[Gate-users] Actor type: FixedForcedDetectionActor does not exist!
Gábor Légrádi
gabor.legradi at 3dhistech.com
Thu Oct 15 14:41:15 CEST 2020
Dear Simon and hsl…,
Now Gate runs and uses ITK-RTK, that is OK. Gate uses GPU as weel – when running purely Monte-Carlo script. However, while using ITK-RTK (using Fixed Forced Detector), GPU does not act. Therefore, I tried to force using GPU while compiling ITK:
sudo cmake -DCMAKE_INSTALL_PREFIX=/usr/share/ITK/itk-install/ -DCMAKE_BUILD_TYPE=RelWithDebInfo -DITK_USE_GPU=ON /usr/share/ITK/itk/
The folloing error message appears in the terminal:
-- Performing Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG - Failed
CMake Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
Could NOT find OpenCL (missing: OPENCL_INCLUDE_DIRS)
Call Stack (most recent call first):
/usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
CMake/FindOpenCL.cmake:89 (FIND_PACKAGE_HANDLE_STANDARD_ARGS)
CMake/itkOpenCL.cmake:2 (find_package)
CMakeLists.txt:342 (include)
I am on Ubuntu-20.04, Nvidia driver: 450.80.02, CUDA: 11.0, gcc version: 9.3.0
And here is the error log:
Performing C SOURCE FILE Test C_HAS_WARNING-Wno-long-double failed with the following output:
Change Dir: /usr/share/ITK/itk-build/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/make cmTC_ea992/fast && /usr/bin/make -f CMakeFiles/cmTC_ea992.dir/build.make CMakeFiles/cmTC_ea992.dir/build
make[1]: Entering directory '/usr/share/ITK/itk-build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_ea992.dir/src.c.o
/usr/bin/cc -DC_HAS_WARNING-Wno-long-double -Wno-long-double -o CMakeFiles/cmTC_ea992.dir/src.c.o -c /usr/share/ITK/itk-build/CMakeFiles/CMakeTmp/src.c
<command-line>: warning: ISO C99 requires whitespace after the macro name
cc1: warning: unrecognized command line option '-Wno-long-double'
Linking C executable cmTC_ea992
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_ea992.dir/link.txt --verbose=1
/usr/bin/cc -DC_HAS_WARNING-Wno-long-double CMakeFiles/cmTC_ea992.dir/src.c.o -o cmTC_ea992
make[1]: Leaving directory '/usr/share/ITK/itk-build/CMakeFiles/CMakeTmp'
Source file was:
int main(void) { return 0; }
Performing C++ SOURCE FILE Test CXX_HAS_WARNING-Wno-long-double failed with the following output:
Change Dir: /usr/share/ITK/itk-build/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/make cmTC_2e73c/fast && /usr/bin/make -f CMakeFiles/cmTC_2e73c.dir/build.make CMakeFiles/cmTC_2e73c.dir/build
make[1]: Entering directory '/usr/share/ITK/itk-build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_2e73c.dir/src.cxx.o
/usr/bin/c++ -DCXX_HAS_WARNING-Wno-long-double -Wno-long-double -std=c++11 -o CMakeFiles/cmTC_2e73c.dir/src.cxx.o -c /usr/share/ITK/itk-build/CMakeFiles/CMakeTmp/src.cxx
<command-line>: warning: ISO C++11 requires whitespace after the macro name
cc1plus: warning: unrecognized command line option '-Wno-long-double'
Linking CXX executable cmTC_2e73c
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_2e73c.dir/link.txt --verbose=1
/usr/bin/c++ -DCXX_HAS_WARNING-Wno-long-double CMakeFiles/cmTC_2e73c.dir/src.cxx.o -o cmTC_2e73c
make[1]: Leaving directory '/usr/share/ITK/itk-build/CMakeFiles/CMakeTmp'
Source file was:
int main() { return 0; }
Performing C++ SOURCE FILE Test CXX_HAS_WARNING-Wno-undefined-var-template failed with the following output:
