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<body dir="ltr" style="font-size:12pt;color:#000000;background-color:#FFFFFF;font-family:Calibri,Arial,Helvetica,sans-serif;">
<p>Hi,<br>
</p>
<p><br>
</p>
<p>I have no idea about that, I am neither used to cmake nor to root.<br>
</p>
<p>Also please use the mailing list as other people may help you or may find useful information.<br>
</p>
<p><br>
</p>
<p>Best<br>
</p>
<p>Simon<br>
</p>
<p><br>
</p>
<div style="color: rgb(33, 33, 33);">
<hr tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De :</b> Xinjie Cao <xinjie.cao@stonybrook.edu><br>
<b>Envoyé :</b> vendredi 27 septembre 2019 18:10<br>
<b>À :</b> STUTE Simon<br>
<b>Objet :</b> Re: [Castor-users] About CASToR Installation</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>Hi Simon,</div>
<div><br>
</div>
<div>Thank you for your reply! I disable the MPI support and but we really want to link it with ROOT to do data process. So I try to link to ROOT when I use CMAKE to configure variables and make install. Here is the error I get when I try to generate binaries:<br>
</div>
<div><br>
</div>
<div>```</div>
<div> CMake Error at CMakeLists.txt:411 (add_executable):<br>
[root@localhost castor_v2.1-build]# " links to item "<br>
<br>
ROOT is built with CMake, see <a href="https://root.cern/building-root">https://root.cern/building-root</a><br>
Please run<br>
mkdir obj" which has leading or trailing whitespace. This is now an<br>
error according to policy CMP0004.<br>
<br>
<br>
<br>
CMake Error at CMakeLists.txt:411 (add_executable):<br>
Target "castor-scannerLUTExplorer" links to item " cd obj" which has<br>
leading or trailing whitespace. This is now an error according to policy<br>
CMP0004.<br>
</div>
<div>```</div>
<div>I have already installed ROOT in another directory under my home directory and set configure path to its configure file, then how do I handle this problem? Thank you!!</div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
</div>
<div dir="ltr"></div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Sep 27, 2019 at 11:12 AM STUTE Simon <<a href="mailto:simon.stute@chu-nantes.fr" target="_blank">simon.stute@chu-nantes.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 dir="ltr" style="font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255); font-family:Calibri,Arial,Helvetica,sans-serif">
<p>I did not realize that you may want to link with ROOT.<br>
</p>
<p>In this case, it is still better to use the CMake.<br>
</p>
<p>Anyway, try again the CMake but just disable the MPI support (do you really need it? Will you launch castor on a cluster of servers or computers?)<br>
</p>
<p>Simon<br>
</p>
<p><br>
</p>
<div style="color:rgb(33,33,33)">
<hr style="display:inline-block; width:98%">
<div id="gmail-m_2845153519592810334gmail-m_1920313804455481799divRplyFwdMsg" dir="ltr">
<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De :</b> Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>><br>
<b>Envoyé :</b> vendredi 27 septembre 2019 16:42<br>
<b>À :</b> STUTE Simon<br>
<b>Objet :</b> Re: [Castor-users] About CASToR Installation</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>Hi Simon,</div>
<div><br>
</div>
<div>Thanks for you quick respond! I delete the build directory for installation used by cmake tool and reunpacked a new CASToR source code. Then I follow your steps and do installation using provided Makefile, but it still failed for some reason. Following
is the shell respond I got this time. I cut most of it and show you 3 most often parts of all respond. Thank you for you kindly help again!<br>
</div>
<div>```</div>
<div>make: root-config: Command not found<br>
make: root-config: Command not found<br>
make: root-config: Command not found<br>
make: root-config: Command not found<br>
make: root-config: Command not found<br>
make: root-config: Command not found<br>
make: root-config: Command not found<br>
make: root-config: Command not found<br>
Making dependencies for castor-recon.cc ...<br>
Making dependencies for toolkits/castor-scannerLUTExplorer.cc ...<br>
Making dependencies for toolkits/castor-datafileExplorer.cc ...<br>
Making dependencies for toolkits/castor-datafileConversionEx.cc ...<br>
Making dependencies for toolkits/castor-PetScannerLutEx.cc ...<br>
make: root-config: Command not found<br>
Making dependencies for toolkits/castor-datafileShuffler.cc ...<br>
Making dependencies for toolkits/castor-GATEMacToGeom.cc ...<br>
make: root-config: Command not found<br>
make: root-config: Command not found<br>
.....<br>
<span style="color:rgb(255,0,0)">toolkits/castor-datafileConversionEx.cc:49:21: fatal error: TROOT.h: No such file or directory<br>
#include "TROOT.h"<br>
^<br>
compilation terminated.<br>
In file included from toolkits/castor-GATERootToCastor.cc:38:0:<br>
include/management/gDataConversionUtilities.hh:44:21: fatal error: TROOT.h: No such file or directory<br>
#include "TROOT.h"<br>
^<br>
In file included from toolkits/castor-GATEMacToGeom.cc:42:0:<br>
include/management/gDataConversionUtilities.hh:44:21: fatal error: TROOT.h: No such file or directory</span><br>
#include "TROOT.h"<br>
^<br>
compilation terminated.<br>
compilation terminated.<br>
make: root-config: Command not found<br>
make: root-config: Command not found<br>
make: root-config: Command not found<br>
Making dependencies for projector/iProjectorClassicSiddon.cc ...<br>
Making dependencies for projector/iProjectorJoseph.cc ...<br>
make: root-config: Command not found<br>
make: root-config: Command not found<br>
......<br>
Compiling datafile/iDataFileCT.cc ...<br>
src/algorithm/oIterativeAlgorithm.cc:575:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]<br>
#pragma omp parallel for private(index) schedule(static, 1)<br>
^<br>
src/algorithm/oIterativeAlgorithm.cc:1009:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]<br>
#pragma omp critical(increment_waiting_threads)<br>
^<br>
src/algorithm/oIterativeAlgorithm.cc:1031:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]<br>
#pragma omp flush(m_releaseThreads)<br>
^<br>
src/algorithm/oIterativeAlgorithm.cc:1050:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]<br>
#pragma omp flush(m_nbThreadsWaiting) // Check any change in m_nbThreadsWaiting<br>
^<br>
src/algorithm/oIterativeAlgorithm.cc:1069:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]<br>
#pragma omp flush(m_releaseThreads) // Make sure the value of m_releaseThreads is propagated to other threads<br>
^<br>
src/algorithm/oIterativeAlgorithm.cc:1071:0: warning: ignoring #pragma omp flush [-Wunknown-pragmas]<br>
#pragma omp flush(m_nbThreadsWaiting) // Same for m_nbThreadsWaiting<br>
^<br>
......<br>
make: root-config: Command not found<br>
make: root-config: Command not found<br>
Compiling image/oImageConvolverManager.cc ...<br>
Compiling image/iDeformationTemplate.cc ...<br>
src/image/vImageConvolver.cc:305:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]<br>
#pragma omp parallel for private(z) schedule(guided)<br>
^<br>
src/image/vImageConvolver.cc:358:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]<br>
#pragma omp parallel for private(z) schedule(guided)<br>
^<br>
make: root-config: Command not found<br>
Compiling management/sRandomNumberGenerator.cc ...<br>
make: *** No rule to make target `build/__src_management/gDataConversionUtilities.d', needed by `build/__src_management/gDataConversionUtilities.o'. Stop.<br>
make: *** Waiting for unfinished jobs....<br>
Compiling management/sOutputManager.cc ...<br>
</div>
<div>```</div>
<div><br>
</div>
<div><br>
</div>
<div>Best,<br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Fri, Sep 27, 2019 at 4:23 AM STUTE Simon <<a href="mailto:simon.stute@chu-nantes.fr" target="_blank">simon.stute@chu-nantes.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 dir="ltr" style="font-size:12pt; color:rgb(0,0,0); background-color:rgb(255,255,255); font-family:Calibri,Arial,Helvetica,sans-serif">
