M Martin | 7 Jul 09:37 2015
Picon

About Gate_v7.1 warning and output comparing the version Gate_v6.1

Thanks Uwe and David for your kind help in my previous question.

Hi All,

I have few queries regarding the .sin files. 
Recently i have changed my machine and also the gate version. Now i am facing the difficulties as mentioned below.

I have executed benchSPECT.mac code in two different machines and in two different versions of GATE, one machine has 4GB RAM along with gate_v6.1, while the other one has 64GB RAM along with gate_v7.1.
Now I am getting two different projection output gate614.sin and gate7164.sin respectively for the 64 frames for the same benchSPECT.mac code. gate7164.sin file shows the projection in all the 64 frames. But gate614.sin file shows the projection in only few frames out of 64 frames. 
Now my question is in gate7164.sin file i am getting all the 64 projections in all the 64 frames because of better 64GB RAM machine comparing to 4GBRAM PC? or is it happening because of the versions? 
Am i supposed to get different projection results for the different gate versions? or
Am i supposed to get different projection results for different configuration machine?

Also, i am getting an warning after initialization in gate_v7.1. The warning is as follows:

[Physic - 0] WARNING: manual physic lists are being deprecated.
Please, use physic list builder mechanism instead. Related documentation can be found at:
http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics

Is this warning hampering my above mentioned execution? or is this warning ignorable?

Please let me know your kind suggestions.


Cheers,
Martin
<div><div dir="ltr">
<span>Thanks Uwe and David for your kind help in my previous question.</span><br><br><span>Hi All,</span><div><br></div>
<div>I have few queries regarding the .sin files.&nbsp;<br>Recently i have changed my machine and also the gate version. Now i am facing the difficulties as mentioned below.<br><br>I have executed benchSPECT.mac code in two different machines and in two different versions of GATE, one machine has 4GB RAM along with gate_v6.1, while the other one has 64GB RAM along with gate_v7.1.<br>Now I am getting two different projection output gate614.sin and gate7164.sin respectively for the 64 frames for the same benchSPECT.mac code. gate7164.sin file shows the projection in all the 64 frames. But gate614.sin file shows the projection in only few frames out of 64 frames.&nbsp;<br>Now my question is in gate7164.sin file i am getting all the 64 projections in all the 64 frames because of better 64GB RAM machine comparing to 4GBRAM PC? or is it happening because of the versions?&nbsp;<br>Am i supposed to get different projection results for the different gate versions? or<br>Am i supposed to get different projection results for different configuration machine?<br><br>
</div>
<div>Also, i am getting an warning after initialization in gate_v7.1. The warning is as follows:<br><br>[Physic - 0] WARNING: manual physic lists are being deprecated.<br>Please, use physic list builder mechanism instead. Related documentation can be found at:<br><a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics" target="_blank">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics</a><br><br>Is this warning hampering my above mentioned execution? or is this warning ignorable?<br><br>Please let me know your kind suggestions.<br><br><br>Cheers,<br>Martin</div>
</div></div>
Steven Michiels | 2 Jul 16:18 2015
Picon

Advice needed using vGate examples - unsupported particle

Hello,

 

After using Gate in the past I started using vGate just now.

 

I installed the virtual machine and wanted to start with the preinstalled radiotherapy examples, but unfortunately none of them works as is. I consistently get the error 'G4HadronCrossSections::GetParticleCode:unsupported particle (see attachment).

 

Could anyone advise ? I don't quite understand why none of the pre-installed examples works on a pre-installed virtual machine.

 

Thanks a lot for any help.

 

Steven

 

 

<div>
<div>
<p>Hello,</p>
<p>&nbsp;</p>
<p>After using Gate in the past I started using vGate just now. </p>
<p>&nbsp;</p>
<p>I installed the virtual machine and wanted to start with the preinstalled radiotherapy examples, but unfortunately none of them works as is. I consistently get the error 'G4HadronCrossSections::GetParticleCode:unsupported particle (see attachment).</p>
<p>&nbsp;</p>
<p>Could anyone advise ? I don't quite understand why none of the pre-installed examples works on a pre-installed virtual machine.</p>
<p>&nbsp;</p>
<p>Thanks a lot for any help.</p>
<p>&nbsp;</p>
<p>Steven</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
</div>
</div>
LORENA VÁZQUEZ CANELAS | 2 Jul 13:39 2015
Picon

MEANING-COLORS-IMAGE

Hi Gaters,

On the picture I send you, I want to know the meaning represented by each color.
The green I think represents the annihilation of the two gammas.
The red, positron range.
BUT, and blue???
Does anyone know?

