Dear all,
I'm having a problem compiling AMBER22 with GCC8/CUDA10.2 and GCC9/CUDA11.2. The first combination was used successfully earlier to compile AMBER22 with CUDA on one machine, however it does not compile now. Furthermore, using the same TAR archives and build environment I am not able to compile it on a different machine.
We are transitioning to GCC9 and CUDA 11.X (currently the default is 11.2, I have also tried 11.4) on the cluster and I have also tried these combinations; unfortunately without luck on both machines.
The TAR sums: 769e13da80489db8c046c45d62d40e9a AmberTools22.tar.bz2, 593ebf62e152f4add0f171b631c18bdc Amber22.tar.bz2
The build environment set through "module load" on both machines running AlmaLinux release 8.5: python/3.8, perl/5.26, gcc/8.2 (9.4 also tried), cmake/3.17 (3.20 also tried), cuda/10.2 (11.2 and 11.4 also tried), openmpi/4.0, automake/1.16, bison/3.7, flex/2.6
The cmake call for serial build, which compiles and passes tests: cmake $AMBER_PREFIX/amber22_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 -DCOMPILER=GNU -DOPTIMIZE=FALSE -DSSE=FALSE -DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE -DDOWNLOAD_MINICONDA=TRUE 2>&1 | tee cmake_serial.log
The cmake call for CUDA build, which fails: cmake $AMBER_PREFIX/amber22_src -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber22 -DCOMPILER=GNU -DOPTIMIZE=FALSE -DSSE=FALSE -DMPI=FALSE -DCUDA=TRUE -DINSTALL_TESTS=TRUE -DDOWNLOAD_MINICONDA=TRUE 2>&1 | tee cmake_serialcuda.log
Please let me know if you have any suggestions for what I should do to compile the CUDA enabled pmemd or if another combination of GCC and CUDA is recommended.
Thank you for your time.
/MH
The following are some outputs from the process:
1) For serial build cmake gives the following warnings, however "make install" proceeds without issue.
#####
CMake Warning at AmberTools/src/cpptraj/src/CMakeLists.txt:129 (add_executable):
Cannot generate a safe runtime search path for target cpptraj because files
in some directories may conflict with libraries in implicit directories:
runtime library [libz.so.1] in /usr/lib64 may be hidden by files in:
/util/opt/anaconda/deployed-conda-envs/packages/cmake/envs/cmake-3.17.0/lib
Some of these libraries may not be found correctly.
CMake Warning at AmberTools/src/cpptraj/src/CMakeLists.txt:137 (add_library):
Cannot generate a safe runtime search path for target libcpptraj because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libz.so.1] in /usr/lib64 may be hidden by files in:
/util/opt/anaconda/deployed-conda-envs/packages/cmake/envs/cmake-3.17.0/lib
Some of these libraries may not be found correctly.
CMake Warning at AmberTools/src/ambpdb/CMakeLists.txt:6 (add_executable):
Cannot generate a safe runtime search path for target ambpdb because files
in some directories may conflict with libraries in implicit directories:
runtime library [libz.so.1] in /usr/lib64 may be hidden by files in:
/util/opt/anaconda/deployed-conda-envs/packages/cmake/envs/cmake-3.17.0/lib
Some of these libraries may not be found correctly.
CMake Warning at AmberTools/src/moft/CMakeLists.txt:3 (add_executable):
Cannot generate a safe runtime search path for target metatwist because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libz.so.1] in /usr/lib64 may be hidden by files in:
/util/opt/anaconda/deployed-conda-envs/packages/cmake/envs/cmake-3.17.0/lib
Some of these libraries may not be found correctly.
2) CUDA build cmake warnings.
#####
-- Configuring done
CMake Warning at AmberTools/src/cpptraj/src/CMakeLists.txt:129 (add_executable):
Cannot generate a safe runtime search path for target cpptraj because files
in some directories may conflict with libraries in implicit directories:
runtime library [libz.so.1] in /usr/lib64 may be hidden by files in:
/util/opt/anaconda/deployed-conda-envs/packages/cmake/envs/cmake-3.17.0/lib
Some of these libraries may not be found correctly.
CMake Warning at AmberTools/src/cpptraj/src/CMakeLists.txt:137 (add_library):
Cannot generate a safe runtime search path for target libcpptraj because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libz.so.1] in /usr/lib64 may be hidden by files in:
/util/opt/anaconda/deployed-conda-envs/packages/cmake/envs/cmake-3.17.0/lib
Some of these libraries may not be found correctly.
CMake Warning at cmake/CopyTarget.cmake:58 (add_executable):
Cannot generate a safe runtime search path for target cpptraj.cuda because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libz.so.1] in /usr/lib64 may be hidden by files in:
/util/opt/anaconda/deployed-conda-envs/packages/cmake/envs/cmake-3.17.0/lib
Some of these libraries may not be found correctly.
