Boost Error in ResourceLog #2898

BifengLei · 2019-02-19T10:16:00Z

In combination with:

GCC 7.3.1
CUDA 9.2.88
Boost 1.68.0 (C++11 build) OR Boost 1.65.1
PIConGPU 0.4.0
centos 7

I have checked the issue here:
#2714 (comment)
But, there is still such err in ResourceLog.hpp:

/trinity/home/b.lei/pic/src/blei/picongpu/include/pmacc/../picongpu/plugins/ResourceLog.hpp(115): here
/trinity/shared/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_pair.h(331): error: identifier "std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage" is undefined in device code

/trinity/shared/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_pair.h(331): error: identifier "std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage" is undefined in device code

2 errors detected in the compilation of "/tmp/tmpxft_0000926d_00000000-6_main.cpp1.ii".
CMake Error at picongpu_generated_main.cpp.o.Release.cmake:279 (message):
  Error generating file
  /trinity/home/b.lei/pic/build/CMakeFiles/picongpu.dir//./picongpu_generated_main.cpp.o

The text was updated successfully, but these errors were encountered:

ax3l · 2019-02-19T10:21:59Z

Thanks for reporting!

PIConGPU 0.4.0+ contains a first work-around from #2721 that should have solved the issue for boost::swap... But I see, that's indeed a regression! Now we still have a std::string signature lurking in device code.

@psychocoderHPC any idea? We definitely missed that the calling boost_swap_impl::swap has exactly the same std::string arguments we tried to get rid off ^^
Maybe we should just add a fat #ifndef __CUDA_ARCH__ guard in our ResourceLog::notify implementation to avoid any traces of boost::property_tree in device code.

ax3l · 2019-02-19T10:33:18Z

@BifengLei in the meantime, you can skip the compilation of the ResourceLog plugin altogether by commenting out these two lines:

diff --git a/include/picongpu/plugins/PluginController.hpp b/include/picongpu/plugins/PluginController.hpp
index ad6543d1c..e174c731f 100644
--- a/include/picongpu/plugins/PluginController.hpp
+++ b/include/picongpu/plugins/PluginController.hpp
@@ -70,7 +70,7 @@
 #endif
 
 #include "picongpu/plugins/Checkpoint.hpp"
-#include "picongpu/plugins/ResourceLog.hpp"
+// include "picongpu/plugins/ResourceLog.hpp"
 
 #include <pmacc/mappings/kernel/MappingDescription.hpp>
 
@@ -181,7 +181,7 @@ private:
 #if (ENABLE_HDF5 == 1)
         , plugins::multi::Master< hdf5::HDF5Writer >
 #endif
-        , ResourceLog
+//        , ResourceLog
     >;

BifengLei · 2019-02-19T10:48:54Z

@BifengLei in the meantime, you can skip the compilation of the ResourceLog plugin altogether by commenting out these two lines:

diff --git a/include/picongpu/plugins/PluginController.hpp b/include/picongpu/plugins/PluginController.hpp
index ad6543d1c..e174c731f 100644
--- a/include/picongpu/plugins/PluginController.hpp
+++ b/include/picongpu/plugins/PluginController.hpp
@@ -70,7 +70,7 @@
 #endif
 
 #include "picongpu/plugins/Checkpoint.hpp"
-#include "picongpu/plugins/ResourceLog.hpp"
+// include "picongpu/plugins/ResourceLog.hpp"
 
 #include <pmacc/mappings/kernel/MappingDescription.hpp>
 
@@ -181,7 +181,7 @@ private:
 #if (ENABLE_HDF5 == 1)
         , plugins::multi::Master< hdf5::HDF5Writer >
 #endif
-        , ResourceLog
+//        , ResourceLog
     >;

@ax3l Thank you so much for replying.
Unfortunately, there is still the err:

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/trinity/shared/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_pair.h(331): error: identifier "std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage" is undefined in device code

/trinity/shared/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_pair.h(331): error: identifier "std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage" is undefined in device code

2 errors detected in the compilation of "/tmp/tmpxft_00018152_00000000-6_main.cpp1.ii".
CMake Error at picongpu_generated_main.cpp.o.Release.cmake:279 (message):
  Error generating file
  /trinity/home/b.lei/pic/build/CMakeFiles/picongpu.dir//./picongpu_generated_main.cpp.o

psychocoderHPC · 2019-02-19T13:04:00Z

@psychocoderHPC any idea? We definitely missed that the calling boost_swap_impl::swap has exactly the same std::string arguments we tried to get rid off ^^
Maybe we should just add a fat #ifndef __CUDA_ARCH__ guard in our ResourceLog::notify implementation to avoid any traces of boost::property_tree in device code.