Thank you

--
LORENA VÁZQUEZ CANELAS
PhD student, Research staff
LRI - Datación (Despacho Técnicos)
Calle Espejo, s/n, 37008 - Salamanca (Spain)
TEL: +34 923 294930 ext:4932 email: lorena.vazquez-M84Vyeb6RnU@public.gmane.org
web: http://campus.usal.es/~lri/
<div><div dir="ltr">
<div class="gmail_default">Hi Gaters,<br><br>On the picture I send you, I want to know the meaning represented by each color.<br>The green I think represents the annihilation of the two gammas.<br>The red, positron range.<br>BUT, and blue???<br>Does anyone know?<br><br>Thank you<br clear="all">
</div>
<br>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">LORENA V&Aacute;ZQUEZ CANELAS<br><span>PhD student, </span><span lang="en">Research staff</span><br>LRI - Dataci&oacute;n (Despacho T&eacute;cnicos)<br>Calle Espejo, s/n, 37008 - Salamanca (Spain)<br>TEL: +34 923 294930 ext:4932 email: <a href="mailto:lorena.vazquez@..." target="_blank">lorena.vazquez@...</a><br>web: <a href="http://campus.usal.es/%7Elri/" target="_blank">http://campus.usal.es/~lri/</a>
</div></div></div></div></div></div></div></div></div></div></div></div></div></div>
</div></div>
M Martin | 1 Jul 12:44 2015
Picon

Examples of the newer versions of GATE

Hi All,

Could someone please share me benchSPECT.mac and benchPET.mac examples for GATE_v7.0 and GATE_v7.1? I got few examples and bechmarks when i installed gate_v6.1 last time. But i didn't get any for the new versions. Also i can see many changes in the physics in the newer version.
it would be great if someone can share me the examples of the new GATE_v7.0 and GATE_v7.1 versions.

Cheers
Martin
<div><div dir="ltr">Hi All,<div><br></div>
<div>Could someone please share me benchSPECT.mac and benchPET.mac examples for GATE_v7.0 and GATE_v7.1? I got few examples and bechmarks when i installed gate_v6.1 last time. But i didn't get any for the new versions. Also i can see many changes in the physics in the newer version.<br>it would be great if someone can share me the examples of the new GATE_v7.0 and GATE_v7.1 versions.</div>
<div><br></div>
<div>Cheers</div>
<div>Martin</div>
</div></div>
Alex Vergara Gil | 26 Jun 17:58 2015
Picon

geant4 10.1 patch 02

Dear All

For those interested I have successfully tested Gate develop branch
against geant4 10.1 with patch 2 without further changes.

Regards
Alex Vergara
tstoole | 26 Jun 17:51 2015

how to define blocks with different numbers of crystals in different layers

Hi, 
I am trying to set up a cylindrical pet system with blocks that 
have two layers of crystals. I am relatively new to gate. I have a simulation working when 
the number of crystals in the inner layer and outer layer are the same, 
say both have 10x10 . Now I am trying to modify the system so that the inner 
layer has a 9x9 array of crystals and the outer layer has an array 
of 10x10 crystals. I attempted to do this with a cubicArray but failed. 
Do I need to use genericRepeater? 

Does anyone have any hints or suggestions on how to accomplish this? 
Or better yet, is there an example around that does something similar? 
I have been looking through the email archive and online documentation 
and have not found the info yet. 

Thanks for any hints or suggestions, 

Terry

P. T. | 24 Jun 00:37 2015
Picon

spatial resolution

Dear gater,

I use GATE 6.1.
When I change spatial resolution of singles by digitizer, I get the
same result !
In the other word, if I use different values for the spatial
resolution, I get the same result. My questions is: can I change the
intrinsic spatial resolution of my detector? If possible, how can I do
it?

In advance, thank you very much.
Pat
Ida Häggström | 22 Jun 14:55 2015
Picon
Picon

Re: gate crash during Materials.xml loading

Hi Pedro!

I know that some people (including myself) have had some problems with patch 01 of geant4.10.01 and gate 7.1, at least when compiling. Dunno if the problem can be related to the patch or not, but you can try the version without the patch: http://geant4.cern.ch/support/source/geant4.10.01.tar.gz

Good luck!
Ida

On Thu, Jun 18, 2015 at 11:19 AM, Pedro Correia <pmcorreia-7Y4ok6tQxkA@public.gmane.org> wrote:
Dear Gaters

Since I was not the only one having this problem (the user Gwennaëlle MARIN had the same experience few weeks ago).
We both used Scientific Linux 6, gate v7.1 and geant4.10.01 (no patch-01).

