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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Using the emstandard_opt3 instead of QGSP physics list seems to work.<br>
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Jared STRYDHORST<br>
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<div style="margin:0"><font face="Calibri,sans-serif" size="2"><span style="font-size:11pt"><font face="Cambria,serif" size="2"><span style="font-size:10pt">Laboratoire Imagerie Moléculaire In Vivo (IMIV)</span></font><font face="Cambria,serif" size="2"><span style="font-size:10pt"><br>
UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS</span></font></span></font></div>
<div style="margin:0"><font face="Calibri,sans-serif" size="2"><span style="font-size:11pt"><font face="Cambria,serif" size="2"><span style="font-size:10pt">CEA/I2BM/Service Hospitalier Frédéric Joliot</span></font></span></font></div>
<div style="margin:0"><font face="Calibri,sans-serif" size="2"><span style="font-size:11pt"><font face="Cambria,serif" size="2"><span style="font-size:10pt">4, place du Général Leclerc</span></font><font face="Cambria,serif" size="2"><span style="font-size:10pt"><br>
91401 ORSAY Cedex</span></font><font face="Cambria,serif" size="2"><span style="font-size:10pt"><br>
</span></font><font face="Cambria,serif" size="2"><span style="font-size:10pt"></span></font><font face="Cambria,serif" size="2"><span style="font-size:10pt"><br>
</span></font><a href="mailto:karima.ait-aissa@cea.fr" target="_blank"><font face="Cambria,serif" size="2"><span style="font-size:10pt"></span></font></a></span></font></div>
<div style="margin:0"><font face="Calibri,sans-serif" size="2"><span style="font-size:11pt"><a href="http://i2bm.cea.fr/dsv/i2bm/shfj/imiv" target="_blank"><font face="Cambria,serif" size="2"><span style="font-size:10pt">http://i2bm.cea.fr/dsv/i2bm/shfj/imiv</span></font></a></span></font></div>
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<div style="direction: ltr;" id="divRpF53295"><font face="Tahoma" color="#000000" size="2"><b>De :</b> gate-users-bounces@lists.opengatecollaboration.org [gate-users-bounces@lists.opengatecollaboration.org] de la part de Michal Knap [knap.michal@yahoo.com]<br>
<b>Envoyé :</b> jeudi 14 janvier 2016 13:35<br>
<b>À :</b> David Boersma; gate-users@lists.opengatecollaboration.org<br>
<b>Objet :</b> [Gate-users] Fw: Problem with 'std::bad_alloc'<br>
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<div id="yiv3203938371yui_3_16_0_1_1452764539431_4758"><span id="yiv3203938371yui_3_16_0_1_1452764539431_6649">Hi All,</span></div>
<div id="yiv3203938371yui_3_16_0_1_1452764539431_4758"><span id="yiv3203938371yui_3_16_0_1_1452764539431_5219">I'm attaching my whole conversation with David and files below.</span></div>
<div id="yiv3203938371yui_3_16_0_1_1452764539431_4758">Could you please help with solving this issue?</div>
<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_4758">It's a strange bug which causes huge consumption of RAM and gives me <span class="yiv3203938371" id="yiv3203938371yui_3_16_0_1_1452764539431_5412" style="font-family:HelveticaNeue,'Helvetica Neue',Helvetica,Arial,'Lucida Grande',sans-serif"> this
error message</span></div>
<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_4758"><span class="yiv3203938371" style="font-family:HelveticaNeue,'Helvetica Neue',Helvetica,Arial,'Lucida Grande',sans-serif"><br clear="none">
</span></div>
<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_4758"><span class="yiv3203938371" id="yiv3203938371yui_3_16_0_1_1452764539431_5414" style="font-family:HelveticaNeue,'Helvetica Neue',Helvetica,Arial,'Lucida Grande',sans-serif"> <i id="yiv3203938371yui_3_16_0_1_1452764539431_5514"> /terminate
called after throwing an instance of 'std::bad_alloc'/</i></span></div>