Change Dir: /usr/share/ITK/itk-build/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/make cmTC_b02a9/fast && /usr/bin/make -f CMakeFiles/cmTC_b02a9.dir/build.make CMakeFiles/cmTC_b02a9.dir/build
make[1]: Entering directory '/usr/share/ITK/itk-build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_b02a9.dir/src.cxx.o
/usr/bin/c++ -DCXX_HAS_WARNING-Wno-undefined-var-template -Wno-undefined-var-template -std=c++11 -o CMakeFiles/cmTC_b02a9.dir/src.cxx.o -c /usr/share/ITK/itk-build/CMakeFiles/CMakeTmp/src.cxx
<command-line>: warning: ISO C++11 requires whitespace after the macro name
cc1plus: warning: unrecognized command line option '-Wno-undefined-var-template'
Linking CXX executable cmTC_b02a9
/usr/bin/cmake -E cmake_link_script CMakeFiles/cmTC_b02a9.dir/link.txt --verbose=1
/usr/bin/c++ -DCXX_HAS_WARNING-Wno-undefined-var-template CMakeFiles/cmTC_b02a9.dir/src.cxx.o -o cmTC_b02a9
make[1]: Leaving directory '/usr/share/ITK/itk-build/CMakeFiles/CMakeTmp'
Source file was:
int main() { return 0; }
Performing C++ SOURCE FILE Test CXX_HAS_DISABLE_OPTIMIZATION_FLAG failed with the following output:
Change Dir: /usr/share/ITK/itk-build/CMakeFiles/CMakeTmp
Run Build Command(s):/usr/bin/make cmTC_ee167/fast && /usr/bin/make -f CMakeFiles/cmTC_ee167.dir/build.make CMakeFiles/cmTC_ee167.dir/build
make[1]: Entering directory '/usr/share/ITK/itk-build/CMakeFiles/CMakeTmp'
Building CXX object CMakeFiles/cmTC_ee167.dir/src.cxx.o
/usr/bin/c++ -DCXX_HAS_DISABLE_OPTIMIZATION_FLAG -std=c++11 -o CMakeFiles/cmTC_ee167.dir/src.cxx.o -c /usr/share/ITK/itk-build/CMakeFiles/CMakeTmp/src.cxx
/usr/share/ITK/itk-build/CMakeFiles/CMakeTmp/src.cxx:1:1: error: expected unqualified-id before ‘-’ token
1 | -O0
| ^
make[1]: *** [CMakeFiles/cmTC_ee167.dir/build.make:66: CMakeFiles/cmTC_ee167.dir/src.cxx.o] Error 1
make[1]: Leaving directory '/usr/share/ITK/itk-build/CMakeFiles/CMakeTmp'
make: *** [Makefile:121: cmTC_ee167/fast] Error 2
Source file was:
-O0
Thank you for your help in advance,
Gabor
Gábor Légrádi
Product Development Manager
3DHISTECH Ltd.<https://www.3dhistech.com/>
H-1141 Budapest, Öv utca 3., HUNGARY
Jabber: gabor.legradi at 3dhistech.com<xmpp:%%Email%%>
Phone: +36 1 467-5600
Fax: +36 1 445-0920
[3DHISTECH Twitter]<https://twitter.com/3DHISTECH_LTD>[3DHISTECH Linkedin]<https://www.linkedin.com/company/3dhistech-ltd-/>[3DHISTECH Facebook]<https://www.facebook.com/3DHISTECH/>[3DHISTECH Instagram]<https://www.instagram.com/3dhistech/> [3DHISTECH Youtube] <https://www.youtube.com/user/3DHISTECH> [3DHISTECH Website] <https://www.3dhistech.com/>
From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr]
Sent: Tuesday, October 13, 2020 5:55 PM
To: Gábor Légrádi <gabor.legradi at 3dhistech.com>
Cc: hsl1196997465 at gmail.com; gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] Actor type: FixedForcedDetectionActor does not exist!
Thanks for reporting. For the record, you can change the GIT_TAG to master in the ITK file Modules/Remote/RTK.remote.cmake to compile ITK directly in RTK or, alternatively, set the ITK cmake option Module_RTK_GIT_TAG to master. This is detailed in INSTALLATION.md<https://github.com/SimonRit/RTK/blob/master/INSTALLATION.md>. But you should obtain the same result as what you did.
On Tue, Oct 13, 2020 at 4:05 PM Gábor Légrádi <gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>> wrote:
Finally, I am able to perform Gate simulations with ffda. I built ITK-5.1.1 instead of 4.13. However, I built it with Module_RTK OFF, and also built RTK-master as of today.
Thank you for your help!
G
Gábor Légrádi
Product Development Manager
3DHISTECH Ltd.<https://www.3dhistech.com/>
H-1141 Budapest, Öv utca 3., HUNGARY
Jabber: gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>
Phone: +36 1 467-5600
Fax: +36 1 445-0920
[3DHISTECH Twitter]<https://twitter.com/3DHISTECH_LTD>[3DHISTECH Linkedin]<https://www.linkedin.com/company/3dhistech-ltd-/>[3DHISTECH Facebook]<https://www.facebook.com/3DHISTECH/>[3DHISTECH Instagram]<https://www.instagram.com/3dhistech/> [3DHISTECH Youtube] <https://www.youtube.com/user/3DHISTECH> [3DHISTECH Website] <https://www.3dhistech.com/>
From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr<mailto:simon.rit at creatis.insa-lyon.fr>]
Sent: Tuesday, October 13, 2020 2:09 PM
To: Gábor Légrádi <gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>>
Cc:hsl1196997465 at gmail.com<mailto:hsl1196997465 at gmail.com>; gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Actor type: FixedForcedDetectionActor does not exist!
FFDA requires RTK so you need to ITK with Module_RTK ON and Gate with GATE_USE_RTK ON. I personally use the master branch of ITK with the develop branch of Gate. At least, I would suggest the latest ITK v5.1.1 and the develop branch of Gate.
Simon
On Tue, Oct 13, 2020 at 1:00 PM Gábor Légrádi <gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>> wrote:
Dear hsl…!
You wrote: ’RTK is required for this function, you should install ITK with RTK ON firstly, and recompile Gate with ITK ON .’
I followed your suggestion: Built ITK with RTK on and then while building Gate GATE_USE_ITK=ON and GATE_USE_RTK=OFF were set. But the issue is the same: ’Actor type: FixedForcedDetectionActor does not exist!’
I did the following:
After building GEANT4-10.6.2 and ROOT:
Downloaded and extracetd ITK 4.13.
sudo ccmake -DITK_USE_REVIEW=ON -DModule_RTK=ON ..
BUILD_EXAMPLES OFF
BUILD_TESTING OFF
INSTALL_GTEST OFF
ITKV3_COMPATIBILITY OFF
ITK_BUILD_DEFAULT_MODULES ON
ITK_WRAP_PYTHON OFF
MEMORYCHECK_COMMAND MEMORYCHECK_COMMAND-NOTFOUND
sudo make -j4
sudo make install
And then:
Downloaded Gate-9.0
sudo ccmake ../gate
BUILD_TESTING ON
CMAKE_BACKWARDS_COMPATIBILITY 2.4
CMAKE_BUILD_TYPE RelWithDebInfo
CMAKE_INSTALL_PREFIX /usr/share/gate/gate-install
EXECUTABLE_OUTPUT_PATH
GATE_COMPILE_WITH_NATIVE OFF
GATE_DOWNLOAD_BENCHMARKS_DATA ON
GATE_USE_DAVIS OFF
GATE_USE_ECAT7 OFF
GATE_USE_GEANT4_UIVIS ON
GATE_USE_ITK ON
GATE_USE_LMF OFF
GATE_USE_OPTICAL ON
GATE_USE_RTK OFF
GATE_USE_SYSTEM_CLHEP OFF
GATE_USE_TORCH OFF
GATE_USE_XRAYLIB OFF
Geant4_DIR /usr/share/geant4/geant4-install/lib/Geant4-10.6.2
ITK_DIR /usr/share/ITK/InsightToolkit-4.13.3/bin
LIBRARY_OUTPUT_PATH
Qt5Core_DIR /usr/lib/x86_64-linux-gnu/cmake/Qt5Core
Qt5Gui_DIR /usr/lib/x86_64-linux-gnu/cmake/Qt5Gui
Qt5OpenGL_DIR /usr/lib/x86_64-linux-gnu/cmake/Qt5OpenGL
Qt5PrintSupport_DIR /usr/lib/x86_64-linux-gnu/cmake/Qt5PrintSupport
Qt5Widgets_DIR /usr/lib/x86_64-linux-gnu/cmake/Qt5Widgets
ROOTCINT_EXECUTABLE /usr/share/cern_root/bin/rootcint
sudo make -j4
sudo make install
source /usr/share/cern_root/bin/thisroot.sh
source /usr/share/geant4/geant4-install/bin/geant4.sh
export PATH=$PATH:/usr/share/gate/gate-install/bin
And then Gate runs properly, can run Monte-Carlo, but not ffda.
