[Castor-users] About CASToR Installation
tmerlin
Thibaut.Merlin at univ-brest.fr
Fri Sep 27 17:54:11 CEST 2019
Hi,
Using the Makefile, you must set the CASTOR_ROOT environment variable to
1 in order to compile with ROOT.
Using Cmake, what are the variables you set to ON ? I will try to
reproduce the missing separator errors you got.
Best,
Thibaut
On 27/09/2019 17:12, STUTE Simon wrote:
>
> I did not realize that you may want to link with ROOT.
>
> In this case, it is still better to use the CMake.
>
> 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?)
>
> Simon
>
>
> ------------------------------------------------------------------------
> *De :* Xinjie Cao <xinjie.cao at stonybrook.edu>
> *Envoyé :* vendredi 27 septembre 2019 16:42
> *À :* STUTE Simon
> *Objet :* Re: [Castor-users] About CASToR Installation
> Hi Simon,
>
> 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!
> ```
> make: root-config: Command not found
> make: root-config: Command not found
> make: root-config: Command not found
> make: root-config: Command not found
> make: root-config: Command not found
> make: root-config: Command not found
> make: root-config: Command not found
> make: root-config: Command not found
> Making dependencies for castor-recon.cc ...
> Making dependencies for toolkits/castor-scannerLUTExplorer.cc ...
> Making dependencies for toolkits/castor-datafileExplorer.cc ...
> Making dependencies for toolkits/castor-datafileConversionEx.cc ...
> Making dependencies for toolkits/castor-PetScannerLutEx.cc ...
> make: root-config: Command not found
> Making dependencies for toolkits/castor-datafileShuffler.cc ...
> Making dependencies for toolkits/castor-GATEMacToGeom.cc ...
> make: root-config: Command not found
> make: root-config: Command not found
> .....
> toolkits/castor-datafileConversionEx.cc:49:21: fatal error: TROOT.h:
> No such file or directory
> #include "TROOT.h"
> ^
> compilation terminated.
> In file included from toolkits/castor-GATERootToCastor.cc:38:0:
> include/management/gDataConversionUtilities.hh:44:21: fatal error:
> TROOT.h: No such file or directory
> #include "TROOT.h"
> ^
> In file included from toolkits/castor-GATEMacToGeom.cc:42:0:
> include/management/gDataConversionUtilities.hh:44:21: fatal error:
> TROOT.h: No such file or directory
> #include "TROOT.h"
> ^
> compilation terminated.
> compilation terminated.
> make: root-config: Command not found
> make: root-config: Command not found
> make: root-config: Command not found
> Making dependencies for projector/iProjectorClassicSiddon.cc ...
> Making dependencies for projector/iProjectorJoseph.cc ...
> make: root-config: Command not found
> make: root-config: Command not found
> ......
> Compiling datafile/iDataFileCT.cc ...
> src/algorithm/oIterativeAlgorithm.cc:575:0: warning: ignoring #pragma
> omp parallel [-Wunknown-pragmas]
> #pragma omp parallel for private(index) schedule(static, 1)
> ^
> src/algorithm/oIterativeAlgorithm.cc:1009:0: warning: ignoring #pragma
> omp critical [-Wunknown-pragmas]
> #pragma omp critical(increment_waiting_threads)
> ^
> src/algorithm/oIterativeAlgorithm.cc:1031:0: warning: ignoring #pragma
> omp flush [-Wunknown-pragmas]
> #pragma omp flush(m_releaseThreads)
> ^
> src/algorithm/oIterativeAlgorithm.cc:1050:0: warning: ignoring #pragma
> omp flush [-Wunknown-pragmas]
> #pragma omp flush(m_nbThreadsWaiting) // Check any change in
> m_nbThreadsWaiting
> ^
> src/algorithm/oIterativeAlgorithm.cc:1069:0: warning: ignoring #pragma
> omp flush [-Wunknown-pragmas]
> #pragma omp flush(m_releaseThreads) // Make sure the value of
> m_releaseThreads is propagated to other threads
> ^
> src/algorithm/oIterativeAlgorithm.cc:1071:0: warning: ignoring #pragma
> omp flush [-Wunknown-pragmas]
> #pragma omp flush(m_nbThreadsWaiting) // Same for m_nbThreadsWaiting
> ^
> ......
> make: root-config: Command not found
> make: root-config: Command not found
> Compiling image/oImageConvolverManager.cc ...
> Compiling image/iDeformationTemplate.cc ...
