I'm trying to compile GenomeWorks using the lastest CUDA version, and there seem to be some breaking changes in thrust that generates some compilation errors, here are the errors reported when doing make -j install:
In file included from /home/qaguado/GenomeWorks/cudaaligner/src/batched_device_matrices.cuh:25,
from /home/qaguado/GenomeWorks/cudaaligner/src/ukkonen_gpu.cu:18:
/home/qaguado/GenomeWorks/common/base/include/claraparabricks/genomeworks/utils/pinned_host_vector.hpp:23:10: fatal error: thrust/system/cuda/experimental/pinned_allocator.h: No such file or directory
23 | #include <thrust/system/cuda/experimental/pinned_allocator.h>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
In file included from /home/qaguado/GenomeWorks/cudaaligner/src/batched_device_matrices.cuh:25,
from /home/qaguado/GenomeWorks/cudaaligner/src/hirschberg_myers_gpu.cuh:20,
from /home/qaguado/GenomeWorks/cudaaligner/src/hirschberg_myers_gpu.cu:17:
/home/qaguado/GenomeWorks/common/base/include/claraparabricks/genomeworks/utils/pinned_host_vector.hpp:23:10: fatal error: thrust/system/cuda/experimental/pinned_allocator.h: No such file or directory
23 | #include <thrust/system/cuda/experimental/pinned_allocator.h>
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
CMake Error at cudaaligner_generated_ukkonen_gpu.cu.o.Release.cmake:220 (message):
Error generating
/home/qaguado/GenomeWorks/build/cudaaligner/CMakeFiles/cudaaligner.dir/src/./cudaaligner_generated_ukkonen_gpu.cu.o
I tried to fix the error by doing the following changes in /common/base/include/claraparabricks/genomeworks/utils/pinned_host_vector.hpp (from this NVIDIA forum answer):
I'm trying to compile GenomeWorks using the lastest CUDA version, and there seem to be some breaking changes in thrust that generates some compilation errors, here are the errors reported when doing
make -j install
:I tried to fix the error by doing the following changes in
/common/base/include/claraparabricks/genomeworks/utils/pinned_host_vector.hpp
(from this NVIDIA forum answer):But it still fails with the following error:
Are there any plans to make GenomeWorks compatible with CUDA 12?
Thanks