<div dir="ltr">Hi Tmerlin,<div><br></div><div>It looks like there is no error now, i will let you know if the error appears again. Thanks!</div><div><br></div><div>Best,</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jun 19, 2020 at 2:56 PM tmerlin <<a href="mailto:Thibaut.Merlin@univ-brest.fr">Thibaut.Merlin@univ-brest.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi Xinjie,</p>
<p>Thanks for your data. I could reproduce your error and it seems
it is linked to the Joseph projector. In particular, there is a
hard-coded tolerance factor used to compute the planes which are
crossed by the lines. Decreasing that factor seems to remove the
crash in my tests. <br>
</p>
<p>So a quick fix may be to reduce that threshold (you can replace
the <i>src/projector/iProjectorJoseph.cc</i> file by the one in
attached, then recompile castor).</p>
<p>I am not sure yet whether the crash is limited to that factor.
Let me know if it fixes the error for you.<br>
</p>
<p>Best,<br>
Thibaut<br>
</p>
<div>On 14/06/2020 02:01, Xinjie Cao wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hi tmerlin,</div>
<div><br>
</div>
<div>Here is my dataset, geometry and entire error log. Hope you
could find something!
<div class="gmail_chip gmail_drive_chip" style="width:396px;height:18px;max-height:18px;background-color:rgb(245,245,245);padding:5px;color:rgb(34,34,34);font-family:arial;font-style:normal;font-weight:bold;font-size:13px;border:1px solid rgb(221,221,221);line-height:1"><a href="https://drive.google.com/a/stonybrook.edu/file/d/1wC4X99y4ATwDWGdrh8OoHfPmeA8l_m2G/view?usp=drive_web" style="display:inline-block;max-width:366px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0px;border:none" target="_blank"><img style="vertical-align: bottom; border: none;" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <span dir="ltr" style="color:rgb(17,85,204);text-decoration:none;vertical-align:bottom">Brain_Double_df.Cdf</span></a><img style="opacity: 0.55; float: right; display: none;"></div>
<div class="gmail_chip gmail_drive_chip" style="width:396px;height:18px;max-height:18px;background-color:rgb(245,245,245);padding:5px;color:rgb(34,34,34);font-family:arial;font-style:normal;font-weight:bold;font-size:13px;border:1px solid rgb(221,221,221);line-height:1"><a href="https://drive.google.com/a/stonybrook.edu/file/d/1CFoCBMTOVrLgbP-chCu4bXVf379jWEQR/view?usp=drive_web" style="display:inline-block;max-width:366px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap;text-decoration:none;padding:1px 0px;border:none" target="_blank"><img style="vertical-align: bottom; border: none;" src="https://ssl.gstatic.com/docs/doclist/images/icon_10_generic_list.png"> <span dir="ltr" style="color:rgb(17,85,204);text-decoration:none;vertical-align:bottom">Brain_Double_df.Cdh</span></a><img style="opacity: 0.55; float: right; display: none;"></div>
</div>
<div><br>
</div>
<div>Best,<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Tue, Jun 9, 2020 at 10:57
AM tmerlin <<a href="mailto:Thibaut.Merlin@univ-brest.fr" target="_blank">Thibaut.Merlin@univ-brest.fr</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi Xinjie,</p>
<p>Does the crash occur directly after you launch the the
reconstruction. Could you run it with -vb 3 to have a bit
more feedback ?</p>
<p>There is no reason why you couldn't change reconstruction
parameters between two consecutive reconstructions. <br>
</p>
<p>Maybe you could send us/upload your dataset &
geometry file so we have a closer look at the problem ?<br>
</p>
<p>Best regards,</p>
<p><br>
</p>
<div>On 08/06/2020 17:20, Xinjie Cao wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Thibaut and Simon,
<div><br>
</div>
<div>I have compiled two different Castor versions for
multi-thread running and single core in
separate directories, respectively. The multi-thread
is running well now, but single core test had a
problem when I move from a lower resolution
configuration to a higher one like below,</div>
<div><br>
</div>
<div><b>First recon try</b>:</div>
<div>```</div>
<div>castor-recon -df Brain_Double_df.Cdh -opti MLEM -it
10:16 -proj joseph -conv gaussian,4.,4.5,3.5::psf -dim
100,100,16 -vox 2.5,2.5,10. -oit -1 -dout
Brain_Double<br>
</div>
<div>.........</div>
<div>iIterativeAlgorithm::StepAfterSubsetLoop() ->
Save image at iteration 10<br>
vAlgorithm::IterateCPU() -> Total time spent |
User: 3699 sec | CPU: 3.6990100e+03 sec<br>
sChronoManager::Display() -> Results from the
profiling<br>
.........<br>
--> Custom update step 1: 00 hours 00 mins 00
secs 000 ms<br>
</div>
<div>```</div>
<div><b>Second recon try</b>:</div>
<div>```</div>
<div>castor-recon -df Brain_Double_df.Cdh -opti MLEM -it
2:10 -proj joseph -conv gaussian,4.,4.5,3.5::psf -dim
200,200,16 -vox 1.25,1.25,10. -oit -1 -dout
Brain_Double_2<br>