> src/image/vImageConvolver.cc:305:0: warning: ignoring #pragma omp
> parallel [-Wunknown-pragmas]
> #pragma omp parallel for private(z) schedule(guided)
> ^
> src/image/vImageConvolver.cc:358:0: warning: ignoring #pragma omp
> parallel [-Wunknown-pragmas]
> #pragma omp parallel for private(z) schedule(guided)
> ^
> make: root-config: Command not found
> Compiling management/sRandomNumberGenerator.cc ...
> make: *** No rule to make target
> `build/__src_management/gDataConversionUtilities.d', needed by
> `build/__src_management/gDataConversionUtilities.o'. Stop.
> make: *** Waiting for unfinished jobs....
> Compiling management/sOutputManager.cc ...
> ```
>
>
> Best,
>
> On Fri, Sep 27, 2019 at 4:23 AM STUTE Simon <simon.stute at chu-nantes.fr
> <mailto:simon.stute at chu-nantes.fr>> wrote:
>
> Hi,
>
>
> Could you try with the standalone Makefile to see what happens ?
>
>
> To do so :
>
> - export the CASTOR_MPI variable using "export CASTOR_MPI=1"
>
> - delete traces of the Cmakefile results
>
> - run "make clean"
>
> - run again "make"
>
>
> Tell us back what happened.
>
>
> Best
>
> Simon
>
>
> ------------------------------------------------------------------------
> *De :* Castor-users <castor-users-bounces at lists.castor-project.org
> <mailto:castor-users-bounces at lists.castor-project.org>> de la part
> de Xinjie Cao <xinjie.cao at stonybrook.edu
> <mailto:xinjie.cao at stonybrook.edu>>
> *Envoyé :* jeudi 26 septembre 2019 22:36
> *À :* castor-users at lists.castor-project.org
> <mailto:castor-users at lists.castor-project.org>
> *Objet :* [Castor-users] About CASToR Installation
> Hi everyone,
>
> 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:
> ```
> [user1 at localhost castor_v2.1-build]$ make -j16
> CMakeFiles/castor-datafileExplorer.dir/flags.make:10: *** missing
> separator. Stop.
> CMakeFiles/castor-datafileConversionEx.dir/flags.make:10: ***
> missing separator. Stop.
> make[1]: *** [CMakeFiles/castor-datafileExplorer.dir/all] Error 2
> make[1]: CMakeFiles/castor-scannerLUTExplorer.dir/flags.make:10:
> *** *** Waiting for unfinished jobs....
> missing separator. Stop.
> make[1]: *** [CMakeFiles/castor-datafileConversionEx.dir/all] Error 2
> make[1]: *** [CMakeFiles/castor-scannerLUTExplorer.dir/all] Error 2
> CMakeFiles/castor-GATEMacToGeom.dir/flags.make:10: *** missing
> separator. Stop.
> make[1]: *** [CMakeFiles/castor-GATEMacToGeom.dir/all] Error 2
> CMakeFiles/castor-GATERootToCastor.dir/flags.make:10: *** missing
> separator. Stop.
> make[1]: *** [CMakeFiles/castor-GATERootToCastor.dir/all] Error 2
> CMakeFiles/castor-PetScannerLutEx.dir/flags.make:10: *** missing
> separator. Stop.
> make[1]: *** [CMakeFiles/castor-PetScannerLutEx.dir/all] Error 2
> CMakeFiles/castor-recon.dir/flags.make:10: *** missing separator.
> Stop.
> make[1]: *** [CMakeFiles/castor-recon.dir/all] Error 2
> make: *** [all] Error 2
> ```
> Anyone can help me? Any reply will be highly appreciated!!!
>
> Best,
>
>
>
> --
> *....................................................*
> *
> *
> Xinjie Cao
> M.E. / Ph.D. student
> Department of Electrical and Computer Engineering & Radiology
> Novel Medical Imaging Technologies Lab
> Health Science Center Level 8
> Stony Brook, NY 11794-8460
> Tel: +1 (631)202-9445
> email: xinjie.cao at stonybrook.edu <mailto:xinjie.cao at stonybrook.edu>
>
>
>
> --
> *....................................................*
> *
> *
> Xinjie Cao
> M.E. / Ph.D. student
> Department of Electrical and Computer Engineering & Radiology
> Novel Medical Imaging Technologies Lab
> Health Science Center Level 8
> Stony Brook, NY 11794-8460
> Tel: +1 (631)202-9445
> email: xinjie.cao at stonybrook.edu <mailto:xinjie.cao at stonybrook.edu>
>
>
> _______________________________________________
> Castor-users mailing list
> Castor-users at lists.castor-project.org
> http://lists.castor-project.org/listinfo/castor-users
--
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
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