Running and Verification

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Set the environment variables of the NAMD executable file.

   export PATH=/path/to/NAMD/NAMD-2.13/build/NAMD_2.13_Source/Linux-ARM64-g++/:$PATH

3. Go to the test case directory.

   cd /path/to/CASE

4. Decompress the test case file.

   tar -xf apoa1.tar.gz

5. Modify the test case file.
   1. Open the test case file.

      vi apoa1/apoa1.namd

   2. Press i to enter the insert mode and add the following content to the end of the apoa1/apoa1.namd file:

      FFTWEstimate yes
      FFTWUseWisdom no

   3. Press Esc, type :wq!, and press Enter to save the file and exit.
6. Perform the test.

   cd apoa1
   mpirun --allow-run-as-root --mca btl ^openib -np 1 namd2 +ppn 32 apoa1.namd +setcpuaffinity 2>&1 |tee -a namd.log

7. If the test must be performed on more than one node, create a hostfile file.
   1. Create hostfile.

      vi hostfile

   2. Press i to enter the insert mode and modify the file as follows:

      Node1
      Node2

      

      Node1 and Node2 are the node names. Change them based on your requirements and ensure that the nodes can ping each other.

   3. Press Esc, type :wq!, and press Enter to save the file and exit.
8. If the test must be performed on more than one node, run the following command to perform the test:

   time mpirun --allow-run-as-root -x PATH=$PATH -x LD_LIBRARY_PATH=$LD_LIBRARY_PATH --hostfile hostfile --mca btl ^openib -np 2 -N 1 namd2 +ppn 32
   apoa1.namd +setcpuaffinity 2>&1 |tee -a namd.log

   Parameter	Description
   -np	Total number of processes used in the test.
   -N	Number of processes running on each server.
   --hostfile	Name of the node to be used.

   The following figure shows the test result: