Closed WassimTenachi closed 2 years ago
lwang-astro
commented
2 years ago I notice that for compiling cuda code, a lot of include pathes from anaconda3 are shown in your log. Not sure whether this is the reason. I have committed a update of Makefile.in in the master branch together with a few updates. Could you try to update PeTar (git pull), configure and make again?
WassimTenachi
commented
2 years ago Hi, Thank you very much for your answer. I 've updated but it seems to give the same kind of errors (here are the first lines) . Do you think it might have something to do with my modules versions (gcc, mpi, cuda) ? I yes do you have a combination that you know works well ? Thanks a lot for your time !
nvcc -std=c++11 -I /usr/local/cuda/cuda-7.5/samples/common/inc -Xcompiler="-O3 -Wall -std=c++11 -fopenmp -D PARTICLE_SIMULATOR_THREAD_PARALLEL -D USE_GPU -D GPU_PROFILE -DINTRINSIC_X86 -march=core-avx2 -D DIV_FIX -D USE_SIMD -D PROFILE -D PARTICLE_SIMULATOR_GPU_MULIT_WALK_INDEX -D USE_QUAD -D SOFT_PERT -D AR_TTL -D AR_SLOWDOWN_TREE -D AR_SLOWDOWN_TIMESCALE -D CLUSTER_VELOCITY -D HARD_CHECK_ENERGY -D HARD_COUNT_NO_NEIGHBOR -D ADJUST_GROUP_PRINT -D TIDAL_TENSOR_3RD -D STELLAR_EVOLUTION -D BSEBBF -D BSE_BASE -D EXTERNAL_POT_IN_PTCL -D RECORD_CM_IN_HEADER -D GALPY " -I ./bse-interface -I./src -I/mypath/PeTar_setup/FDPS/src -I/mypath/PeTar_setup/SDAR/src -c ./src/force_gpu_cuda.cu -o build/force_gpu_cuda.o /usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/type_traits(1049): error: identifier "__is_assignable" is undefined
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/type_traits(1049): error: type name is not allowed
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/type_traits(1049): error: type name is not allowed
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/utility(307): error: identifier "__integer_pack" is undefined
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/utility(307): error: pack expansion does not make use of any argument packs
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/functional(545): error: expression must have a constant value
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/functional(549): error: expression must have a constant value
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/stl_tree.h(452): error: expression must have a constant value
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/stl_tree.h(1679): error: identifier "_Compare" is undefined
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/stl_tree.h(2012): error: identifier "_Compare" is undefined
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/type_traits(2431): error: class "std::enable_if<
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/x86_64-pc-linux-gnu/bits/basic_file.h(80): error: no instance of overloaded function "std::swap" matches the argument list argument types are: (__nv_bool, __nv_bool)
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/stl_pair.h(378): error: invalid redeclaration of member function "std::pair<_T1, _T2>::operator=(std::conditional<std::and_<std::is_copy_assignable<_T1>, std::is_copy_assignable<_T2>>::value, const std::pair<_T1, _T2> &, const std::__nonesuch_no_braces &>::type) [with _T1=nv_bool, _T2=std::size_t]" (367): here detected during instantiation of class "std::pair<_T1, _T2> [with _T1=__nv_bool, _T2=std::size_t]" /usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/hashtable_policy.h(582): here
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/stl_pair.h(378): error: invalid redeclaration of member function "std::pair<_T1, _T2>::operator=(std::conditional<std::and_<std::is_copy_assignable<_T1>, std::is_copy_assignable<_T2>>::value, const std::pair<_T1, _T2> &, const std::__nonesuch_no_braces &>::type) [with _T1=nv_bool, _T2=int]" (367): here detected during instantiation of class "std::pair<_T1, _T2> [with _T1=__nv_bool, _T2=int]" /usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/hashtable_policy.h(594): here
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/hashtable.h(192): error: expression must have a constant value
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/hashtable.h(195): error: expression must have a constant value
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/hashtable.h(197): error: expression must have a constant value
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/hashtable.h(1383): error: identifier "_H1" is undefined
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/hashtable.h(1384): error: identifier "_Equal" is undefined
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/bits/stl_tree.h(700): error: identifier "_Node_allocator" is undefined
detected during instantiation of "std::_Rb_tree<_Key, _Val, _KeyOfValue, _Compare, _Alloc>::_Rb_tree_impl<_Key_compare,
lwang-astro
commented
2 years ago I can succesfully compile the code with CUDA on Ubuntu 18.04/20.04 LTS, where the gcc/g++ version is 9.4.0 and cuda version is 11.0. From your error message, I guess that your g++ version may not match your cuda (nvcc) version.
WassimTenachi
commented
2 years ago Hi, I was able to make it work with cuda disabled ! :) Thanks again for your help.
Hello,
I am trying to install PeTar and I think I might have missed something regarding the c++ requirements.