Call Stack (most recent call first):
AmberTools/src/cpptraj/src/CMakeLists.txt:319 (copy_target)
CMake Warning at cmake/CopyTarget.cmake:43 (add_library):
Cannot generate a safe runtime search path for target libcpptraj_cuda
because files in some directories may conflict with libraries in implicit
directories:
runtime library [libz.so.1] in /usr/lib64 may be hidden by files in:
/util/opt/anaconda/deployed-conda-envs/packages/cmake/envs/cmake-3.17.0/lib
Some of these libraries may not be found correctly.
Call Stack (most recent call first):
AmberTools/src/cpptraj/src/CMakeLists.txt:320 (copy_target)
CMake Warning at AmberTools/src/ambpdb/CMakeLists.txt:6 (add_executable):
Cannot generate a safe runtime search path for target ambpdb because files
in some directories may conflict with libraries in implicit directories:
runtime library [libz.so.1] in /usr/lib64 may be hidden by files in:
/util/opt/anaconda/deployed-conda-envs/packages/cmake/envs/cmake-3.17.0/lib
Some of these libraries may not be found correctly.
CMake Warning at AmberTools/src/moft/CMakeLists.txt:3 (add_executable):
Cannot generate a safe runtime search path for target metatwist because
files in some directories may conflict with libraries in implicit
directories:
runtime library [libz.so.1] in /usr/lib64 may be hidden by files in:
/util/opt/anaconda/deployed-conda-envs/packages/cmake/envs/cmake-3.17.0/lib
Some of these libraries may not be found correctly.
-- Generating done
3) CUDA build "make install" error
#####
[ 95%] Building NVCC (Device) object src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
/util/opt/cuda/10.2/include/thrust/detail/allocator/allocator_traits.h(245): error: class "thrust::detail::device_delete_allocator" has no member "value_type"
detected during:
instantiation of class "thrust::detail::allocator_traits<Alloc> [with Alloc=thrust::detail::device_delete_allocator]"
(398): here
instantiation of class "thrust::detail::allocator_system<Alloc> [with Alloc=thrust::detail::device_delete_allocator]"
/util/opt/cuda/10.2/include/thrust/detail/allocator/destroy_range.inl(137): here
instantiation of "thrust::detail::allocator_traits_detail::enable_if_destroy_range_case2<Allocator, Pointer>::type thrust::detail::allocator_traits_detail::destroy_range(Allocator &, Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator, Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
/util/opt/cuda/10.2/include/thrust/detail/allocator/destroy_range.inl(158): here
instantiation of "void thrust::detail::destroy_range(Allocator &, Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator, Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
/util/opt/cuda/10.2/include/thrust/detail/device_delete.inl(42): here
instantiation of "void thrust::device_delete(thrust::device_ptr<T>, size_t) [with T=xray::Sym33]"
/Software/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu(116): here
/util/opt/cuda/10.2/include/thrust/detail/type_traits.h(442): error: class "thrust::iterator_system<<error-type> *>" has no member "type"
detected during:
instantiation of class "thrust::detail::eval_if<false, Then, Else> [with Then=thrust::detail::allocator_traits_detail::nested_system_type<thrust::detail::device_delete_allocator>, Else=thrust::iterator_system<<error-type> *>]"
/util/opt/cuda/10.2/include/thrust/detail/allocator/allocator_traits.h(320): here
instantiation of class "thrust::detail::allocator_traits<Alloc> [with Alloc=thrust::detail::device_delete_allocator]"
/util/opt/cuda/10.2/include/thrust/detail/allocator/allocator_traits.h(398): here
instantiation of class "thrust::detail::allocator_system<Alloc> [with Alloc=thrust::detail::device_delete_allocator]"
/util/opt/cuda/10.2/include/thrust/detail/allocator/destroy_range.inl(137): here
instantiation of "thrust::detail::allocator_traits_detail::enable_if_destroy_range_case2<Allocator, Pointer>::type thrust::detail::allocator_traits_detail::destroy_range(Allocator &, Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator, Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
/util/opt/cuda/10.2/include/thrust/detail/allocator/destroy_range.inl(158): here
instantiation of "void thrust::detail::destroy_range(Allocator &, Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator, Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
/util/opt/cuda/10.2/include/thrust/detail/device_delete.inl(42): here
instantiation of "void thrust::device_delete(thrust::device_ptr<T>, size_t) [with T=xray::Sym33]"
/Software/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu(116): here
/util/opt/cuda/10.2/include/thrust/detail/allocator/allocator_traits.h(407): error: class "thrust::detail::eval_if<<error-constant>, thrust::detail::add_reference<<error-type>>, thrust::detail::identity_<<error-type>>>" has no member "type"