While I’m waiting for response, I build RTK too and build Gate with RTK ON too…
Thanks in advance,
Gabor
Gábor Légrádi
Product Development Manager
3DHISTECH Ltd.<https://www.3dhistech.com/>
H-1141 Budapest, Öv utca 3., HUNGARY
Jabber: gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>
Phone: +36 1 467-5600
Fax: +36 1 445-0920
[3DHISTECH Twitter]<https://twitter.com/3DHISTECH_LTD>[3DHISTECH Linkedin]<https://www.linkedin.com/company/3dhistech-ltd-/>[3DHISTECH Facebook]<https://www.facebook.com/3DHISTECH/>[3DHISTECH Instagram]<https://www.instagram.com/3dhistech/> [3DHISTECH Youtube] <https://www.youtube.com/user/3DHISTECH> [3DHISTECH Website] <https://www.3dhistech.com/>
From: Gate-users [mailto:gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>] On Behalf Of Gábor Légrádi
Sent: Monday, October 12, 2020 5:43 PM
To: Simon Rit <simon.rit at creatis.insa-lyon.fr<mailto:simon.rit at creatis.insa-lyon.fr>>
Cc:gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Actor type: FixedForcedDetectionActor does not exist!
Dear Simon,
Yes, the suggestion in issue 254 did help. Thank you!
Gabor
Gábor Légrádi
Product Development Manager
3DHISTECH Ltd.<https://www.3dhistech.com/>
H-1141 Budapest, Öv utca 3., HUNGARY
Jabber: gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>
Phone: +36 1 467-5600
Fax: +36 1 445-0920
[3DHISTECH Twitter]<https://twitter.com/3DHISTECH_LTD>[3DHISTECH Linkedin]<https://www.linkedin.com/company/3dhistech-ltd-/>[3DHISTECH Facebook]<https://www.facebook.com/3DHISTECH/>[3DHISTECH Instagram]<https://www.instagram.com/3dhistech/> [3DHISTECH Youtube] <https://www.youtube.com/user/3DHISTECH> [3DHISTECH Website] <https://www.3dhistech.com/>
From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr]
Sent: Monday, October 12, 2020 12:49 PM
To: Gábor Légrádi <gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>>
Cc:gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Actor type: FixedForcedDetectionActor does not exist!
That seems to be a root problem. Can you check if the suggestion in issue 254<https://github.com/OpenGATE/Gate/issues/254> helps you?
On Mon, Oct 12, 2020 at 11:49 AM Gábor Légrádi <gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>> wrote:
Thank you, Simon, for your answer!