@ax3l yes we can try it

ax3l · 2019-02-19T13:12:21Z

@BifengLei can you post one line more regarding the new error? Which PIConGPU file includes the first line?

BifengLei · 2019-02-19T13:22:17Z

@ax3l Here is all of build information:

-- Found CUDA: /trinity/shared/opt/cuda-9.2 (found suitable version "9.2", minimum required is "7.0") 
-- ALPAKA_ACC_GPU_CUDA_ONLY_MODE
-- ALPAKA_ACC_GPU_CUDA_ENABLED
-- _cupla_COMPILE_OPTIONS_PUBLIC: -std=c++11;-ftemplate-depth-512;-Wall;-Wextra;-Wno-unknown-pragmas;-Wno-unused-parameter;-Wno-unused-local-typedefs;-Wno-attributes;-Wno-reorder;-Wno-sign-compare
-- _cupla_COMPILE_DEFINITIONS_PUBLIC: ALPAKA_ACC_GPU_CUDA_ONLY_MODE;ALPAKA_ACC_GPU_CUDA_ENABLED;ALPAKA_DEBUG=0;CUPLA_STREAM_ASYNC_ENABLED=1
-- _cupla_INCLUDE_DIRECTORIES_PUBLIC: /trinity/shared/opt/cuda-9.2/include;/trinity/home/b.lei/pic/src/blei/picongpu/thirdParty/alpaka/include;/trinity/home/b.lei/pic/src/blei/picongpu/thirdParty/cupla/include
-- _cupla_LINK_LIBRARIES_PUBLIC: Boost::boost;general;/trinity/shared/opt/cuda-9.2/lib64/libcudart.so;general;pthread;general;rt
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   filesystem
--   system
--   math_tr1
-- Boost: result_of with TR1 style and decltype fallback
-- Found OpenMP_C: -fopenmp  
-- Found OpenMP_CXX: -fopenmp  
-- Found OpenMP: TRUE   
-- Found CUDA: /trinity/shared/opt/cuda-9.2 (found suitable version "9.2", minimum required is "5.0") 
-- Boost version: 1.68.0
-- Found OpenMP_C: -fopenmp  
-- Found OpenMP_CXX: -fopenmp  
-- Boost version: 1.68.0
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   program_options
--   regex
--   filesystem
--   system
--   math_tr1
--   serialization
-- Found CUDA: /trinity/shared/opt/cuda-9.2 (found version "9.2") 
-- Could NOT find NVML (missing: NVML_LIBRARY) 
-- Boost version: 1.68.0
-- Found the following Boost libraries:
--   program_options
-- Can NOT find 'adios_config' - set ADIOS_ROOT or check your PATH
-- Could NOT find ADIOS (missing: ADIOS_LIBRARIES ADIOS_INCLUDE_DIRS) (Required is at least version "1.13.1")
-- HDF5: Using hdf5 compiler wrapper to determine C configuration
-- Found Splash: /trinity/home/b.lei/lib/gcc-7.3.1/splash-1.68.0/lib/cmake/Splash
-- Found PNGwriter: /trinity/home/b.lei/lib/gcc-7.3.1/pngwriter/lib/cmake/PNGwriter
-- Could NOT find ISAAC - set ISAAC_DIR or check your CMAKE_PREFIX_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /trinity/home/b.lei/pic/build
[  4%] Built target cupla
[  8%] Linking CXX executable cuda_memtest
[ 20%] Built target mpiInfo
[ 50%] Built target picongpu-hostonly
/trinity/shared/opt/rh/devtoolset-7/root/usr/bin/../libexec/gcc/x86_64-redhat-linux/7/ld: warning: libmpi.so.12, needed by /trinity/home/b.lei/lib/gcc-7.3.1/zlib/lib/libz.so, may conflict with libmpi.so.40
[ 62%] Built target cuda_memtest
[ 66%] Building NVCC (Device) object CMakeFiles/picongpu.dir/picongpu_generated_main.cpp.o
/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/mpl/map/aux_/item.hpp(54): warning: "boost::mpl::aux::type_wrapper<T> operator/(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/mpl/map/aux_/item.hpp(55): warning: "boost::mpl::aux::type_wrapper<boost::mpl::pair<Key, T>> operator|(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::next<Base::order>::type *)" declares a non-template function -- add <> to refer to a template instance

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/mpl/map/aux_/item.hpp(56): warning: "char (&operator||(const boost::mpl::m_item<Key, T, Base> &, boost::mpl::aux::type_wrapper<Key> *))[boost::mpl::next<Base::order>::type::value]" declares a non-template function -- add <> to refer to a template instance