<i id="yiv3203938371yui_3_16_0_1_1452764539431_6027"><span class="yiv3203938371" id="yiv3203938371yui_3_16_0_1_1452764539431_5416" style="font-family:HelveticaNeue,'Helvetica Neue',Helvetica,Arial,'Lucida Grande',sans-serif"> / what():
std::bad_alloc/</span><br class="yiv3203938371" id="yiv3203938371yui_3_16_0_1_1452764539431_5418" style="font-family:HelveticaNeue,'Helvetica Neue',Helvetica,Arial,'Lucida Grande',sans-serif" clear="none">
</i>
<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_5421"><span id="yiv3203938371yui_3_16_0_1_1452764539431_5422" style="font-family:HelveticaNeue,'Helvetica Neue',Helvetica,Arial,'Lucida Grande',sans-serif"><i id="yiv3203938371yui_3_16_0_1_1452764539431_6028"> /Przerwane
(core dumped)/</i></span></div>
<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_5421"><br clear="none">
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<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_5421">My visualization doesn't even start but it is the smallest problem.</div>
<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_5421"><br>
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<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_5421">I run benchmark simulation just to check if is everything all right with my Gate and it all works (benchmarkSPECT.mac with visualization works fine).</div>
<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_5421"><br>
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<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_5421">I'm working on ubuntu 14.04 LTS / Geant4.9.6.p04 / Gate_v7.0/ ROOT 5.34.34.</div>
<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_5421"><font id="yiv3203938371yui_3_16_0_1_1452764539431_6164" size="3">On<font id="yiv3203938371yui_3_16_0_1_1452764539431_6137" face="HelveticaNeue, Helvetica Neue, Helvetica, Arial, Lucida Grande, sans-serif">
machine with i5VPRO/2.4GHz/8GB/128 SSD. </font></font></div>
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<font id="yiv3203938371yui_3_16_0_1_1452764539431_6165" size="3">Can anybody help me with this issue?</font></div>
<div class="yiv3203938371qtdSeparateBR" id="yiv3203938371yui_3_16_0_1_1452764539431_4571">
<font size="3">I'll be very thankful.</font></div>
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<font id="yui_3_16_0_1_1452764539431_9395" size="3">Best Regards&Thanks</font></div>
<div class="yiv3203938371qtdSeparateBR" id="yiv3203938371yui_3_16_0_1_1452764539431_4571">
<font id="yui_3_16_0_1_1452764539431_9396" size="3">Michał Knap<br id="yiv3203938371yui_3_16_0_1_1452764539431_6140" clear="none">
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<div id="yiv3203938371yui_3_16_0_1_1452764539431_4562" style="font-family:HelveticaNeue,Helvetica Neue,Helvetica,Arial,Lucida Grande,sans-serif; font-size:16px">
<div dir="ltr" id="yiv3203938371yui_3_16_0_1_1452764539431_4561"><font id="yiv3203938371yui_3_16_0_1_1452764539431_4560" face="Arial" size="2">13:07 czwartek, 2016-1-14, David Boersma <david.boersma@physics.uu.se> napisał(a):<br clear="none">
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Hi,<br clear="none">
<br clear="none">
All:<br clear="none">
<br clear="none">
Could other people please have a look at Michał's problem? I could run <br clear="none">
his macro (see his previous mail) and Gate indeed consumes excessive <br clear="none">
amounts of RAM, but it is not clear to me why that happens. See below <br clear="none">
for my observations. I have to work on other things now.<br clear="none">
<br clear="none">
<br clear="none">
Michał:<br clear="none">
<br clear="none">
Yes, I could run your macro. I disabled all the lines with "/vis" in <br clear="none">
them, ran the command "Gate ./minigamma1pointsourceoncollimator.mac" and <br clear="none">
then observed in a separate window with "htop" how things were going, <br clear="none">
resource-wise.<br clear="none">
<br clear="none">