Anyway, it was not ccmake which crashed with error but the build (make). Here you are the very end of it:
[100%] Linking CXX executable Gate
/usr/bin/ld: warning: libtbb.so.2, needed by /usr/share/cern_root/lib/libImt.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::initialize(int)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_root_with_context_proxy::free(tbb::task&) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_additional_child_of_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::isolate_within_arena(tbb::interface7::internal::delegate_base&, long)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::default_num_threads()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_continuation_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::initialize(int, unsigned long)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_root_with_context_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface5::internal::task_base::destroy(tbb::task&)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::cancel_group_execution()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task::note_affinity(unsigned short)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::terminate()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `typeinfo for tbb::task'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::init()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::get_initial_auto_partitioner_divisor()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::~task_group_context()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_child_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_additional_child_of_proxy::free(tbb::task&) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::is_group_execution_cancelled() const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::throw_exception_v4(tbb::internal::exception_id)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::reset()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_terminate()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_initialize()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_execute(tbb::interface7::internal::delegate_base&) const'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/GateDigit_singles_sorter.dir/build.make:1628: GateDigit_singles_sorter] Error 1
make[1]: *** [CMakeFiles/Makefile2:217: CMakeFiles/GateDigit_singles_sorter.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
/usr/bin/ld: warning: libtbb.so.2, needed by /usr/share/cern_root/lib/libImt.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::initialize(int)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_root_with_context_proxy::free(tbb::task&) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_additional_child_of_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::isolate_within_arena(tbb::interface7::internal::delegate_base&, long)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::default_num_threads()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_continuation_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::initialize(int, unsigned long)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_root_with_context_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface5::internal::task_base::destroy(tbb::task&)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::cancel_group_execution()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task::note_affinity(unsigned short)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::terminate()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `typeinfo for tbb::task'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::init()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::get_initial_auto_partitioner_divisor()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::~task_group_context()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_child_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_additional_child_of_proxy::free(tbb::task&) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::is_group_execution_cancelled() const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::throw_exception_v4(tbb::internal::exception_id)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::reset()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_terminate()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_initialize()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_execute(tbb::interface7::internal::delegate_base&) const'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/GateDigit_hits_digitizer.dir/build.make:1628: GateDigit_hits_digitizer] Error 1
make[1]: *** [CMakeFiles/Makefile2:190: CMakeFiles/GateDigit_hits_digitizer.dir/all] Error 2
/usr/bin/ld: warning: libtbb.so.2, needed by /usr/share/cern_root/lib/libImt.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::initialize(int)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_root_with_context_proxy::free(tbb::task&) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_additional_child_of_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::isolate_within_arena(tbb::interface7::internal::delegate_base&, long)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::default_num_threads()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_continuation_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::initialize(int, unsigned long)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_root_with_context_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface5::internal::task_base::destroy(tbb::task&)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::cancel_group_execution()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task::note_affinity(unsigned short)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::terminate()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `typeinfo for tbb::task'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::init()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::get_initial_auto_partitioner_divisor()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::~task_group_context()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_child_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_additional_child_of_proxy::free(tbb::task&) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::is_group_execution_cancelled() const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::throw_exception_v4(tbb::internal::exception_id)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::reset()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_terminate()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_initialize()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_execute(tbb::interface7::internal::delegate_base&) const'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/GateDigit_coincidence_processor.dir/build.make:1628: GateDigit_coincidence_processor] Error 1
make[1]: *** [CMakeFiles/Makefile2:163: CMakeFiles/GateDigit_coincidence_processor.dir/all] Error 2
/usr/bin/ld: warning: libtbb.so.2, needed by /usr/share/cern_root/lib/libImt.so, not found (try using -rpath or -rpath-link)
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::initialize(int)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_root_with_context_proxy::free(tbb::task&) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_additional_child_of_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::isolate_within_arena(tbb::interface7::internal::delegate_base&, long)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::default_num_threads()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_continuation_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::initialize(int, unsigned long)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_root_with_context_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface5::internal::task_base::destroy(tbb::task&)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::cancel_group_execution()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task::note_affinity(unsigned short)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_scheduler_init::terminate()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `typeinfo for tbb::task'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::init()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::get_initial_auto_partitioner_divisor()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::~task_group_context()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_child_proxy::allocate(unsigned long) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::allocate_additional_child_of_proxy::free(tbb::task&) const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::is_group_execution_cancelled() const'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::internal::throw_exception_v4(tbb::internal::exception_id)'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::task_group_context::reset()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_terminate()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_initialize()'
/usr/bin/ld: /usr/share/cern_root/lib/libImt.so: undefined reference to `tbb::interface7::internal::task_arena_base::internal_execute(tbb::interface7::internal::delegate_base&) const'
collect2: error: ld returned 1 exit status
make[2]: *** [CMakeFiles/Gate.dir/build.make:1628: Gate] Error 1
make[1]: *** [CMakeFiles/Makefile2:676: CMakeFiles/Gate.dir/all] Error 2
make: *** [Makefile:141: all] Error 2
Gábor Légrádi
Product Development Manager
3DHISTECH Ltd.<https://www.3dhistech.com/>
H-1141 Budapest, Öv utca 3., HUNGARY
Jabber: gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>
Phone: +36 1 467-5600
Fax: +36 1 445-0920
[3DHISTECH Twitter]<https://twitter.com/3DHISTECH_LTD>[3DHISTECH Linkedin]<https://www.linkedin.com/company/3dhistech-ltd-/>[3DHISTECH Facebook]<https://www.facebook.com/3DHISTECH/>[3DHISTECH Instagram]<https://www.instagram.com/3dhistech/> [3DHISTECH Youtube] <https://www.youtube.com/user/3DHISTECH> [3DHISTECH Website] <https://www.3dhistech.com/>
From: Simon Rit [mailto:simon.rit at creatis.insa-lyon.fr<mailto:simon.rit at creatis.insa-lyon.fr>]
Sent: Monday, October 12, 2020 9:24 AM
To: Gábor Légrádi <gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>>
Cc:gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: Re: [Gate-users] Actor type: FixedForcedDetectionActor does not exist!