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/mpl/map/aux_/item.hpp(71): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator/(const boost::mpl::m_mask<Key, Base> &, boost::mpl::aux::type_wrapper<Key> *)" declares a non-template function -- add <> to refer to a template instance

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/mpl/map/aux_/item.hpp(72): warning: "boost::mpl::aux::type_wrapper<mpl_::void_> operator|(const boost::mpl::m_mask<Key, Base> &, boost::mpl::x_order_impl<Base, Key>::type *)" declares a non-template function -- add <> to refer to a template instance

/trinity/home/b.lei/pic/src/blei/picongpu/include/pmacc/../pmacc/particles/memory/dataTypes/Particle.hpp(167): warning: __device__ annotation is ignored on a function("operator=") that is explicitly defaulted on its first declaration

/trinity/home/b.lei/pic/src/blei/picongpu/include/pmacc/../pmacc/particles/memory/dataTypes/Particle.hpp(167): warning: __host__ annotation is ignored on a function("operator=") that is explicitly defaulted on its first declaration

/trinity/home/b.lei/pic/src/blei/picongpu/include/pmacc/../picongpu/fields/LaserPhysics.hpp(147): warning: pointless comparison of unsigned integer with zero

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/fusion/support/unused.hpp(25): warning: __host__ annotation is ignored on a function("unused_type") that is explicitly defaulted on its first declaration

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/fusion/support/unused.hpp(25): warning: __device__ annotation is ignored on a function("unused_type") that is explicitly defaulted on its first declaration

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/fusion/support/unused.hpp(31): warning: __host__ annotation is ignored on a function("unused_type") that is explicitly defaulted on its first declaration

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/fusion/support/unused.hpp(31): warning: __device__ annotation is ignored on a function("unused_type") that is explicitly defaulted on its first declaration

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/fusion/container/vector/vector.hpp(189): warning: __host__ annotation is ignored on a function("vector_data") that is explicitly defaulted on its first declaration

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/fusion/container/vector/vector.hpp(189): warning: __device__ annotation is ignored on a function("vector_data") that is explicitly defaulted on its first declaration

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/fusion/container/vector/vector.hpp(276): warning: __host__ annotation is ignored on a function("vector") that is explicitly defaulted on its first declaration

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/fusion/container/vector/vector.hpp(276): warning: __device__ annotation is ignored on a function("vector") that is explicitly defaulted on its first declaration

/trinity/home/b.lei/lib/gcc-7.3.1/boost-1.68.0/include/boost/regex/v4/basic_regex_parser.hpp(48): warning: integer conversion resulted in a change of sign

/trinity/shared/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_pair.h(331): error: identifier "std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage" is undefined in device code

/trinity/shared/opt/rh/devtoolset-7/root/usr/include/c++/7/bits/stl_pair.h(331): error: identifier "std::basic_string<char, std::char_traits<char>, std::allocator<char> >::_Rep::_S_empty_rep_storage" is undefined in device code

2 errors detected in the compilation of "/tmp/tmpxft_0005f9c5_00000000-6_main.cpp1.ii".
CMake Error at picongpu_generated_main.cpp.o.Release.cmake:279 (message):
  Error generating file
  /trinity/home/b.lei/pic/build/CMakeFiles/picongpu.dir//./picongpu_generated_main.cpp.o


make[2]: *** [CMakeFiles/picongpu.dir/picongpu_generated_main.cpp.o] Error 1
make[1]: *** [CMakeFiles/picongpu.dir/all] Error 2
make: *** [all] Error 2

ax3l · 2019-02-19T13:30:33Z

Hm, that's indeed all we got here...

I expect it's coming from include/picongpu/initialization/ParserGridDistribution.hpp where we can replace <boost/regex.hpp> with C++11 <regex> these days (GCC 4.9+ and the like).

Until then, and if you don't use the --gridDist feature for static load balancing, you can hack this out via:

diff --git a/include/picongpu/initialization/ParserGridDistribution.hpp b/include/picongpu/initialization/ParserGridDistribution.hpp
index e41a8cdc6..53c395952 100644
--- a/include/picongpu/initialization/ParserGridDistribution.hpp
+++ b/include/picongpu/initialization/ParserGridDistribution.hpp
@@ -24,7 +24,7 @@
 #include <string>   // std::string
 #include <iterator> // std::distance
 
-#include <boost/regex.hpp>
+// include <boost/regex.hpp>
 #include <boost/lexical_cast.hpp>
 
 
@@ -142,6 +142,9 @@ private:
     value_type
     parse( std::string const s ) const
     {
+        value_type newInput;
+
+#if 0
         boost::regex regFind( "[0-9]+(\\{[0-9]+\\})*",
                               boost::regex_constants::perl );
 