<p>Hi,<br>
</p>
<p><br>
</p>
<p>Could you try with the standalone Makefile to see what happens ?<br>
</p>
<p><br>
</p>
<p>To do so :<br>
</p>
<p> - export the CASTOR_MPI variable using "export CASTOR_MPI=1"<br>
</p>
<p> - delete traces of the Cmakefile results<br>
</p>
<p> - run "make clean"<br>
</p>
<p> - run again "make"<br>
</p>
<p><br>
</p>
<p>Tell us back what happened.<br>
</p>
<p><br>
</p>
<p>Best<br>
</p>
<p>Simon<br>
</p>
<p><br>
</p>
<div style="color:rgb(33,33,33)">
<hr style="display:inline-block; width:98%">
<div id="gmail-m_2845153519592810334gmail-m_1920313804455481799gmail-m_7954195775106884535divRplyFwdMsg" dir="ltr">
<font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>De :</b> Castor-users <<a href="mailto:castor-users-bounces@lists.castor-project.org" target="_blank">castor-users-bounces@lists.castor-project.org</a>> de la part de Xinjie Cao <<a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">xinjie.cao@stonybrook.edu</a>><br>
<b>Envoyé :</b> jeudi 26 septembre 2019 22:36<br>
<b>À :</b> <a href="mailto:castor-users@lists.castor-project.org" target="_blank">
castor-users@lists.castor-project.org</a><br>
<b>Objet :</b> [Castor-users] About CASToR Installation</font>
<div> </div>
</div>
<div>
<div dir="ltr">
<div>Hi everyone,<br>
</div>
<div><br>
</div>
<div>I am installing CASToR for our PET research, but I met some problems with it. When I use Cmake to configure compilation of CASToR, the MPI cannot be built in CASToR, and cmake always gave error messages like this:</div>
<div>```<br>
</div>
<div>[user1@localhost castor_v2.1-build]$ make -j16<br>
CMakeFiles/castor-datafileExplorer.dir/flags.make:10: *** missing separator. Stop.<br>
CMakeFiles/castor-datafileConversionEx.dir/flags.make:10: *** missing separator. Stop.<br>
make[1]: *** [CMakeFiles/castor-datafileExplorer.dir/all] Error 2<br>
make[1]: CMakeFiles/castor-scannerLUTExplorer.dir/flags.make:10: *** *** Waiting for unfinished jobs....<br>
missing separator. Stop.<br>
make[1]: *** [CMakeFiles/castor-datafileConversionEx.dir/all] Error 2<br>
make[1]: *** [CMakeFiles/castor-scannerLUTExplorer.dir/all] Error 2<br>
CMakeFiles/castor-GATEMacToGeom.dir/flags.make:10: *** missing separator. Stop.<br>
make[1]: *** [CMakeFiles/castor-GATEMacToGeom.dir/all] Error 2<br>
CMakeFiles/castor-GATERootToCastor.dir/flags.make:10: *** missing separator. Stop.<br>
make[1]: *** [CMakeFiles/castor-GATERootToCastor.dir/all] Error 2<br>
CMakeFiles/castor-PetScannerLutEx.dir/flags.make:10: *** missing separator. Stop.<br>
make[1]: *** [CMakeFiles/castor-PetScannerLutEx.dir/all] Error 2<br>
CMakeFiles/castor-recon.dir/flags.make:10: *** missing separator. Stop.<br>
make[1]: *** [CMakeFiles/castor-recon.dir/all] Error 2<br>
make: *** [all] Error 2</div>
<div>```</div>
<div>Anyone can help me? Any reply will be highly appreciated!!!</div>
<div><br>
</div>
<div>Best,<br>
</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
-- <br>
<div dir="ltr" class="gmail-m_2845153519592810334gmail-m_1920313804455481799gmail-m_7954195775106884535gmail_signature">
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<div><b><font color="#000000" style="background-color:rgb(255,255,255)">....................................................</font></b></div>
<div><b><font color="#000000" style="background-color:rgb(255,255,255)"><br>
</font></b></div>
<font size="1" face="arial black, sans-serif" color="#990000">Xinjie Cao</font>
<div><font size="1" face="arial black, sans-serif">M.E. / Ph.D. student</font></div>
<div><font size="1" face="arial black, sans-serif">Department of Electrical and Computer Engineering & Radiology </font></div>
<div><font size="1" face="arial black, sans-serif">Novel Medical Imaging Technologies Lab</font></div>
