Hi,
On Sat, Jun 25, 2022 at 05:17:19AM +0000, Hashemi, Mohtadin via AMBER wrote:
> 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
If the tests generally pass then i suspect the warnings in 1 can be ignored.
For 3 try this workaround:
cd amber22_src/src/pmemd/src
mv CMakeLists.txt CMakeLists.txt.original
cp CMakeLists.txt.noxray CMakeLists.txt
# rebuild
cd amber22_src/build
./clean_build
./run_cmake
make
This problem was detected during beta testing on various platforms:
RHELS 7.9 with GNU 9.1.0 and nvcc's 11.2.152, 11.1.105, 11.0.221;
CentOS 7.9 with GNU 10.2.0 and nvcc 11.1.74.
And was reported by user Felix Bangerter
on CentOS 7.8 with GNU 7.1.0 and CUDA 10.2.89.
For him the same problems did not occur when using CUDA 11.4.1.
good luck,
scott
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Received on Thu Aug 04 2022 - 13:33:12 PDT