I ran this on a machine with 16 GiB of RAM, Ubuntu 14.04, Geant <br clear="none">
4.9.6.p04. It took about a minute to fill up all the RAM, and then it <br clear="none">
started to eat up the swap space. When it had eaten up 90% of the swap <br clear="none">
space I killed the program (from within htop; I was not able to kill <br clear="none">
Gate with ctrl-C).<br clear="none">
<br clear="none">
I think we can conclude that "something" in Gate is allocating too much <br clear="none">
memory. It could be a spectacular memory leak, or it could be some <br clear="none">
missconfigured component in your macro that causes excessive resource <br clear="none">
consumption. For the latter hypothesis I looked at your macro for <br clear="none">
suspicious things, but the most segmented thing I could find was the <br clear="none">
"projection" output, and replacing 128*128 by 4*4 did not help at all. I <br clear="none">
reduced the time slice from 1s to 0.001s and the time stop from 60s to <br clear="none">
0.002s, but that did not seem to change anything either.<br clear="none">
<br clear="none">
Maybe there is some implicit/default setting that is wrong for your <br clear="none">
application. I am not an imaging expert (I use gate for radiotherapy), <br clear="none">
so maybe someone else has an idea.<br clear="none">
<br clear="none">
I ran it in "gdb" (the GNU debugger) and stopped the program by sending <br clear="none">
it a signal, while it was eating memory, and checked with "bt" <br clear="none">
(backtrace) in which function it was running at the moment I stopped it. <br clear="none">
I repeated this several times and got different backtraces every time, <br clear="none">
so this did not provide any useful hints for finding out which part of <br clear="none">
the code is responsible.<br clear="none">
<br clear="none">
This is as far as I could get, and the problem is not yet solved. I hope <br clear="none">
someone else on the list can take over to help you solve this. Maybe <br clear="none">
someone should run it with "valgrind", but that can be pretty time <br clear="none">
consuming, and maybe someone actually already knows, that would be much <br clear="none">
more efficient.<br clear="none">
<br clear="none">
Good luck,<br clear="none">
David B.<br clear="none">
<br clear="none">
<br clear="none">
Den 13/01/2016 kl. 20:26, skrev Michal Knap:<br clear="none">
> Hi David,<br clear="none">
> It would be really great if you could take a look on my mac file.<br clear="none">
> Please see the attachment.<br clear="none">
> I'm a little bit confused about this bug.<br clear="none">
><br clear="none">
> I will try to try out your idea with much simplified version and will<br clear="none">
> return with the results.<br clear="none">
><br clear="none">
> Thanks&Regards<br clear="none">
> Michał Knap<br clear="none">
><br clear="none">
><br clear="none">
><br clear="none">
> 12:00 środa, 2016-1-13, David Boersma <<a rel="nofollow" shape="rect" href="mailto:david.boersma@physics.uu.se" target="_blank">david.boersma@physics.uu.se</a>><br clear="none">
> napisał(a):<br clear="none">
><br clear="none">
><br clear="none">
> Hi Michał,<br clear="none">
><br clear="none">
> On 2016-01-13 07:04, Michal Knap wrote:<br clear="none">
> > Hi David,<br clear="none">
> > I have only one version of Gate and Geant4 installed - Gate v7.0 and<br clear="none">
> > Geant4.9.6.p04.<br clear="none">
> ><br clear="none">
> > I successfully run benchmark simulation - benchmarkSPECT, with or<br clear="none">
> > without visualization.<br clear="none">
> ><br clear="none">
> > So it's somthing with my code i think. What can i disable/enable to fix<br clear="none">
> > this bug?<br clear="none">
><br clear="none">
> If there is indeed something wrong with your code then we can only help<br clear="none">
> you by looking at your code.<br clear="none">
