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Fix for multiblock GPU dists (#99)
* Fix for multiblock GPU dists Rectangular parts were being transposed to the wrong size, overwriting some elements and leaving others as uninitialised * Bump cuda version for azure pipelines
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3 files changed

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azure-pipelines.yml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -37,7 +37,7 @@ steps:
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# pushd src && make && make install && popd
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- script: |
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source activate pp_env
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export CUDA_HOME=/usr/local/cuda-12.6
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export CUDA_HOME=/usr/local/cuda-12.8
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export PATH=${CUDA_HOME}/bin${PATH:+:${PATH}}
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export LD_LIBRARY_PATH=${CUDA_HOME}/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
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export SKETCHLIB_INSTALL=azure
@@ -46,7 +46,7 @@ steps:
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- script: |
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source activate pp_env
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export CUDA_HOME=/usr/local/cuda-12.6
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export CUDA_HOME=/usr/local/cuda-12.8
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export PATH=${CUDA_HOME}/bin${PATH:+:${PATH}}
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export LD_LIBRARY_PATH=${CUDA_HOME}/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
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cd test && python run_test.py

pp_sketch/__init__.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -3,4 +3,4 @@
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'''PopPUNK sketching functions'''
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__version__ = '2.1.4'
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__version__ = '2.1.5'

src/gpu/gpu_api.cpp

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -201,8 +201,8 @@ void longToSquareBlock(NumpyMatrix &coreSquare, NumpyMatrix &accessorySquare,
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dummy_query_query, num_threads);
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} else {
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square_form = Eigen::Map<NumpyMatrix, 0, Eigen::InnerStride<2>>(
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blockMat.data(), sketch_subsample.ref_size,
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sketch_subsample.query_size);
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blockMat.data(), sketch_subsample.query_size,
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sketch_subsample.ref_size);
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}
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// Only update the upper triangle
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coreSquare.block(sketch_subsample.query_offset, sketch_subsample.ref_offset,
@@ -214,8 +214,8 @@ void longToSquareBlock(NumpyMatrix &coreSquare, NumpyMatrix &accessorySquare,
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dummy_query_query, num_threads);
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} else {
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square_form = Eigen::Map<NumpyMatrix, 0, Eigen::InnerStride<2>>(
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blockMat.data() + 1, sketch_subsample.ref_size,
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sketch_subsample.query_size);
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blockMat.data() + 1, sketch_subsample.query_size,
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sketch_subsample.ref_size);
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}
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accessorySquare.block(
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sketch_subsample.query_offset, sketch_subsample.ref_offset,

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