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NVIDIA-Genomics-Research / GenomeWorks

SDK for GPU accelerated genome assembly and analysis
https://clara-parabricks.github.io/GenomeWorks/
Apache License 2.0
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@GW_USE_DEVICE_ALLOCATOR_FILE@ #634

Open pb-cdunn opened 3 years ago

pb-cdunn commented 3 years ago

Set @GW_USE_DEVICE_ALLOCATOR_FILE@ based on gw_enable_caching_allocator, to include only one DefaultDeviceAllocator for a given installation.

This way, after the library is built and installed, the user does not need to specify -DGW_ENABLE_CACHING_ALLOCATOR, which would currently select the DefaultDeviceAllocator to use.

I have not tested this yet. (I think we will need to add the build-directory to the include path.) I wanted to get opinions on this idea first.

To be clear, here is the error that can hit if we fail to use the same compilation flags as when the library was installed:

src/libpancake.so.1.1.0: undefined reference to
`claraparabricks::genomeworks::cudaaligner::create_aligner(
    claraparabricks::genomeworks::cudaaligner::AlignmentType, int, CUstream_st*, int,
    claraparabricks::genomeworks::CudaMallocAllocator<char>, long)'
GPUtester commented 3 years ago

Can one of the admins verify this patch?

ahehn-nv commented 3 years ago

HI @pb-cdunn , thanks for submitting this PR. This certainly is a problem that needs to be addressed. We are evaluating your PR and will get back to you soon.

ohadmo commented 3 years ago

ok to test