_dvolgyes.patch.gz

The second patch contains Gate wrappers to all the missing Geant4 solid objects 
from

http://geant4.web.cern.ch/geant4/UserDocumentation/UsersGuides/ForApplicationDeveloper/html/ch04.html 
.
With this patch the following extra shapes will be available: cut tube, 
elliptical cone, generic trapezoid, hyperbolic tube, parallelepiped, paraboloid 
tube, tetrahedron, torus, twisted box, twisted trapezoid, generic twisted 
trapezoid and twisted tube segment.
[2] https://dl.dropboxusercontent.com/u/43097994/gate7/geant4-geometry.patch.gz

The third patch is a heavy modification of the Interfile reader. Besides some 
code cleaning and refactoring, it solves the following issues:
- if the key 'name of data file' is present in the header file then it won't 
guess the name
- the 'number of bytes per pixel' key (1,2,4,8...) is implemented
- the 'data offset in bytes' key is implemented
- the 'number format' key now accepts 'signed integer', 'unsigned integer', 
'short float', 'long float' and (for convenience) 'float', as seen in the 
Interfile 3.3 standard.
The interfile reader thus accepts signed or unsigned 8, 16, 32 or 64 bit integer 
as well as 32 (float) or 64 bit (double) floating point data from little or big 
endian binary file.
[3] https://dl.dropboxusercontent.com/u/43097994/gate7/interfile.patch.gz

cheers,
  Gergely

---
Gergely Patay
physicist
Mediso Medical Imaging Systems Ltd.
Hungary
_______________________________________________
Gate-users mailing list
Gate-users <at> lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
Hojjat Mahani | 17 Jun 23:12 2014
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Neutron Tomography using GATE

Dear Gate users,

I was wondering if one can model a 'neutron' tomographic system in Gate using the predefined, generalized 'Scanner' system? 
I would be extremely grateful if you kindly share your experiences with me.

Thank you in advance,
 
Hojjat 

<div><div>
<div>Dear <span>Gate users</span>,</div>
<div><br></div>
<div>I was wondering if one can model a 'neutron' tomographic system in Gate using the predefined, generalized 'Scanner' system?&nbsp;</div>
<div>I would be extremely grateful if you kindly share your experiences with me.</div>
<div><br></div>
<div>Thank you in advance,</div>
<div></div>
<div>&nbsp;</div>
<div><span>Hojjat&nbsp;</span></div>
<div><br></div>
</div></div>

Gmane