</div>
<div><br>
</div>
<div>*** Break *** segmentation violation<br>
===========================================================<br>
There was a crash.<br>
This is the entire stack trace of all threads:<br>
===========================================================<br>
#0 0x00007fc5feb0641c in waitpid () from
/lib64/libc.so.6<br>
#1 0x00007fc5fea83f12 in do_system () from
/lib64/libc.so.6<br>
#2 0x00007fc60384e0c4 in TUnixSystem::StackTrace() ()
from /home/goldan/GATE/root/lib/libCore.so.6.18<br>
#3 0x00007fc6038507fc in
TUnixSystem::DispatchSignals(ESignals) () from
/home/goldan/GATE/root/lib/libCore.so.6.18<br>
#4 <signal handler called><br>
#5 0x00007fc5feac6eec in free () from
/lib64/libc.so.6<br>
#6 0x000000000044e9ba in
oSensitivityGenerator::ComputeSensitivityFromScanner(int)
()<br>
#7 0x000000000044f425 in
oSensitivityGenerator::LaunchCPU() ()<br>
#8 0x000000000042b7bc in main ()<br>
===========================================================<br>
<br>
<br>
The lines below might hint at the cause of the crash.<br>
You may get help by asking at the ROOT forum <a href="http://root.cern.ch/forum" target="_blank">http://root.cern.ch/forum</a><br>
Only if you are really convinced it is a bug in ROOT
then please submit a<br>
report at <a href="http://root.cern.ch/bugs" 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>
#5 0x00007fc5feac6eec in free () from
/lib64/libc.so.6<br>
#6 0x000000000044e9ba in
oSensitivityGenerator::ComputeSensitivityFromScanner(int)
()<br>
#7 0x000000000044f425 in
oSensitivityGenerator::LaunchCPU() ()<br>
#8 0x000000000042b7bc in main ()<br>
===========================================================<br>
</div>
<div>````</div>
<div>Does that mean I cannot modify the iteration
setting or any setting between two consecutive
reconstructions? Or was there something wrong other
than configurations? Thank you!</div>
<div><br>
</div>
<div>Best,</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, May 29, 2020
at 3:07 PM tmerlin <<a href="mailto:Thibaut.Merlin@univ-brest.fr" target="_blank">Thibaut.Merlin@univ-brest.fr</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Hi Xinjie,</p>
<p>Hard to say what's going wrong without having the
data because memory errors could come from a wide
number of things, but we didn't experienced this
kind of issue with reconstructing large images.<br>
</p>
<p>As Simon suggested, in the case you compiled the
code multiple time with the castor makefile, such
errors could occur if the files generated from the
previous compilation are not cleaned.</p>
<p>Best,<br>
Thibaut<br>
</p>
<p><br>
</p>
<div>On 28/05/2020 16:35, Xinjie Cao wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Thibaut,
<div><br>
</div>
<div>Thanks for your response! I am trying to
recon a list-mode data in root. I got this
problem when I changed my recon parameters to
a higher resolution, like from 6mm voxel size
to 1.5mm voxel size.</div>
<div><br>
</div>
<div>Best,</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, May
28, 2020 at 7:04 AM Thibaut Merlin <<a href="mailto:Thibaut.Merlin@univ-brest.fr" target="_blank">Thibaut.Merlin@univ-brest.fr</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="font-family:Arial;font-size:14px">
<p> Hi Xinjie,<br>
<br>
On which kind of dataset did you get this
problem ? Did it occur on every data you
tried to reconstruct or just some of them
?<br>
<br>
Best,<br>
Thibaut<br>
<br>
Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>>
a écrit :</p>
<blockquote style="border-left:2px solid blue;margin-left:2px;padding-left:12px" type="cite">
<div dir="ltr">
<div dir="ltr"> Dear all,
<div> </div>
<div> I am testing CASToR performance
on multi-thread running, but it
looks like using the multi-thread
function is not very stable. </div>
<div> Before applying multi-thread to
recon, every job was good. But recon
jobs always dumped with unrecognized
problem since I used multi-thread as
below:</div>
<div> ```</div>
<div> *** Error in `castor-recon':
munmap_chunk(): invalid pointer:
0x0000000002259380 ***</div>
<div> ```</div>
<div> Did anyone ever see this problem
before? </div>
<div> Any answer will be highly
appreciated! Thank you!</div>
<div> </div>
<div> Best,</div>
<div> </div>
</div>
</div>
</blockquote>
<br>
<br>
</div>
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<pre cols="72">--
Thibaut MERLIN -- PhD
Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
Institut Brestois de recherche en Bio-Santé (IBRBS)
12 Avenue Foch, 29200 Brest, FRANCE
Tel: 06.75.12.24.90</pre>
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<div><b><font color="#000000">....................................................</font></b><br>
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<div><b><span>Xinjie Cao</span></b><br>
</div>
