feat: GPU keep-on-device + kvikio (GDS) reader + pipeline GPU wiring#112
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FIrgolitsch wants to merge 13 commits intosphinx-configfrom
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feat: GPU keep-on-device + kvikio (GDS) reader + pipeline GPU wiring#112FIrgolitsch wants to merge 13 commits intosphinx-configfrom
FIrgolitsch wants to merge 13 commits intosphinx-configfrom
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linumpy/gpu/kvikio_zarr.py: read_zarr_v2_to_gpu() loads an uncompressed zarr v2 array directly into a CuPy array using kvikio.CuFile.pread, bypassing the host bounce buffer when GDS is active. scripts/linum_benchmark_kvikio_zarr.py: benchmarks the GDS path against the conventional zarr.open + numpy + cupy.asarray path; supports synthetic dataset generation. Prototype scope: zarr v2, compressor=None, order=C. Compressed chunks (blosc/lz4) need nvCOMP for on-device decompression and are out of scope here.
CuFile.pread requires a contiguous device buffer; out[slices] is generally non-contiguous. Read each chunk into a single reused chunk-shaped scratch and copy into the output.
… in gpu_zarr_context
…focal curvature roll
…c_grid process Co-authored-by: Copilot <copilot@github.com>
This was referenced Apr 30, 2026
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PR — GPU keep-on-device + kvikio (GDS) reader + pipeline GPU wiring
Extends the GPU stack with end-to-end on-device data flow for the OCT reconstruction pipeline and adds a GPUDirect Storage (GDS) reader as a fast path for reading uncompressed zarr arrays straight into device memory.
GPU keep-on-device
linumpy.gpu.zarr_iowithgpu_zarr_context()(useszarr.config.enable_gpu()) andread_zarr_to_gpu(...)with auto backend selection (kvikio when available, zarr-gpu otherwise).linumpy.gpu.interpolation: device-preservingresize,affine_transform,map_coordinates.linumpy.gpu.interfacewith a GPU implementation offind_tissue_interface(no-mask path) usingcupyxfilters.linumpy.geometry.interface.find_tissue_interface(..., use_gpu=...)andlinumpy.mosaic.stacking.find_z_overlap(..., use_gpu=...)now route to GPU when requested.linum_aip.pyandlinum_resample_mosaic_grid.pyusegpu_zarr_contextto keep tiles on-device through the slab loop and writer.linum_detect_focal_curvature.py: vectorized roll viatake_along_axis(xpdispatch) and--use_gpu/--no-use_gpu.linum_stack_slices_motor.py:--use_gpu/--no-use_gpuplumbed tofind_z_overlap.kvikio (GDS) reader (prototype)
linumpy/gpu/kvikio_zarr.py: GDS reader for raw uncompressed zarr v2 + v3.Corder, mismatched endian) withNotImplementedError.CuFile.pread.scripts/linum_benchmark_kvikio_zarr.py: benchmark with kvikio andzarr.config.enable_gpu()paths for comparison.read_zarr_to_gpufalls back to zarr-gpu when kvikio is in compat mode, when arrays aren't GDS-compatible, or on any runtime failure.Server / build
shell_scripts/server_setup/nvfs_kernel7_patch.sh: nvidia-fs 2.28.4 patch for kernel 7.0; symvers helper now also handles.ko.zst.pyproject.toml: bumpome-zarrto>=0.16.0(NGFF 0.5).Nextflow pipeline GPU wiring
fix_focal_curvatureandstackprocesses pass--use_gpu/--no-use_gpufromparams.use_gpu.nextflow.config:withName: "fix_focal_curvature"getsmaxForks = params.use_gpu ? 4 : null.withName: "resample_mosaic_grid":maxForks = params.use_gpu ? 6 : null(measured ~1 GB GPU mem per fork; IO-gated)._run_pipelined: prefetch + GPU compute pipeline; periodic free of cupy memory pool.