running_on_nusc_cluster.md

0. Download cmake 3.20 (already done):

   • https://github.com/Kitware/CMake/releases/download/v3.20.3/cmake-3.20.3-linux-x86_64.tar.gz
   • tar -xvzf cmake-3.20.3-linux-x86_64.tar.gz

1. Download and unpack source files: https://github.com/friofry/motif_finder_cuda/archive/refs/tags/v1.0.zip

2. Run the a6500g10q node:

qsub -I -l walltime=00:30:00 -l select=1:ngpus=4:ncpus=12:mem=40gb -q a6500g10q@vm-pbs2

3. Unpack the sources:

unzip motif_finder_cuda-1.0.zip -d .

4. Navigate to the sourcedir:

cd motif_finder_cuda-1.0

5. Create build dir and navigate to it:

mkdir build
cd build

6. Configure:

Easy way: ~/cmake-3.20.3-linux-x86_64/bin/cmake -DCMAKE_BUILD_TYPE=Release ..

If it doesn't work:

• Add to CUDA_COMPILER to path:

export PATH="/opt/shared/nvidia/cuda-10.2.89/bin:$PATH";

• Configure the project:

export CC=gcc-8; export CXX=g++-8; ~/cmake-3.20.3-linux-x86_64/bin/cmake -DCMAKE_CUDA_HOST_COMPILER=/usr/bin/g++-8 -DCUDA_TOOLKIT_ROOT_DIR=/opt/shared/nvidia/cuda-10.2.89/  -DCMAKE_BUILD_TYPE=Release ..

7. Build:

~/cmake-3.20.3-linux-x86_64/bin/cmake --build . -j

8. Run:

• Copy test data:

cp ../motif_finder_gpu/init.ini ../motif_finder_gpu/test_12.fst motif_finder_gpu/

• Run:

cd motif_finder_gpu
./motif_finder_gpu