@@ -179,7 +182,7 @@ private:
             };
             newInput.emplace_back( g );
         }
-
+#endif
         return newInput;
     }

BifengLei · 2019-02-19T13:56:13Z

With gcc-4.9.2, not any err here.
But, with gcc-7.3.1 together with this temporal solution, the same err is still there.

psychocoderHPC · 2019-02-19T14:43:14Z

@ax3l If ParserGridDistribution is the reason than we can create a cpp file and interfacing to it via a *.hpp file.
I will open a PR for it.

fix ComputationalRadiationPhysics#2898 Split the grid parser into a interface file `hpp` and the implementation `cpp` to avoid that boost regex is parsed by nvcc. Boost regex is very often the root of compile issues because nvcc is not able to split the host and device part correctly. Split `ParserGridDistribution` to avoid t

fix ComputationalRadiationPhysics#2898 Split the grid parser into a interface file `hpp` and the implementation `cpp` to avoid that boost regex is parsed by nvcc. Boost regex is very often the root of compile issues because nvcc is not able to split the host and device part correctly.

ax3l · 2019-02-19T16:10:25Z

@BifengLei please be aware that GCC 7.3.1 is newer than what NVCC 9.2 "knew" (think: "could test against") at its release (May 2018).
GCC 7.3.0 was released on Jan 25, 2018 and might be the last reliably working version for that release of CUDA.

BifengLei · 2019-02-19T16:24:46Z

@ax3l Thanks a lot. I will try GCC7.3.0 or lower version later.

fix ComputationalRadiationPhysics#2898 Split the grid parser into a interface file `hpp` and the implementation `cpp` to avoid that boost regex is parsed by nvcc. Boost regex is very often the root of compile issues because nvcc is not able to split the host and device part correctly.

ax3l · 2019-02-27T16:15:16Z

@BifengLei this problem should be solved in our dev branch with #2899 .
Thanks @psychocoderHPC for the fix!

fix ComputationalRadiationPhysics#2898 Split the grid parser into a interface file `hpp` and the implementation `cpp` to avoid that boost regex is parsed by nvcc. Boost regex is very often the root of compile issues because nvcc is not able to split the host and device part correctly.

ax3l added bug a bug in the project's code component: plugin in PIConGPU plugin component: third party third party libraries that are shipped and/or linked labels Feb 19, 2019

ax3l added this to the 0.4.0: CPU Support, Filter & Merging milestone Feb 19, 2019

ax3l added the affects latest release a bug that affects the latest stable release label Feb 19, 2019

ax3l added the backend: cuda CUDA backend label Feb 19, 2019

psychocoderHPC mentioned this issue Feb 19, 2019

split ParserGridDistribution into hpp/cpp file #2899

Merged

sbastrakov closed this as completed Jan 16, 2020

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Boost Error in ResourceLog #2898

Boost Error in ResourceLog #2898

BifengLei commented Feb 19, 2019

ax3l commented Feb 19, 2019 •

edited

Loading

ax3l commented Feb 19, 2019

BifengLei commented Feb 19, 2019

psychocoderHPC commented Feb 19, 2019

ax3l commented Feb 19, 2019 •

edited

Loading

BifengLei commented Feb 19, 2019

ax3l commented Feb 19, 2019 •

edited

Loading

BifengLei commented Feb 19, 2019

psychocoderHPC commented Feb 19, 2019 •

edited

Loading

ax3l commented Feb 19, 2019 •

edited

Loading

BifengLei commented Feb 19, 2019

ax3l commented Feb 27, 2019

Boost Error in ResourceLog #2898

Boost Error in ResourceLog #2898

Comments

BifengLei commented Feb 19, 2019

ax3l commented Feb 19, 2019 • edited Loading

ax3l commented Feb 19, 2019

BifengLei commented Feb 19, 2019

psychocoderHPC commented Feb 19, 2019

ax3l commented Feb 19, 2019 • edited Loading

BifengLei commented Feb 19, 2019

ax3l commented Feb 19, 2019 • edited Loading

BifengLei commented Feb 19, 2019

psychocoderHPC commented Feb 19, 2019 • edited Loading

ax3l commented Feb 19, 2019 • edited Loading

BifengLei commented Feb 19, 2019

ax3l commented Feb 27, 2019

ax3l commented Feb 19, 2019 •

edited

Loading

ax3l commented Feb 19, 2019 •

edited

Loading

ax3l commented Feb 19, 2019 •

edited

Loading

psychocoderHPC commented Feb 19, 2019 •

edited

Loading

ax3l commented Feb 19, 2019 •

edited

Loading