<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">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">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">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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</blockquote>
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<div>
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<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
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>
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</div>
</div>
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</div>
</div>
</div>
</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>