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cuda 12 build fails with missing header pinned_allocator.h #80

@rfox-mbl

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@rfox-mbl

My builds against cuda 12 are failing with the following:

[ 9%] Building NVCC (Device) object _deps/genomeworks-build/cudaaligner/CMakeFiles/cudaaligner.dir/src/cudaaligner_generated_hirschberg_myers_gpu.cu.o In file included from /bioware/root/SOURCES/racon/1.5.0/builds/x86_64/racon-1.5.0/build/_deps/genomeworks-src/cudaaligner/src/batched_device_matrices.cuh:25, from /bioware/root/SOURCES/racon/1.5.0/builds/x86_64/racon-1.5.0/build/_deps/genomeworks-src/cudaaligner/src/hirschberg_myers_gpu.cuh:20, from /bioware/root/SOURCES/racon/1.5.0/builds/x86_64/racon-1.5.0/build/_deps/genomeworks-src/cudaaligner/src/hirschberg_myers_gpu.cu:17: /bioware/root/SOURCES/racon/1.5.0/builds/x86_64/racon-1.5.0/build/_deps/genomeworks-src/common/base/include/claraparabricks/genomeworks/utils/pinned_host_vector.hpp:20:10: fatal error: thrust/system/cuda/experimental/pinned_allocator.h: No such file or directory 20 | #include <thrust/system/cuda/experimental/pinned_allocator.h> | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ compilation terminated. CMake Error at cudaaligner_generated_hirschberg_myers_gpu.cu.o.Release.cmake:220 (message):

As far as I have been able to determine, not having knowledge of cuda development, it seems that the cuda libraries may have changed in version 12 but I haven't been able to find release notes that detail the change. Also, this looks like it's a bundled package so I'm not positive I'm reporting this in the right place. Nevertheless, my racon build is breaking since there is no experimental subdirectory in the thrust/system/cuda directory and hence no relevant include files.
https://github.com/NVIDIA/thrust/tree/main/thrust/system/cuda

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