I’m assuming that is not an issue with Geant4, because I found nothing related with this in the Geant4 forum.
Is it possible that the Gate developers take a look to this?

Cheers, Pedro




No dia 16/06/2015, às 18:50, pedro correia <pmcorreia-7Y4ok6tQxkA@public.gmane.org<mailto:pmcorreia-7Y4ok6tQxkA@public.gmane.org>> escreveu:

Dear Gaters

I’m having some problems with Gate7.1 and geant4.10.01.

I compile both softwares apparently with no erros, just few warnings in Gate, and when I try to run Gate with some macro file (PET_CylindricalPET_System.mac for example), I got the following output.
I tried to reinstall Root, Geant4 and Gate several times, but I always get the same output. The optical flag is ON.
I think that may be something related with libxml2 library, do you have any suggestion?

Best regards,
Pedro Correia

[Core-0] You are using Geant4 version 10.1.0
[Core-0] Starting macro Optical_System.mac
===== XML PATH ====: ./Materials.xml

*** Break *** segmentation violation



===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================

Thread 2 (Thread 0x7eff492f8700 (LWP 9249)):
#0  0x00000039a54df0d3 in poll () from /lib64/libc.so.6
#1  0x00000039a8409aaa in ?? () from /usr/lib64/libxcb.so.1
#2  0x00000039a840b1c8 in xcb_wait_for_event () from /usr/lib64/libxcb.so.1
#3  0x00007eff4b3f23a1 in ?? () from /usr/lib64/qt5/plugins/platforms/libqxcb.so
#4  0x00007eff52fe6819 in ?? () from /usr/lib64/libQt5Core.so.5
#5  0x00000039b40aa754 in ?? () from /usr/lib64/nvidia/libGL.so.1
#6  0x00000039a5c079d1 in start_thread () from /lib64/libpthread.so.0
#7  0x00000039a54e88fd in clone () from /lib64/libc.so.6

Thread 1 (Thread 0x7eff519e4240 (LWP 9248)):
#0  0x00000039a54ac65d in waitpid () from /lib64/libc.so.6
#1  0x00000039a543e609 in do_system () from /lib64/libc.so.6
#2  0x00000039a543e940 in system () from /lib64/libc.so.6
#3  0x0000003867a6a454 in TUnixSystem::StackTrace() () from /usr/lib64/root/libCore.so
#4  0x0000003867a69873 in TUnixSystem::DispatchSignals(ESignals) () from /usr/lib64/root/libCore.so
#5  <signal handler called>
#6  0x00000039a5529170 in __strncmp_sse42 () from /lib64/libc.so.6
#7  0x00007eff54d5f885 in __xmlParserInputBufferCreateFilename () from /usr/lib64/libxml2.so.2
#8  0x00007eff54d3480d in xmlNewInputFromFile () from /usr/lib64/libxml2.so.2
#9  0x00007eff54d389f6 in xmlCreateURLParserCtxt () from /usr/lib64/libxml2.so.2
#10 0x00007eff54d4d6ae in xmlSAXParseFileWithData () from /usr/lib64/libxml2.so.2
#11 0x00000000008c981a in GateXMLDocument::GateXMLDocument(G4String const&) ()
#12 0x00000000005f0345 in GateMaterialDatabase::ReadMaterialFromDBFile(G4String const&) ()
#13 0x00000000005f24c3 in GateMaterialDatabase::GetMaterial(G4String const&) ()
#14 0x00000000005825cb in GateVVolume::DefineOwnMaterials() ()
#15 0x000000000061edc0 in GateVolumeMessenger::SetNewValue(G4UIcommand*, G4String) ()
#16 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#17 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#18 0x00007eff564c5a97 in G4UIbatch::ExecCommand(G4String const&) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#19 0x00007eff564c6a2b in G4UIbatch::SessionStart() () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#20 0x00007eff564de303 in G4UImanager::ExecuteMacroFile(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#21 0x00007eff564d9648 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#22 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#23 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#24 0x00000000004f83fb in main ()
===========================================================


