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

Author: johnlees

azure-pipelines.yml

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

pp_sketch/__init__.py

@@ -3,4 +3,4 @@
 
 '''PopPUNK sketching functions'''
 
-__version__ = '2.1.4'
+__version__ = '2.1.5'

src/gpu/gpu_api.cpp

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