Hi,
Gate does not suport GEANT4_BUILD_MULTITHREADED and you should get a meaningful message when configuring Gate, see here<https://github.com/OpenGATE/Gate/blob/develop/CMakeLists.txt#L70>.
Fixed forced detection only works on one voxelized volume with the rest (world, detector material, etc) being made of one material only. It supports x-ray spectrum and detector response, following the example in GateContrib.
You can always do a pure Monte Carlo simulation instead if you prefer mathematical descriptions, see the analog simulation<https://github.com/OpenGATE/GateContrib/blob/master/imaging/CT/fixedForcedDetectionCT/mac/monteCarloCT.mac> of the fixed forced detection example.
Please report the meaningless messages if you get any...
Simon
On Sun, Oct 11, 2020 at 12:19 PM Gábor Légrádi <gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>> wrote:
Thank you, hsl...!
Anyway, may I ask some more general questions?
1. I plan to use GATE for one definite purpose. I am to simulate microCT acquisitions with mathematical phantoms which means that I need to be able to simulate
- X-ray source with spectrum.
- Interaction of X-ray and matter below 130keV, i.e. photoelectric effect, Compton- and Raleigh-scatter.
- Detector response.
In this case what flags and settings do you recommend for GEANT4 and GATE4 build?
2. Anyway, how can I find out myself such dependencies? Meanwhile I succeeded to compile GEANT4 with the following flags:
sudo cmake -DCMAKE_INSTALL_PREFIX=/PAHT/TO/geant4/geant4-install/ -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_QT=ON -DGEANT4_USE_OPENGL_X11=ON -DGEANT4_USE_SYSTEM_EXPAT=OFF CMAKE_BUILD_TYPE=RelWithDebInfo GEANT4_BUILD_MULTITHREADED=ON GEANT4_USE_RAYTRACER_X11=ON GEANT4_USE_INVENTOR=ON GEANT4_USE_XM=ON /PATH/TO/geant4/geant4/
However, this case my GATE compilation crashes with meaningless error message. It would be really demanding to try out one-by-one which flag is really helpful in my case and which causes the crash. It is very likely, that crash is caused by some settings which are, on the other hand, absolutely useless for X-ray modelling in GATE.
Hoping that my point is clear,
Gabor
Gábor Légrádi
Product Development Manager
3DHISTECH Ltd.<https://www.3dhistech.com/>
H-1141 Budapest, Öv utca 3., HUNGARY
Jabber: gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>
Phone: +36 1 467-5600
Fax: +36 1 445-0920
[3DHISTECH Twitter]<https://twitter.com/3DHISTECH_LTD>[3DHISTECH Linkedin]<https://www.linkedin.com/company/3dhistech-ltd-/>[3DHISTECH Facebook]<https://www.facebook.com/3DHISTECH/>[3DHISTECH Instagram]<https://www.instagram.com/3dhistech/> [3DHISTECH Youtube] <https://www.youtube.com/user/3DHISTECH> [3DHISTECH Website] <https://www.3dhistech.com/>
On Sat, Oct 10, 2020 at 11:47 AM hsl1196997465 at gmail.com<mailto:hsl1196997465 at gmail.com> <hsl1196997465 at gmail.com<mailto:hsl1196997465 at gmail.com>> wrote:
RTK is required for this function, you should install ITK with RTK ON firstly, and recompile Gate with ITK ON .
