[Castor-users] About CASToR Installation

Mon Sep 30 09:31:37 CEST 2019

Hi,

I have no idea about that, I am neither used to cmake nor to root.

Also please use the mailing list as other people may help you or may find useful information.

Best

Simon

________________________________
De : Xinjie Cao <xinjie.cao at stonybrook.edu>
Envoyé : vendredi 27 septembre 2019 18:10
À : STUTE Simon
Objet : Re: [Castor-users] About CASToR Installation

Hi Simon,

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:

```
 CMake Error at CMakeLists.txt:411 (add_executable):
[root at localhost castor_v2.1-build]# " links to item "

     ROOT is built with CMake, see https://root.cern/building-root
     Please run
mkdir obj" which has leading or trailing whitespace.  This is now an
 error according to policy CMP0004.

 CMake Error at CMakeLists.txt:411 (add_executable):
   Target "castor-scannerLUTExplorer" links to item " cd obj" which has
   leading or trailing whitespace.  This is now an error according to policy
   CMP0004.
```
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!!

Best,

On Fri, Sep 27, 2019 at 11:12 AM STUTE Simon <simon.stute at chu-nantes.fr<mailto:simon.stute at chu-nantes.fr>> 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<mailto: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>

 [https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ]    [https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download]

--
....................................................

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>

 [https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ]    [https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download]

--
....................................................

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>

 [https://docs.google.com/uc?export=download&id=12iMPAuaMtpKRdkcmBleVsP6iWiM4wlm_&revid=0B_TLWOu4jP1eWnFFRW9qQXlicTY3ZTVzWnR5QkRVY3RRT3JVPQ]    [https://drive.google.com/a/stonybrook.edu/uc?id=17TB1Ha3enD8HC5e_Ez238vpeBF92aCgH&export=download]
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