Remove the mismatched version warning (#97)

* Remove the mismatched version warning

* Add setuptools to requirements

* Two attempts at nvcc CI

* Two fix attempts

* Try newer cuda version

* Replace hardcoded CUDA path in Makefile

* Unpin cuda in environment.yaml

* Remove CUDA_HOME export in workflow

* Still seem to need explicit CUDA_HOME in with 12.6

Goes in azure config which is better at least

Author: johnlees

.github/workflows/azure_ci.yml

@@ -3,7 +3,7 @@
 # Add steps that analyze code, save the dist with the build record, publish to a PyPI-compatible index, and more:
 # https://docs.microsoft.com/azure/devops/pipelines/languages/python
 
-name: Run tests
+name: Run tests (CPU)
 
 on: [push]
 

azure-pipelines.yml

@@ -4,7 +4,7 @@ trigger:
 - master
 
 pool:
-  vmImage: 'ubuntu-20.04'
+  vmImage: 'ubuntu-22.04'
 strategy:
   matrix:
     Python38:
@@ -24,12 +24,10 @@ steps:
   displayName: Add conda to PATH
 
 - script: |
-    wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
-    sudo mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
-    sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
-    sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
+    wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-keyring_1.1-1_all.deb
+    sudo dpkg -i cuda-keyring_1.1-1_all.deb
     sudo apt-get update
-    sudo apt-get -y install cuda=11.2.2-1
+    sudo apt-get -y install cuda-toolkit
   displayName: Install nvcc
 
 - bash: conda env create --file environment.yml
@@ -39,7 +37,7 @@ steps:
 # pushd src && make && make install && popd
 - script: |
     source activate pp_env
-    export CUDA_HOME=/usr/local/cuda-11.2
+    export CUDA_HOME=/usr/local/cuda-12.6
     export PATH=${CUDA_HOME}/bin${PATH:+:${PATH}}
     export LD_LIBRARY_PATH=${CUDA_HOME}/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
     export SKETCHLIB_INSTALL=azure
@@ -48,7 +46,7 @@ steps:
 
 - script: |
     source activate pp_env
-    export CUDA_HOME=/usr/local/cuda-11.2
+    export CUDA_HOME=/usr/local/cuda-12.6
     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

environment.yml

@@ -7,6 +7,7 @@ channels:
 dependencies:
   - python
   - pip
+  - setuptools
   - numpy
   - scipy
   - docopt
@@ -21,4 +22,4 @@ dependencies:
   - openblas
   - libgfortran-ng
   - nvcc_linux-64
-  - cudatoolkit==11.2 # This is pinned due to version install on azure, see azure-pipelines.yml
+  - cudatoolkit # This is pinned due to version install on azure, see azure-pipelines.yml

requirements.txt

@@ -3,3 +3,4 @@ numpy
 pybind11
 scipy
 docopt
+setuptools

src/Makefile

@@ -34,7 +34,7 @@ CUDAFLAGS +=-std=c++17 -Xcompiler -fPIC --cudart static --relocatable-device-cod
 ifdef GPU
 	CXXFLAGS += -DGPU_AVAILABLE
 	CUDAFLAGS += -gencode arch=compute_86,code=sm_86
-	CUDA_LDFLAGS += -L/usr/local/cuda-11.2/lib64
+	CUDA_LDFLAGS += -L${CUDA_HOME}/lib64
 endif
 
 PYTHON_LIB = pp_sketchlib$(shell python3-config --extension-suffix)

src/sketchlib_bindings.cpp

@@ -99,11 +99,6 @@ NumpyMatrix queryDatabase(const std::string &ref_db_name,
     throw std::runtime_error(
         "Extracting Jaccard distances not supported on GPU");
   }
-  if (!same_db_version(ref_db_name, query_db_name)) {
-    std::cerr << "WARNING: versions of input databases sketches are different,"
-                 " results may not be compatible"
-              << std::endl;
-  }
 
   std::vector<Reference> ref_sketches =
       load_sketches(ref_db_name, ref_names, kmer_lengths, false);