<div><font size="1" face="arial black, sans-serif">Health Science Center Level 8</font></div>
<div><font size="1" face="arial black, sans-serif">Stony Brook, NY 11794-8460 </font></div>
<div><font size="1" face="arial black, sans-serif">Tel: +1 (631)202-9445</font></div>
<div><font size="1" face="arial black, sans-serif">email: <a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">
xinjie.cao@stonybrook.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 width="200" height="28" src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ"> <img width="200" height="33" src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download"></div>
</div>
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</div>
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</blockquote>
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-- <br>
<div dir="ltr" class="gmail-m_2845153519592810334gmail-m_1920313804455481799gmail_signature">
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<div><b><font color="#000000" style="background-color:rgb(255,255,255)">....................................................</font></b></div>
<div><b><font color="#000000" style="background-color:rgb(255,255,255)"><br>
</font></b></div>
<font size="1" face="arial black, sans-serif" color="#990000">Xinjie Cao</font>
<div><font size="1" face="arial black, sans-serif">M.E. / Ph.D. student</font></div>
<div><font size="1" face="arial black, sans-serif">Department of Electrical and Computer Engineering & Radiology </font></div>
<div><font size="1" face="arial black, sans-serif">Novel Medical Imaging Technologies Lab</font></div>
<div><font size="1" face="arial black, sans-serif">Health Science Center Level 8</font></div>
<div><font size="1" face="arial black, sans-serif">Stony Brook, NY 11794-8460 </font></div>
<div><font size="1" face="arial black, sans-serif">Tel: +1 (631)202-9445</font></div>
<div><font size="1" face="arial black, sans-serif">email: <a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">
xinjie.cao@stonybrook.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 width="200" height="28" src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ"> <img width="200" height="33" src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download"></div>
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-- <br>
<div dir="ltr" class="gmail-m_2845153519592810334gmail_signature">
<div dir="ltr">
<div>
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<div dir="ltr">
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<div><b><font color="#000000" style="background-color:rgb(255,255,255)">....................................................</font></b></div>
<div><b><font color="#000000" style="background-color:rgb(255,255,255)"><br>
</font></b></div>
<font size="1" face="arial black, sans-serif" color="#990000">Xinjie Cao</font>
<div><font size="1" face="arial black, sans-serif">M.E. / Ph.D. student</font></div>
<div><font size="1" face="arial black, sans-serif">Department of Electrical and Computer Engineering & Radiology </font></div>
<div><font size="1" face="arial black, sans-serif">Novel Medical Imaging Technologies Lab</font></div>
<div><font size="1" face="arial black, sans-serif">Health Science Center Level 8</font></div>
<div><font size="1" face="arial black, sans-serif">Stony Brook, NY 11794-8460 </font></div>
<div><font size="1" face="arial black, sans-serif">Tel: +1 (631)202-9445</font></div>
<div><font size="1" face="arial black, sans-serif">email: <a href="mailto:xinjie.cao@stonybrook.edu" target="_blank">
xinjie.cao@stonybrook.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 width="200" height="28" src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ"> <img width="200" height="33" src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download"></div>
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