Running and Verification

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Create a working directory.

   mkdir -p path/to/CASE

3. Go to the working directory.

   cd /path/to/CASE

4. Obtain the test case and the binary file.

   wget https://www.ks.uiuc.edu/Research/namd/utilities/stmv.tar.gz
   wget https://www.ks.uiuc.edu/Research/namd/2.13/benchmarks/stmv_nve_cuda.namd

5. Decompress stmv.tar.gz.

   tar xvf stmv.tar.gz

6. Copy stmv_nve_cuda.namd to the stmv directory.

   cp stmv_nve_cuda.namd stmv

7. Run the test case to start a test.

   cd stmv
   /path/to/NAMD/NAMD_2.14_Source/Linux-ARM64-g++/namd2 +p96 +setcpuaffinity +maffinity +isomalloc_sync +devices 0,1 stmv_nve_cuda.namd

   View the value of day/ns in the log. A smaller value indicates a higher performance.