><br clear="none">
> So, as I wrote in my previous mail, it would be nice if you could make a<br clear="none">
> short and strongly simplified version of your macro which still crashes<br clear="none">
> in the same way. Preferably it only uses input data from the examples<br clear="none">
> and benchmarks. E.g. you define only a very crude geometry and a gamma<br clear="none">
> source, and a number of primaries, no visualization. If that throws the<br clear="none">
> same bad_alloc exception, then please send that to us, we can try to<br clear="none">
> reproduce and tell you what's wrong. Of course it is possible that the<br clear="none">
> problem disappears after you take out certain parts of the macro. If you<br clear="none">
> can nail it down to one particular line or set of lines that makes the<br clear="none">
> difference between crashing and not crashing, then quote those lines to<br clear="none">
> us. That is less helpful the first option, but could still provide a hint.<br clear="none">
><br clear="none">
> David B.<br clear="none">
><br clear="none">
><br clear="none">
> ><br clear="none">
> > Best regards<br clear="none">
> > Michał Knap<br clear="none">
> ><br clear="none">
> ><br clear="none">
> > 18:11 wtorek, 2016-1-12, David Boersma <<a rel="nofollow" shape="rect" href="mailto:david.boersma@physics.uu.se" target="_blank">david.boersma@physics.uu.se</a><br clear="none">
> <mailto:<a rel="nofollow" shape="rect" href="mailto:david.boersma@physics.uu.se" target="_blank">david.boersma@physics.uu.se</a>>><br clear="none">
> > napisał(a):<br clear="none">
> ><br clear="none">
> ><br clear="none">
> > Hi Michał,<br clear="none">
> ><br clear="none">
> > Some more simple questions:<br clear="none">
> ><br clear="none">
> > * Can you run macros from the example directory successfully, or do some<br clear="none">
> > of them result in this same error?<br clear="none">
> ><br clear="none">
> ><br clear="none">
> > * Do you have multiple versions of Geant4 and/or Root installed? If yes,<br clear="none">
> > could you check with the following command:<br clear="none">
> ><br clear="none">
> > ldd $(which Gate)<br clear="none">
> ><br clear="none">
> > that your Gate executable gets indeed linked to the same versions as the<br clear="none">
> > ones you configured during installation of Gate? If the versions do not<br clear="none">
> > match: then fix your environment, or reinstall Gate (from scratch).<br clear="none">
> ><br clear="none">
> ><br clear="none">
> ><br clear="none">
> > If these simple questions do not help, then I think the next step is to<br clear="none">
> > make a minimalistic version of your macro that demonstrates the error<br clear="none">
> > you are seeing and post it here on the list, so that other people have a<br clear="none">
> > chance to reproduce this problem. Please also specify how you run the<br clear="none">
> > Gate command (with which options).<br clear="none">
> ><br clear="none">
> > HTH,<br clear="none">
> > David Boersma<br clear="none">
> ><br clear="none">
> > Den 12/01/2016 kl. 17:35, skrev Michal Knap:<br clear="none">
> > > Hi David,<br clear="none">
> > > I checked you idea but i use only 50-60% RAM memory.<br clear="none">
> > > While i'm running simulation i do not use any other apps.<br clear="none">
> > > Even browser is closed.<br clear="none">
> > ><br clear="none">
> > > I have intel i5 vPRO, 8GB RAM, 120 GB SSD<br clear="none">
> > > Ubuntu 14.04 LTS, Geant4.9.6.p04,Gate7.0,Root 5.34.34<br clear="none">
> > ><br clear="none">
> > > Kind regards<br clear="none">
> > ><br clear="none">
> > ><br clear="none">
> > > 17:01 wtorek, 2016-1-12, David Boersma<br clear="none">
> <<a rel="nofollow" shape="rect" href="mailto:david.boersma@physics.uu.se" target="_blank">david.boersma@physics.uu.se</a> <mailto:<a rel="nofollow" shape="rect" href="mailto:david.boersma@physics.uu.se" target="_blank">david.boersma@physics.uu.se</a>><br clear="none">