The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug report at
http://root.cern.ch/bugs. Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#6  0x00000039a5529170 in __strncmp_sse42 () from /lib64/libc.so.6
#7  0x00007eff54d5f885 in __xmlParserInputBufferCreateFilename () from /usr/lib64/libxml2.so.2
#8  0x00007eff54d3480d in xmlNewInputFromFile () from /usr/lib64/libxml2.so.2
#9  0x00007eff54d389f6 in xmlCreateURLParserCtxt () from /usr/lib64/libxml2.so.2
#10 0x00007eff54d4d6ae in xmlSAXParseFileWithData () from /usr/lib64/libxml2.so.2
#11 0x00000000008c981a in GateXMLDocument::GateXMLDocument(G4String const&) ()
#12 0x00000000005f0345 in GateMaterialDatabase::ReadMaterialFromDBFile(G4String const&) ()
#13 0x00000000005f24c3 in GateMaterialDatabase::GetMaterial(G4String const&) ()
#14 0x00000000005825cb in GateVVolume::DefineOwnMaterials() ()
#15 0x000000000061edc0 in GateVolumeMessenger::SetNewValue(G4UIcommand*, G4String) ()
#16 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#17 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#18 0x00007eff564c5a97 in G4UIbatch::ExecCommand(G4String const&) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#19 0x00007eff564c6a2b in G4UIbatch::SessionStart() () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#20 0x00007eff564de303 in G4UImanager::ExecuteMacroFile(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#21 0x00007eff564d9648 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#22 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#23 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so
#24 0x00000000004f83fb in main ()
===========================================================