My config:
1) slurm/slurm(latest) 2) gcc/gcc-8 3) openmpi/openmpi-3.1.gcc8 4) cuda/cuda-7.5
My python path looks like:
/mypath/PeTar_setup/include
My path looks like:
/usr/local/bin: /usr/local/cuda/cuda-7.5/bin: /usr/local/openmpi/openmpi-3.1.3-g8/bin: /usr/local/gcc/gcc-8.2.0/bin: /mypath/anaconda3/bin: /mypath/anaconda3/condabin: /usr/local/bin: /usr/local/Modules/5.0.1/bin: /usr/lib64/qt-3.3/bin: /usr/local/bin: /usr/bin: /usr/local/sbin: /usr/sbin: /usr/local/slurm/bin: /mypath/bin: /mypath/PeTar_setup/bin: /mypath/anaconda3/lib/python3.9/site-packages/galpy:
I am running this command to create the makefile:
./configure --with-fdps-prefix=/mypath/PeTar_setup/FDPS --with-sdar-prefix=/mypath/PeTar_setup/SDAR --with-mpi=yes --with-external=galpy --with-galpy-prefix=/mypath/anaconda3/lib/python3.9/site-packages/galpy --with-interrupt=bse --enable-cuda --with-cuda-sdk-prefix=/usr/local/cuda/cuda-7.5 CC=mpic++
When running make I get the following output:
nvcc -std=c++17 -I /usr/local/cuda/cuda-7.5/samples/common/inc -Xcompiler="-O3 -Wall -std=c++17 -fopenmp -D PARTICLE_SIMULATOR_THREAD_PARALLEL -D USE_GPU -D GPU_PROFILE -DINTRINSIC_X86 -march=core-avx2 -D DIV_FIX -D USE_SIMD -D PROFILE -D PARTICLE_SIMULATOR_GPU_MULIT_WALK_INDEX -D USE_QUAD -D SOFT_PERT -D AR_TTL -D AR_SLOWDOWN_TREE -D AR_SLOWDOWN_TIMESCALE -D CLUSTER_VELOCITY -D HARD_CHECK_ENERGY -D HARD_COUNT_NO_NEIGHBOR -D ADJUST_GROUP_PRINT -D TIDAL_TENSOR_3RD -D STELLAR_EVOLUTION -D BSEBBF -D BSE_BASE -D EXTERNAL_POT_IN_PTCL -D RECORD_CM_IN_HEADER -D GALPY" -I ./bse-interface -I ./galpy-interface -I/mypath/anaconda3/lib/python3.9/site-packages/galpy -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/snapshot -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/snapshot/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/orbit -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/orbit/orbit_c_ext -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/orbit/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/util -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/util/interp_2d -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/util/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/df -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/df/data -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/df/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/actionAngle -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/actionAngle/actionAngle_c_ext -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/actionAngle/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/actionAngle/actionAngleTorus_c_ext -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/potential -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/potential/potential_c_ext -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/potential/interppotential_c_ext -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/potential/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/pycache -I/mypath/anaconda3/include -I./src -I/mypath/PeTar_setup/FDPS/src -I/mypath/PeTar_setup/SDAR/src -c ./src/force_gpu_cuda.cu -o build/force_gpu_cuda.o nvcc fatal : Value 'c++17' is not defined for option 'std' make: *** [build/force_gpu_cuda.o] Error 1
I noticed that in the makefile c++17 is used, I tried replacing it with c++11 (as c++11 is mentioned in the readme) which gives me the following output (sorry for the long output) see below. Do you have an idea of how to solve this problem ? Thanks a lot for your help and sorry if this is a silly question.
nvcc -std=c++11 -I /usr/local/cuda/cuda-7.5/samples/common/inc -Xcompiler="-O3 -Wall -std=c++11 -fopenmp -D PARTICLE_SIMULATOR_THREAD_PARALLEL -D USE_GPU -D GPU_PROFILE -DINTRINSIC_X86 -march=core-avx2 -D DIV_FIX -D USE_SIMD -D PROFILE -D PARTICLE_SIMULATOR_GPU_MULIT_WALK_INDEX -D USE_QUAD -D SOFT_PERT -D AR_TTL -D AR_SLOWDOWN_TREE -D AR_SLOWDOWN_TIMESCALE -D CLUSTER_VELOCITY -D HARD_CHECK_ENERGY -D HARD_COUNT_NO_NEIGHBOR -D ADJUST_GROUP_PRINT -D TIDAL_TENSOR_3RD -D STELLAR_EVOLUTION -D BSEBBF -D BSE_BASE -D EXTERNAL_POT_IN_PTCL -D RECORD_CM_IN_HEADER -D GALPY" -I ./bse-interface -I ./galpy-interface -I/mypath/anaconda3/lib/python3.9/site-packages/galpy -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/snapshot -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/snapshot/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/orbit -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/orbit/orbit_c_ext -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/orbit/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/util -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/util/interp_2d -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/util/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/df -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/df/data -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/df/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/actionAngle -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/actionAngle/actionAngle_c_ext -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/actionAngle/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/actionAngle/actionAngleTorus_c_ext -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/potential -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/potential/potential_c_ext -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/potential/interppotential_c_ext -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/potential/pycache -I/mypath/anaconda3/lib/python3.9/site-packages/galpy/pycache -I/mypath/anaconda3/include -I./src -I/mypath/PeTar_setup/FDPS/src -I/mypath/PeTar_setup/SDAR/src -c ./src/force_gpu_cuda.cu -o build/force_gpu_cuda.o /usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/type_traits(1049): error: identifier "__is_assignable" is undefined
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/type_traits(1049): error: type name is not allowed
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/type_traits(1049): error: type name is not allowed
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/utility(307): error: identifier "__integer_pack" is undefined
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/utility(307): error: pack expansion does not make use of any argument packs
/usr/local/gcc/gcc-8.2.0/include/c++/8.2.0/functional(545): error: expression must have a constant value