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<p>Hi,</p>
<p><br>
</p>
<p>Using the Makefile, you must set the CASTOR_ROOT environment
variable to 1 in order to compile with ROOT.<br>
<br>
Using Cmake, what are the variables you set to ON ? I will try to
reproduce the missing separator errors you got.</p>
<p><br>
</p>
<p>Best,</p>
<p>Thibaut<br>
</p>
<p><br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 27/09/2019 17:12, STUTE Simon wrote:<br>
</div>
<blockquote type="cite" cite="mid:1569597262244.93281@chu-nantes.fr">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<style type="text/css" style="display:none"><!-- p { margin-top: 0px; margin-bottom: 0px; }--></style>
<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 tabindex="-1" style="display:inline-block; width:98%">
<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>De :</b>
Xinjie Cao <a class="moz-txt-link-rfc2396E" href="mailto:xinjie.cao@stonybrook.edu"><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"
moz-do-not-send="true">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_7954195775106884535divRplyFwdMsg"
dir="ltr"><font style="font-size:11pt"
face="Calibri, sans-serif" color="#000000"><b>De :</b>
Castor-users <<a
href="mailto:castor-users-bounces@lists.castor-project.org"
target="_blank" moz-do-not-send="true">castor-users-bounces@lists.castor-project.org</a>>
de la part de Xinjie Cao <<a
href="mailto:xinjie.cao@stonybrook.edu"
target="_blank" moz-do-not-send="true">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" moz-do-not-send="true">
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_7954195775106884535gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div><b><font
style="background-color:rgb(255,255,255)"
color="#000000">....................................................</font></b></div>
<div><b><font
style="background-color:rgb(255,255,255)"
color="#000000"><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"
moz-do-not-send="true">
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
src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ"
moz-do-not-send="true"
width="200" height="28"> <img
src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download"
moz-do-not-send="true"
width="200" height="33"></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br clear="all">
<br>
-- <br>
<div dir="ltr" class="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div><b><font
style="background-color:rgb(255,255,255)"
color="#000000">....................................................</font></b></div>
<div><b><font
style="background-color:rgb(255,255,255)"
color="#000000"><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" moz-do-not-send="true">
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
src="https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ"
moz-do-not-send="true" width="200"
height="28"> <img
src="https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download"
moz-do-not-send="true" width="200"
height="33"></div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Castor-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Castor-users@lists.castor-project.org">Castor-users@lists.castor-project.org</a>
<a class="moz-txt-link-freetext" href="http://lists.castor-project.org/listinfo/castor-users">http://lists.castor-project.org/listinfo/castor-users</a>
</pre>
</blockquote>
<pre class="moz-signature" 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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