Running and Verification

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Switch to the test directory.

   cd /path/to/CASE

3. Decompress the test case file.

   tar -zxvf  Amber20_Benchmark_Suite.tar.gz

4. Go to the directory generated after the decompression.

   cd PME/Cellulose_production_NPT_4fs/

5. Run the Amber tests.

   cp ../Coordinates/Cellulose.inpcrd inpcrd
   cp ../Topologies/Cellulose.prmtop prmtop

   mpirun -np 96 $AMBERHOME/exe/pmemd -O -i mdin.CPU -o mdout.CPU -p prmtop -c inpcrd

   $AMBERHOME/exe/pmemd.cuda -O -i mdin.GPU -o mdout.GPU -p prmtop -c inpcrd

   View the value of ns/day under Performance in the mdout.CPU file. A higher value indicates higher performance.

   The following is an example of the test result:

   Final Performance Info:
   |     -----------------------------------------------------
   |     Average timings for last      10 steps:
   |     Elapsed(s) =      40.80 Per Step(ms) =    4079.94
   |         ns/day =       0.08   seconds/ns = 1019985.72
   |
   |     Average timings for all steps:
   |     Elapsed(s) =     783.10 Per Step(ms) =    3915.48
   |         ns/day =       0.09   seconds/ns =  978871.00