<div>
<div dir="ltr">Hi Pedro!<div><br></div>
<div>I know that some people (including myself) have had some problems with patch 01 of geant4.10.01 and gate 7.1, at least when compiling. Dunno if the problem can be related to the patch or not, but you can try the version without the patch:&nbsp;<a href="http://geant4.cern.ch/support/source/geant4.10.01.tar.gz" rel="noreferrer" target="_blank">http://<span class="">geant4</span>.cern.ch/support/source/≤span class="">geant4</span>.10.01.tar.gz</a>
</div>
<div><br></div>
<div>Good luck!</div>
<div>Ida</div>
</div>
<div class="gmail_extra">
<br><div class="gmail_quote">On Thu, Jun 18, 2015 at 11:19 AM, Pedro Correia <span dir="ltr">&lt;<a href="mailto:pmcorreia@..." target="_blank">pmcorreia@...</a>&gt;</span> wrote:<br><blockquote class="gmail_quote">Dear Gaters<br><br>
Since I was not the only one having this problem (the user Gwenna&euml;lle MARIN had the same experience few weeks ago).<br>
We both used Scientific Linux 6, gate v7.1 and geant4.10.01 (no patch-01).<br><br>
I&rsquo;m assuming that is not an issue with Geant4, because I found nothing related with this in the Geant4 forum.<br>
Is it possible that the Gate developers take a look to this?<br><br>
Cheers, Pedro<br><div class="HOEnZb"><div class="h5">
<br><br><br><br>
No dia 16/06/2015, &agrave;s 18:50, pedro correia &lt;<a href="mailto:pmcorreia@...">pmcorreia@...</a>&lt;mailto:<a href="mailto:pmcorreia@...">pmcorreia@...</a>&gt;&gt; escreveu:<br><br>
Dear Gaters<br><br>
I&rsquo;m having some problems with Gate7.1 and geant4.10.01.<br><br>
I compile both softwares apparently with no erros, just few warnings in Gate, and when I try to run Gate with some macro file (PET_CylindricalPET_System.mac for example), I got the following output.<br>
I tried to reinstall Root, Geant4 and Gate several times, but I always get the same output. The optical flag is ON.<br>
I think that may be something related with libxml2 library, do you have any suggestion?<br><br>
Best regards,<br>
Pedro Correia<br><br>
[Core-0] You are using Geant4 version 10.1.0<br>
[Core-0] Starting macro Optical_System.mac<br>
===== XML PATH ====: ./Materials.xml<br><br>
*** Break *** segmentation violation<br><br><br><br>
===========================================================<br>
There was a crash.<br>
This is the entire stack trace of all threads:<br>
===========================================================<br><br>
Thread 2 (Thread 0x7eff492f8700 (LWP 9249)):<br>
#0&nbsp; 0x00000039a54df0d3 in poll () from /lib64/libc.so.6<br>
#1&nbsp; 0x00000039a8409aaa in ?? () from /usr/lib64/libxcb.so.1<br>
#2&nbsp; 0x00000039a840b1c8 in xcb_wait_for_event () from /usr/lib64/libxcb.so.1<br>
#3&nbsp; 0x00007eff4b3f23a1 in ?? () from /usr/lib64/qt5/plugins/platforms/libqxcb.so<br>
#4&nbsp; 0x00007eff52fe6819 in ?? () from /usr/lib64/libQt5Core.so.5<br>
#5&nbsp; 0x00000039b40aa754 in ?? () from /usr/lib64/nvidia/libGL.so.1<br>
#6&nbsp; 0x00000039a5c079d1 in start_thread () from /lib64/libpthread.so.0<br>
#7&nbsp; 0x00000039a54e88fd in clone () from /lib64/libc.so.6<br><br>
Thread 1 (Thread 0x7eff519e4240 (LWP 9248)):<br>
#0&nbsp; 0x00000039a54ac65d in waitpid () from /lib64/libc.so.6<br>
#1&nbsp; 0x00000039a543e609 in do_system () from /lib64/libc.so.6<br>
#2&nbsp; 0x00000039a543e940 in system () from /lib64/libc.so.6<br>
#3&nbsp; 0x0000003867a6a454 in TUnixSystem::StackTrace() () from /usr/lib64/root/libCore.so<br>
#4&nbsp; 0x0000003867a69873 in TUnixSystem::DispatchSignals(ESignals) () from /usr/lib64/root/libCore.so<br>
#5&nbsp; &lt;signal handler called&gt;<br>
#6&nbsp; 0x00000039a5529170 in __strncmp_sse42 () from /lib64/libc.so.6<br>
#7&nbsp; 0x00007eff54d5f885 in __xmlParserInputBufferCreateFilename () from /usr/lib64/libxml2.so.2<br>
#8&nbsp; 0x00007eff54d3480d in xmlNewInputFromFile () from /usr/lib64/libxml2.so.2<br>
#9&nbsp; 0x00007eff54d389f6 in xmlCreateURLParserCtxt () from /usr/lib64/libxml2.so.2<br>
#10 0x00007eff54d4d6ae in xmlSAXParseFileWithData () from /usr/lib64/libxml2.so.2<br>
#11 0x00000000008c981a in GateXMLDocument::GateXMLDocument(G4String const&amp;) ()<br>
#12 0x00000000005f0345 in GateMaterialDatabase::ReadMaterialFromDBFile(G4String const&amp;) ()<br>
#13 0x00000000005f24c3 in GateMaterialDatabase::GetMaterial(G4String const&amp;) ()<br>
#14 0x00000000005825cb in GateVVolume::DefineOwnMaterials() ()<br>
#15 0x000000000061edc0 in GateVolumeMessenger::SetNewValue(G4UIcommand*, G4String) ()<br>
#16 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#17 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#18 0x00007eff564c5a97 in G4UIbatch::ExecCommand(G4String const&amp;) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#19 0x00007eff564c6a2b in G4UIbatch::SessionStart() () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#20 0x00007eff564de303 in G4UImanager::ExecuteMacroFile(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#21 0x00007eff564d9648 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#22 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#23 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#24 0x00000000004f83fb in main ()<br>
===========================================================<br><br><br>
The lines below might hint at the cause of the crash.<br>
If they do not help you then please submit a bug report at<br><a href="http://root.cern.ch/bugs" rel="noreferrer" target="_blank">http://root.cern.ch/bugs</a>. Please post the ENTIRE stack trace<br>
from above as an attachment in addition to anything else<br>
that might help us fixing this issue.<br>
===========================================================<br>
#6&nbsp; 0x00000039a5529170 in __strncmp_sse42 () from /lib64/libc.so.6<br>
#7&nbsp; 0x00007eff54d5f885 in __xmlParserInputBufferCreateFilename () from /usr/lib64/libxml2.so.2<br>
#8&nbsp; 0x00007eff54d3480d in xmlNewInputFromFile () from /usr/lib64/libxml2.so.2<br>
#9&nbsp; 0x00007eff54d389f6 in xmlCreateURLParserCtxt () from /usr/lib64/libxml2.so.2<br>
#10 0x00007eff54d4d6ae in xmlSAXParseFileWithData () from /usr/lib64/libxml2.so.2<br>
#11 0x00000000008c981a in GateXMLDocument::GateXMLDocument(G4String const&amp;) ()<br>
#12 0x00000000005f0345 in GateMaterialDatabase::ReadMaterialFromDBFile(G4String const&amp;) ()<br>
#13 0x00000000005f24c3 in GateMaterialDatabase::GetMaterial(G4String const&amp;) ()<br>
#14 0x00000000005825cb in GateVVolume::DefineOwnMaterials() ()<br>
#15 0x000000000061edc0 in GateVolumeMessenger::SetNewValue(G4UIcommand*, G4String) ()<br>
#16 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#17 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#18 0x00007eff564c5a97 in G4UIbatch::ExecCommand(G4String const&amp;) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#19 0x00007eff564c6a2b in G4UIbatch::SessionStart() () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#20 0x00007eff564de303 in G4UImanager::ExecuteMacroFile(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#21 0x00007eff564d9648 in G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#22 0x00007eff564d32bb in G4UIcommand::DoIt(G4String) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#23 0x00007eff564e06a7 in G4UImanager::ApplyCommand(char const*) () from /home/Pedro/GEANT4/geant4.10.01-install/lib64/libG4intercoms.so<br>
#24 0x00000000004f83fb in main ()<br>
===========================================================<br><br><br><br>
</div></div>
</blockquote>
</div>
<br>
</div>
</div>
soomaAlsanea | 21 Jun 09:57 2015
Picon