---Original---
From: "Gábor Légrádi"<gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>>
Date: Sat, Oct 10, 2020 06:41 AM
To: "gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>"<gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>;
Subject: [Gate-users] Actor type: FixedForcedDetectionActor does not exist!
Dear All,
I am new to GATE. Until now, I have been playing with vGATE, on Virtual Machine. Now I am testing my newly compiled GATE on my host machine. I tried to execute a macro which runs properly on vGATE. You may find it in GateContrib Github folder: https://github.com/OpenGATE/GateContrib/tree/master/imaging/CT/fixedForcedDetectionCT .
On my host Gate can not accomplish this line:
/gate/actor/addActor FixedForcedDetectionActor ffda
Warning message:
*** WARNING *** Actor type: FixedForcedDetectionActor does not exist!
And then, naturally, ffda can not be attached and Gate stops with error:
/gate/actor/ffda/attachTo world
[G4-cerr] command not found
Any hint?
I installed the whole stuff on Ubuntu 20.04. Here are my notes about the installation:
**** GEANT4 ****
sudo apt-get update
sudo apt upgrade
sudo apt install cmake
Downloaded and unzipped: https://geant4.web.cern.ch/support/download -> GNU or Linux tar format, compressed using gzip (33.2Mb, 34833550 bytes)
[...]
cmake command:
cmake -DCMAKE_INSTALL_PREFIX=/home/lg/geant4.10.06.p02 -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_SYSTEM_EXPAT=OFF /home/lg/work/geant4.10.06.p02
make -j4
make install
**** ROOT ****
sudo apt-get install libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev (elvileg dpkg-dev cmake g++ gcc binutils már fenn vannak)
Binary loaded from here and extracted: https://root.cern/install/all_releases/ -> Release 6.22/02 - 17 Aug 2020
**** GATE ****
sudo apt install cmake-curses-gui
sudo apt-get install libxml2-dev
sudo apt-get install libc6-dev libssl-dev dpkg-dev debhelper fakeroot libxml2-dev libxslt1-dev
Downloaded and extracted: https://github.com/OpenGATE/Gate/archive/v9.0.zip
[...]
cd gate_v9.0
ccmake ../Gate-9.0-dwnld
Then I set these settings:
BUILD_TESTING: ON
CMAKE_BACKWARD_COMPATIBILITY: 2.4
CMAKE_BUILD_TYPE: Release
CMAKE_INSTALL_PREFIX:
EXECUTABLE_OUTPUT_PATH:
GATE_COMPILE_WITH_NATIVE: OFF
GATE_DOWNLOAD_BENCHMARKS_DATA: ON
GATE_USE_DAVIS: OFF
GATE_USE_ECAT7: OFF
GATE_USE_GEANT4_UIVUS: ON
GATE_USE_ITK: OFF
GATE_USE_LMF: OFF
GATE_USE_OPTICAL: ON
GATE_USE_RTK: OFF
GATE_USE_SYSTEM_CLHEP: OFF
GATE_USE_TORCH: OFF
GATE_USE_XRAYLIB: OFF
Geant4_DIR:
LIBRARY_OUTPUT_PATH:
ROOTCINT_EXECUTABLE:
g: Generate and exit
make -j4
make install
source /home/lg/root/bin/thisroot.sh
source /home/lg/geant4.10.06.p02/bin/geant4.sh
export PATH=$PATH:/home/lg/gate_v9.0/bin
Gábor Légrádi
Product Development Manager
3DHISTECH Ltd.
H-1141 Budapest, Öv utca 3., HUNGARY
Jabber: gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>
Phone: +36 1 467-5600
Fax: +36 1 445-0920
_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
________________________________
From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>> on behalf of Gábor Légrádi <gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>>
Sent: Saturday, October 10, 2020 12:41:34 AM
To:gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] Actor type: FixedForcedDetectionActor does not exist!
Dear All,
I am new to GATE. Until now, I have been playing with vGATE, on Virtual Machine. Now I am testing my newly compiled GATE on my host machine. I tried to execute a macro which runs properly on vGATE. You may find it in GateContrib Github folder: https://github.com/OpenGATE/GateContrib/tree/master/imaging/CT/fixedForcedDetectionCT .
On my host Gate can not accomplish this line:
/gate/actor/addActor FixedForcedDetectionActor ffda
Warning message:
<!> *** WARNING *** <!> Actor type: FixedForcedDetectionActor does not exist!