detected during:
instantiation of class "thrust::detail::allocator_system<Alloc> [with Alloc=thrust::detail::device_delete_allocator]"
/util/opt/cuda/10.2/include/thrust/detail/allocator/destroy_range.inl(137): here
instantiation of "thrust::detail::allocator_traits_detail::enable_if_destroy_range_case2<Allocator, Pointer>::type thrust::detail::allocator_traits_detail::destroy_range(Allocator &, Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator, Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
/util/opt/cuda/10.2/include/thrust/detail/allocator/destroy_range.inl(158): here
instantiation of "void thrust::detail::destroy_range(Allocator &, Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator, Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
/util/opt/cuda/10.2/include/thrust/detail/device_delete.inl(42): here
instantiation of "void thrust::device_delete(thrust::device_ptr<T>, size_t) [with T=xray::Sym33]"
/Software/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu(116): here
/util/opt/cuda/10.2/include/thrust/detail/allocator/allocator_traits.inl(359): error: more than one instance of overloaded function "thrust::detail::allocator_traits_detail::system" matches the argument list:
function template "thrust::detail::enable_if<thrust::detail::allocator_traits_detail::has_member_system<Alloc>::value, thrust::detail::allocator_system<Alloc>::type &>::type thrust::detail::allocator_traits_detail::system(Alloc &)"
function template "thrust::detail::disable_if<thrust::detail::allocator_traits_detail::has_member_system<Alloc>::value, thrust::detail::allocator_system<Alloc>::type>::type thrust::detail::allocator_traits_detail::system(Alloc &)"
argument types are: (thrust::detail::device_delete_allocator)
detected during:
instantiation of "thrust::detail::allocator_system<Alloc>::get_result_type thrust::detail::allocator_system<Alloc>::get(Alloc &) [with Alloc=thrust::detail::device_delete_allocator]"
/util/opt/cuda/10.2/include/thrust/detail/allocator/destroy_range.inl(137): here
instantiation of "thrust::detail::allocator_traits_detail::enable_if_destroy_range_case2<Allocator, Pointer>::type thrust::detail::allocator_traits_detail::destroy_range(Allocator &, Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator, Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
/util/opt/cuda/10.2/include/thrust/detail/allocator/destroy_range.inl(158): here
instantiation of "void thrust::detail::destroy_range(Allocator &, Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator, Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
/util/opt/cuda/10.2/include/thrust/detail/device_delete.inl(42): here
instantiation of "void thrust::device_delete(thrust::device_ptr<T>, size_t) [with T=xray::Sym33]"
/Software/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu(116): here
/util/opt/cuda/10.2/include/thrust/detail/allocator/destroy_range.inl(137): error: no instance of overloaded function "thrust::for_each_n" matches the argument list
argument types are: (<error-type>, thrust::device_ptr<xray::Sym33>, size_t, thrust::detail::allocator_traits_detail::gozer)
detected during:
instantiation of "thrust::detail::allocator_traits_detail::enable_if_destroy_range_case2<Allocator, Pointer>::type thrust::detail::allocator_traits_detail::destroy_range(Allocator &, Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator, Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
(158): here
instantiation of "void thrust::detail::destroy_range(Allocator &, Pointer, Size) [with Allocator=thrust::detail::device_delete_allocator, Pointer=thrust::device_ptr<xray::Sym33>, Size=size_t]"
/util/opt/cuda/10.2/include/thrust/detail/device_delete.inl(42): here
instantiation of "void thrust::device_delete(thrust::device_ptr<T>, size_t) [with T=xray::Sym33]"
/Software/amber22_src/src/pmemd/src/xray/cuda/src/xray/BulkMaskGPU.cu(116): here
5 errors detected in the compilation of "/tmp/tmpxft_0025d7fc_00000000-11_BulkMaskGPU.compute_61.cpp1.ii".
CMake Error at pmemd_xray_cuda_generated_BulkMaskGPU.cu.o.RELEASE.cmake:278 (message):
Error generating file
/Software/amber22_src/build/src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/./pmemd_xray_cuda_generated_BulkMaskGPU.cu.o
make[2]: *** [src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/build.make:82: src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/src/xray/pmemd_xray_cuda_generated_BulkMaskGPU.cu.o] Error 1
make[2]: Leaving directory '/Software/amber22_src/build'
make[1]: *** [CMakeFiles/Makefile2:8776: src/pmemd/src/xray/cuda/CMakeFiles/pmemd_xray_cuda.dir/all] Error 2
make[1]: Leaving directory '/Software/amber22_src/build'
make: *** [Makefile:169: all] Error 2
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Received on Thu Aug 04 2022 - 13:33:11 PDT