error&warning.txt

Hi Gaters,
I am quite new in using GATE . I am trying to build a PET system using vGATE . but when I run my macro only the World box is appearing with a list of warnings . The PET simulated image doesn't appear . I am trying to find the solution for almost month and I am failing..
please help me to solve this problem

the warning list like this, and it attached as txt file 
----------------------------------
You are using Geant4 version 9.6.3 Idle> /control/execute test.mac libGL error: pci id for fd 11: 80ee:beef, driver (null) OpenGL Warning: glFlushVertexArrayRangeNV not found in mesa table OpenGL Warning: glVertexArrayRangeNV not found in mesa table OpenGL Warning: glCombinerInputNV not found in mesa table OpenGL Warning: glCombinerOutputNV not found in mesa table OpenGL Warning: glCombinerParameterfNV not found in mesa table OpenGL Warning: glCombinerParameterfvNV not found in mesa table OpenGL Warning: glCombinerParameteriNV not found in mesa table OpenGL Warning: glTestFenceNV not found in mesa table libGL error: core dri or dri2 extension not found libGL error: failed to load driver: vboxvideo G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font -adobe-courier-bold-r-normal--10-100-75-75-m-60-iso8859-1 G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font -adobe-courier-bold-r-normal--11-80-100-100-m-60-iso8859-1 G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font -adobe-courier-bold-r-normal--12-120-75-75-m-70-iso8859-1 OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU /tracking/storeTrajectory 1 Attributes available for modeling and filtering with "/vis/modeling/trajectories/create/drawByAttribute" and "/vis/filtering/trajectories/create/attributeFilter" 
You are using Geant4 version 9.6.3
Idle> /control/execute test.mac
libGL error: pci id for fd 11: 80ee:beef, driver (null)
OpenGL Warning: glFlushVertexArrayRangeNV not found in mesa table
OpenGL Warning: glVertexArrayRangeNV not found in mesa table
OpenGL Warning: glCombinerInputNV not found in mesa table
OpenGL Warning: glCombinerOutputNV not found in mesa table
OpenGL Warning: glCombinerParameterfNV not found in mesa table
OpenGL Warning: glCombinerParameterfvNV not found in mesa table
OpenGL Warning: glCombinerParameteriNV not found in mesa table
OpenGL Warning: glCombinerParameterivNV not found in mesa table
OpenGL Warning: glFinalCombinerInputNV not found in mesa table
OpenGL Warning: glGetCombinerInputParameterfvNV not found in mesa table
OpenGL Warning: glGetCombinerInputParameterivNV not found in mesa table
OpenGL Warning: glGetCombinerOutputParameterfvNV not found in mesa table
OpenGL Warning: glGetCombinerOutputParameterivNV not found in mesa table
OpenGL Warning: glGetFinalCombinerInputParameterfvNV not found in mesa table
OpenGL Warning: glGetFinalCombinerInputParameterivNV not found in mesa table
OpenGL Warning: glDeleteFencesNV not found in mesa table
OpenGL Warning: glFinishFenceNV not found in mesa table
OpenGL Warning: glGenFencesNV not found in mesa table
OpenGL Warning: glGetFenceivNV not found in mesa table
OpenGL Warning: glIsFenceNV not found in mesa table
OpenGL Warning: glSetFenceNV not found in mesa table
OpenGL Warning: glTestFenceNV not found in mesa table
libGL error: core dri or dri2 extension not found
libGL error: failed to load driver: vboxvideo
G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--10-100-75-75-m-60-iso8859-1
G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--11-80-100-100-m-60-iso8859-1
G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--12-120-75-75-m-70-iso8859-1
G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--14-100-100-100-m-90-iso8859-1
G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--17-120-100-100-m-100-iso8859-1
G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--18-180-75-75-m-110-iso8859-1
G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--20-140-100-100-m-110-iso8859-1
G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--24-240-75-75-m-150-iso8859-1
G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--25-180-100-100-m-150-iso8859-1
G4OpenGLXViewer::CreateFontLists XLoadQueryFont failed for font
  -adobe-courier-bold-r-normal--34-240-100-100-m-200-iso8859-1
OpenGL Warning: No pincher, please call crStateSetCurrentPointers() in your SPU
/tracking/storeTrajectory 1
Attributes available for modeling and filtering with
  "/vis/modeling/trajectories/create/drawByAttribute" and
  "/vis/filtering/trajectories/create/attributeFilter" commands:
G4TrajectoriesModel:
  Event ID (EventID): G4int
G4Trajectory:
  Charge (Ch): unit: e+ (G4double)
  Track ID (ID): G4int
  Initial kinetic energy (IKE): G4BestUnit (G4double)
  Initial momentum magnitude (IMag): G4BestUnit (G4double)
  Initial momentum (IMom): G4BestUnit (G4ThreeVector)
  No. of points (NTP): G4int
  PDG Encoding (PDG): G4int
  Parent ID (PID): G4int
  Particle Name (PN): G4String
G4TrajectoryPoint:
  Position (Pos): G4BestUnit (G4ThreeVector)
WARNING: Trajectory storing has been requested.  This action may be
  reversed with "/tracking/storeTrajectory 0".
WARNING: The vis manager will keep up to 100 events.
  This may use a lot of memory.
  It may be changed with, e.g., "/vis/scene/endOfEventAction accumulate 10".
 CREATED THE COMMAND /gate/systems/cylindricalPET/addAnewRsector
===== XML PATH ====: ./Materials.xml
===== XML PATH ====: 0x1af2da0