> > <mailto:<a rel="nofollow" shape="rect" href="mailto:david.boersma@physics.uu.se" target="_blank">david.boersma@physics.uu.se</a><br clear="none">
> <mailto:<a rel="nofollow" shape="rect" href="mailto:david.boersma@physics.uu.se" target="_blank">david.boersma@physics.uu.se</a>>>><br clear="none">
> > > napisał(a):<br clear="none">
> > ><br clear="none">
> > ><br clear="none">
> > ><br clear="none">
> > ><br clear="none">
> > > Hi Michał,<br clear="none">
> > ><br clear="none">
> > > My first guess would be a memory problem. Could you check with some<br clear="none">
> > > resource monitor ("top" or "htop" on linux, "Activity Monitory" on<br clear="none">
> > > MacOSX) how much RAM is used on your machine, by which programs?<br clear="none">
> > ><br clear="none">
> > > It could be that other programs than GATE (e.g. a web browser) are<br clear="none">
> using<br clear="none">
> > > so much RAM that there is not enough available for your GATE<br clear="none">
> > > application. Then this is easily solved by quitting those other<br clear="none">
> programs.<br clear="none">
> > ><br clear="none">
> > > It could be that you configured GATE too optimistically, e.g. using a<br clear="none">
> > > scoring volume with too many voxels. Then you should either use a more<br clear="none">
> > > modest configuration, or run on a bigger machine.<br clear="none">
> > ><br clear="none">
> > > There are many other possible causes, but these are the easiest<br clear="none">
> ones, I<br clear="none">
> > > can think of. It would be good if you could tell us whether these are<br clear="none">
> > > already ruled out.<br clear="none">
> > ><br clear="none">
> > > Also: when reporting problems and asking for help, it could be helpful<br clear="none">
> > > if you would add some basic specs about the OS (+version) and the<br clear="none">
> > > hardware (in particular how much RAM your have). Which version of GATE<br clear="none">
> > > are you using, with which version of Geant4? How did you install<br clear="none">
> it? Did<br clear="none">
> > > you install it recently or long ago?<br clear="none">
> > ><br clear="none">
> > > HTH,<br clear="none">
> > > David<br clear="none">
> > ><br clear="none">
> > > Den 12/01/2016 kl. 15:55, skrev Michal Knap:<br clear="none">
> > > > Hi All,<br clear="none">
> > > > As i'm trying to simulate a minigammacamera i'm getting this error<br clear="none">
> > > message.<br clear="none">
> > > > I still do not know how to fix this.<br clear="none">
> > > > Can anybody know what is wrong?<br clear="none">
> > > > //<br clear="none">
> > > > /[Acquisition-0] Slice 0 from 0 to 37.5 s [slice=37.5 s], final<br clear="none">
> > stop at<br clear="none">
> > > > 150 s./<br clear="none">
> > > > /terminate called after throwing an instance of 'std::bad_alloc'/<br clear="none">
> > > > / what(): std::bad_alloc/<br clear="none">
> > > > /Przerwane (core dumped)/<br clear="none">
> > > > /<br clear="none">
> > > > /<br clear="none">
> > > > I'll be very thankful for any help.<br clear="none">
> > > ><br clear="none">
> > > > Thanks in advance<br clear="none">
> > > ><br clear="none">
> > > > Kind regards<br clear="none">
> > > > Michał Knap<br clear="none">
> > ><br clear="none">
> > > ><br clear="none">
> > > ><br clear="none">
> > > > _______________________________________________<br clear="none">
> > > > Gate-users mailing list<br clear="none">
> > > > <a rel="nofollow" shape="rect" href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">
Gate-users@lists.opengatecollaboration.org</a><br clear="none">
> <mailto:<a rel="nofollow" shape="rect" id="yiv3203938371yui_3_16_0_1_1452764539431_5361" href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a>><br clear="none">
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