And then, naturally, ffda can not be attached and Gate stops with error:
/gate/actor/ffda/attachTo world
[G4-cerr] command </gate/actor/ffda/attachTo world> not found
Any hint?
I installed the whole stuff on Ubuntu 20.04. Here are my notes about the installation:
**** GEANT4 ****
sudo apt-get update
sudo apt upgrade
sudo apt install cmake
Downloaded and unzipped: https://geant4.web.cern.ch/support/download -> GNU or Linux tar format, compressed using gzip (33.2Mb, 34833550 bytes)
[...]
cmake command:
cmake -DCMAKE_INSTALL_PREFIX=/home/lg/geant4.10.06.p02 -DGEANT4_INSTALL_DATA=ON -DGEANT4_USE_SYSTEM_EXPAT=OFF /home/lg/work/geant4.10.06.p02
make -j4
make install
**** ROOT ****
sudo apt-get install libx11-dev libxpm-dev libxft-dev libxext-dev libssl-dev (elvileg dpkg-dev cmake g++ gcc binutils már fenn vannak)
Binary loaded from here and extracted: https://root.cern/install/all_releases/ -> Release 6.22/02 - 17 Aug 2020
**** GATE ****
sudo apt install cmake-curses-gui
sudo apt-get install libxml2-dev
sudo apt-get install libc6-dev libssl-dev dpkg-dev debhelper fakeroot libxml2-dev libxslt1-dev
Downloaded and extracted: https://github.com/OpenGATE/Gate/archive/v9.0.zip
[...]
cd gate_v9.0
ccmake ../Gate-9.0-dwnld
Then I set these settings:
BUILD_TESTING: ON
CMAKE_BACKWARD_COMPATIBILITY: 2.4
CMAKE_BUILD_TYPE: Release
CMAKE_INSTALL_PREFIX: <IT WAS SET PROPERLY>
EXECUTABLE_OUTPUT_PATH: <NONE>
GATE_COMPILE_WITH_NATIVE: OFF
GATE_DOWNLOAD_BENCHMARKS_DATA: ON
GATE_USE_DAVIS: OFF
GATE_USE_ECAT7: OFF
GATE_USE_GEANT4_UIVUS: ON
GATE_USE_ITK: OFF
GATE_USE_LMF: OFF
GATE_USE_OPTICAL: ON
GATE_USE_RTK: OFF
GATE_USE_SYSTEM_CLHEP: OFF
GATE_USE_TORCH: OFF
GATE_USE_XRAYLIB: OFF
Geant4_DIR: <IT WAS SET PROPERLY>
LIBRARY_OUTPUT_PATH: <NONE>
ROOTCINT_EXECUTABLE: <IT WAS SET PROPERLY>
g: Generate and exit
make -j4
make install
source /home/lg/root/bin/thisroot.sh
source /home/lg/geant4.10.06.p02/bin/geant4.sh
export PATH=$PATH:/home/lg/gate_v9.0/bin
Gábor Légrádi
Product Development Manager
3DHISTECH Ltd.
H-1141 Budapest, Öv utca 3., HUNGARY
Jabber: gabor.legradi at 3dhistech.com<mailto:gabor.legradi at 3dhistech.com>
Phone: +36 1 467-5600
Fax: +36 1 445-0920
_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
_______________________________________________
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
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This e-mail may contain confidential and/or privileged information and should only be read by those persons to whom it is addressed. If you are not the intended recipient or have received this e-mail in error, please notify the sender (3DHISTECH Ltd., info at 3dhistech.com) immediately and erase this e-mail from your system. If you are not the intended recipient you are hereby notified that any form of copying, dissemination, disclosure, modification, distribution and/or publication or any action taken in reliance on this email is prohibited and may be unlawful. Moreover, to the extent that a non-disclosure agreement exists between 3DHISTECH Ltd. and you, the recipient, the contents of this email and any attachments hereto are governed by the terms of said non-disclosure agreement and are considered confidential and proprietary to 3DHISTECH Ltd. as defined by such agreement. Any form of copying, dissemination, disclosure, modification, distribution and/or publication of this e-mail message without preliminary permission is strictly prohibited.
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