with my regards,
Ebtesam Alsanea

Sent from my iPa
<div>
<div></div>
<div>
<div></div>
<div>
<span></span><br><span></span><br><span></span><br><span>with my regards,</span><br><span>Ebtesam Alsanea</span><br><span></span><br><span>Sent from my iPa</span>
</div>
</div>
</div>
M.R Teimoori | 18 Jun 06:58 2015
Picon

PET GPU example: Empty output

Hi All,

I just got Gate 7.1 installed on Ubuntu 14.04 with the GPU flag on for my project involving PET simulations. The results of the PET Benchmark were quite consistent with what it's supposed to be, so I am hoping that the installation process was quite successful. Then I tried the PET GPU Example to make sure that GPU is also working properly. Surprisingly, the output is just an empty file, although based on the summary file, generated after the simulation, there are almost 250,000 coincidences recorded for the acquisition time of 0.01 sec. 

Does anyone have any similar experience and know what is going on here? 
Has anyone tried the PET GPU Example in Gate 7.1 and got consistent results with the CPU one?

Here are a few things to note:

* The default output format in this example is ASCII - I switched to Root and still the output is just an empty file. If I increase the acquisition time, the run time would also increase, so would the number of coincidences (according to the generated summary file). However, the output file is still an empty file.
* The number of recorded coincidences varies every time that I run the GPU sample macro file, even though the macro file (including the random number generator seed) remains the same.
* Because the output is always an entirely empty file, I am not able to double check the source location too,
* There is no hardware issue and the GPU was functional in Gate 7 on this system.