<div><b><font size="1" face="arial black,
sans-serif">M.E. /
Ph.D. student</font></b></div>
<div><b><font size="1" face="arial black,
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Medical Imaging
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<div><b><font size="1" face="arial black,
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Science Center Level
8</font></b></div>
<div><b><font size="1" face="arial black,
sans-serif">Stony
Brook, NY
11794-8460 </font></b></div>
<div><b><font size="1" face="arial black,
sans-serif">Tel: +1
(631)202-9445</font></b></div>
<div><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><b><font size="1" face="arial
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<div>
<div><b><font color="#000000">....................................................</font></b></div>
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</blockquote>
<pre cols="72">--
Thibaut MERLIN -- PhD
Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
Institut Brestois de recherche en Bio-Santé (IBRBS)
12 Avenue Foch, 29200 Brest, FRANCE
Tel: 06.75.12.24.90</pre>
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<div dir="ltr">
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<div dir="ltr">
<div><b><font color="#000000">....................................................</font></b><br>
</div>
<div><b><span>Xinjie Cao</span></b><br>
</div>
<div><b><font size="1" face="arial
black, sans-serif">M.E. /
Ph.D. student</font></b></div>
<div><b><font size="1" face="arial
black, sans-serif">Research
Project Assistant</font></b></div>
<div><b><font size="1" face="arial
black, sans-serif">Department
of Electrical and Computer
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<div><b><font size="1" face="arial
black, sans-serif">Novel
Medical Imaging Technologies
Lab</font></b></div>
<div><b><font size="1" face="arial
black, sans-serif">Health
Science Center Level 8</font></b></div>
<div><b><font size="1" face="arial
black, sans-serif">Stony
Brook, NY 11794-8460 </font></b></div>
<div><b><font size="1" face="arial
black, sans-serif">Tel: +1
(631)202-9445</font></b></div>
<div><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><b><font size="1" face="arial black,
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<div>
<div><b><font color="#000000">....................................................</font></b></div>
<div>It is prohibited to
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</blockquote>
<pre cols="72">--
Thibaut MERLIN -- PhD
Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
Institut Brestois de recherche en Bio-Santé (IBRBS)
12 Avenue Foch, 29200 Brest, FRANCE
Tel: 06.75.12.24.90</pre>
</div>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" 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 dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div><b><font color="#000000">....................................................</font></b><br></div><div><b><span style="color:rgb(153,0,0);font-family:"arial black",sans-serif;font-size:x-small">Xinjie Cao</span></b><br></div><div><b><font size="1" face="arial black, sans-serif">M.E. / Ph.D. student</font></b></div><div><b><font size="1" face="arial black, sans-serif">Research Project Assistant</font></b></div><div><b><font size="1" face="arial black, sans-serif">Department of Electrical and Computer Engineering & Radiology </font></b></div><div><b><font size="1" face="arial black, sans-serif">Novel Medical Imaging Technologies Lab</font></b></div><div><b><font size="1" face="arial black, sans-serif">Health Science Center Level 8</font></b></div><div><b><font size="1" face="arial black, sans-serif">Stony Brook, NY 11794-8460 </font></b></div><div><b><font size="1" face="arial black, sans-serif">Tel: +1 (631)202-9445</font></b></div><div><a href="https://you.stonybrook.edu/goldan/people/" target="_blank">you.stonybrook.edu/goldan/people/</a><b><font size="1" face="arial black, sans-serif"><br></font></b></div><div><font size="1" face="arial black, sans-serif"><b>email: </b><a href="mailto:xinjie.cao@stonybrook.edu" target="_blank"><b>xinjie.cao@stonybroo</b>k.edu</a></font></div><div><font size="1" face="arial black, sans-serif"><br></font></div><div><font size="1" face="arial black, sans-serif"> </font><img src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ" width="200" height="28"> <img src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download" width="200" height="33"></div><div><div><b><font color="#000000">....................................................</font></b></div><div>It is prohibited to distribute or publish the files attached to any other people unless you get permission from the writer himself. All rights reserved.</div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>