Any thoughts would be greatly appreciated,

Cheers,
Reza


<div><div dir="ltr">Hi All,<div><br></div>
<div>I just got Gate 7.1 installed on Ubuntu 14.04 with the GPU flag on for my project involving PET simulations. The results of the PET Benchmark were quite consistent with what it's supposed to be, so I am hoping that the installation process was quite successful. Then I tried the PET GPU Example to make sure that GPU is also working properly. Surprisingly, the output is just an empty file,&nbsp;although&nbsp;based on the summary file, generated after the simulation, there are almost 250,000 coincidences recorded for the acquisition time of 0.01 sec.&nbsp;</div>
<div><br></div>
<div>Does anyone have any similar experience and know what is going on here?&nbsp;</div>
<div>
<span>Has anyone tried the PET GPU Example in Gate 7.1 and got consistent results with the CPU one?</span><br>
</div>
<div><br></div>
<div>Here are a few things to note:</div>
<div><br></div>
<div>* The default output format in this example is ASCII - I switched to Root and still the output is just an empty file. If I increase the acquisition time, the run time would also increase, so would the number of coincidences (according to the generated summary file). However, the output file is still an empty file.</div>
<div>* The number of recorded coincidences varies every time that I run the GPU sample macro file, even though the macro file (including the random number generator seed) remains the same.</div>
<div>* Because the output is always an&nbsp;entirely&nbsp;empty file, I am not able to double check the source location too,</div>
<div>* There is no hardware issue and the GPU was functional in Gate 7 on this system.</div>
<div><br></div>
<div>Any thoughts would be greatly appreciated,</div>
<div><br></div>
<div>Cheers,</div>
<div>Reza</div>
<div><br></div>
<div><br></div>
</div></div>
Charles A. Maitz | 17 Jun 22:17 2015
Picon

lists and leaks

Greetings GATE-users,

 

I am new to GATE (self-taught for about 4 months, but did attend the Geant4 training course last fall in Catania).  I am running Gate 7.1 with geant4 10.1.0.  I am able to run simulations with manually defined physics processes, but whenever I run a simulation using the physic list builder, it seems to run, and I get events defined in my stat.txt file, with the same number of tracks and steps, which makes me think that interactions are not registering.  I also get no hits, singles or coincidences in my .root output files.

 

I think this is a general issue, but I am using GATE for radiopharmaceutical dosimetry purposes, and so my sources tend to be ion source decays.

 

In an unrelated issue, I also have a bad case memory leaks whenever I try to employ dose or spectrum actors.  I am typically employing a dose and a spectrum actor to both the tumor and the patient.  I am no computer expert.  I’ve attached the valgrind leak output, and it seems as though it may have something to do with my geant4 installation.

 

Thanks,

-charlie

 

 

Charles A. Maitz, DVM, PhD, DACVR-RO

Assistant Professor of Radiation Oncology

Department of Veterinary Medicine and Surgery and Radiology

International Institute of Nano & Molecular Medicine

University of Missouri - Columbia

maitzc-807GuYrz9FD2fBVCVOL8/A@public.gmane.org

(573)882-7821

 

Attachment (valgrind leak): application/octet-stream, 80 KiB
<div><div class="WordSection1">
<p class="MsoNormal">Greetings GATE-users,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">I am new to GATE (self-taught for about 4 months, but did attend the Geant4 training course last fall in Catania).&nbsp; I am running Gate 7.1 with geant4 10.1.0.&nbsp; I am able to run simulations with manually defined physics processes, but whenever I run a simulation using the physic list builder, it seems to run, and I get events defined in my stat.txt file, with the same number of tracks and steps, which makes me think that interactions are not registering. &nbsp;I also get no hits, singles or coincidences in my .root output files.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">I think this is a general issue, but I am using GATE for radiopharmaceutical dosimetry purposes, and so my sources tend to be ion source decays.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">In an unrelated issue, I also have a bad case memory leaks whenever I try to employ dose or spectrum actors.&nbsp; I am typically employing a dose and a spectrum actor to both the tumor and the patient.&nbsp; I am no computer expert.&nbsp; I&rsquo;ve attached the valgrind leak output, and it seems as though it may have something to do with my geant4 installation.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">Thanks,<p></p></p>
<p class="MsoNormal">-charlie<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal"><span>Charles A. Maitz, DVM, PhD, DACVR-RO</span><span><p></p></span></p>
<p class="MsoNormal"><span>Assistant Professor of Radiation Oncology<p></p></span></p>
<p class="MsoNormal"><span>Department of Veterinary Medicine and Surgery and Radiology<p></p></span></p>
<p class="MsoNormal"><span>International Institute of Nano &amp; Molecular Medicine<p></p></span></p>
<p class="MsoNormal"><span>University of Missouri - Columbia<p></p></span></p>
<p class="MsoNormal"><span><a href="mailto:maitzc@...">maitzc@...</a><p></p></span></p>
<p class="MsoNormal"><span>(573)882-7821</span><span><p></p></span></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div></div>

Gmane