Skip to content

Run NAMD3 Docker Application

This guide describes how to run the NAMD3 Docker application. Go to the Application Configuration screen.

apoa1 benchmark

Paste the following into the Run Script text box to run the apoa1 benchmark on all GPUs on an 8-GPU node.

cd /examples
BENCHMARK=/examples/apoa1/apoa1.namd
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 0 --CUDASOAintegrate on +devices 0 2>&1 > gpu0 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 8 --CUDASOAintegrate on +devices 1 2>&1 > gpu1 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 16 --CUDASOAintegrate on +devices 2 2>&1 > gpu2 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 32 --CUDASOAintegrate on +devices 3 2>&1 > gpu3 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 64 --CUDASOAintegrate on +devices 4 2>&1 > gpu4 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 72 --CUDASOAintegrate on +devices 5 2>&1 > gpu5 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 80 --CUDASOAintegrate on +devices 6 2>&1 > gpu6 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 88 --CUDASOAintegrate on +devices 7 2>&1 > gpu7
wait
./ns_per_day.py gpu0
./ns_per_day.py gpu1
./ns_per_day.py gpu2
./ns_per_day.py gpu3
./ns_per_day.py gpu4
./ns_per_day.py gpu5
./ns_per_day.py gpu6
./ns_per_day.py gpu7

Compute figure of merit (FOM)

From the completed Workloads list, open your completed NAMD3 job and open the STDOUT tab. The FOM for an 8-GPU NAMD3 workload is the sum of the eight "Nanoseconds per day" values. Example: 862.694 Nanoseconds per day (8 × 107.9 approx.).


Nanoseconds per day: 107.972
Mean time per step: 0.00160041
Standard deviation: 1.9379e-05
Nanoseconds per day: 107.949
Mean time per step: 0.00160076
Standard deviation: 1.59461e-05
Nanoseconds per day: 107.228
Mean time per step: 0.00161151
Standard deviation: 1.59286e-05
Nanoseconds per day: 107.572
Mean time per step: 0.00160637
Standard deviation: 6.90183e-06
Nanoseconds per day: 107.163
Mean time per step: 0.00161249
Standard deviation: 1.22992e-05
Nanoseconds per day: 108.366
Mean time per step: 0.0015946
Standard deviation: 1.39513e-05
Nanoseconds per day: 108.35
Mean time per step: 0.00159483
Standard deviation: 1.61872e-05
Nanoseconds per day: 108.094
Mean time per step: 0.00159861
Standard deviation: 1.68244e-05

jac benchmark

Copy the following code block in the Run Script text to run jac benchmark concurrently on all GPUs on an 8-GPU compute node.

cd /examples
BENCHMARK=/examples/jac/jac.namd
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 0 --CUDASOAintegrate on +devices 0 2>&1 > gpu0 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 8 --CUDASOAintegrate on +devices 1 2>&1 > gpu1 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 16 --CUDASOAintegrate on +devices 2 2>&1 > gpu2 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 32 --CUDASOAintegrate on +devices 3 2>&1 > gpu3 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 64 --CUDASOAintegrate on +devices 4 2>&1 > gpu4 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 72 --CUDASOAintegrate on +devices 5 2>&1 > gpu5 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 80 --CUDASOAintegrate on +devices 6 2>&1 > gpu6 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 88 --CUDASOAintegrate on +devices 7 2>&1 > gpu7
wait
./ns_per_day.py gpu0
./ns_per_day.py gpu1
./ns_per_day.py gpu2
./ns_per_day.py gpu3
./ns_per_day.py gpu4
./ns_per_day.py gpu5
./ns_per_day.py gpu6
./ns_per_day.py gpu7

Compute figure of merit (FOM)

From the completed Workloads list, select your completed NAMD3 job. Select the STDOUT tab to view stdout logs. The FOM for NAMD3 8-GPU workload is the sum of the eight Nanoseconds per day numbers.

f1atpase benchmark

Copy the following code block in the Run Script text box to run f1atpase benchmark concurrently on all GPUs on an 8-GPU compute node.

cd /examples
BENCHMARK=/examples/f1atpase/f1atpase.namd
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 0 --CUDASOAintegrate on +devices 0 2>&1 > gpu0 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 8 --CUDASOAintegrate on +devices 1 2>&1 > gpu1 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 16 --CUDASOAintegrate on +devices 2 2>&1 > gpu2 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 32 --CUDASOAintegrate on +devices 3 2>&1 > gpu3 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 64 --CUDASOAintegrate on +devices 4 2>&1 > gpu4 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 72 --CUDASOAintegrate on +devices 5 2>&1 > gpu5 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 80 --CUDASOAintegrate on +devices 6 2>&1 > gpu6 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 88 --CUDASOAintegrate on +devices 7 2>&1 > gpu7
wait
./ns_per_day.py gpu0
./ns_per_day.py gpu1
./ns_per_day.py gpu2
./ns_per_day.py gpu3
./ns_per_day.py gpu4
./ns_per_day.py gpu5
./ns_per_day.py gpu6
./ns_per_day.py gpu7

Compute figure of merit (FOM)

From the completed Workloads list, select your completed NAMD3 job. Select the STDOUT tab to view stdout logs. The FOM for NAMD3 8-GPU workload is the sum of the eight Nanoseconds per day numbers.

stmv benchmark

Copy the following code block in the Run Script text box to run stmv benchmark concurrently on all GPUs on an 8-GPU compute node.

cd /examples
BENCHMARK=/examples/stmv/stmv.namd
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 0 --CUDASOAintegrate on +devices 0 2>&1 > gpu0 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 8 --CUDASOAintegrate on +devices 1 2>&1 > gpu1 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 16 --CUDASOAintegrate on +devices 2 2>&1 > gpu2 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 32 --CUDASOAintegrate on +devices 3 2>&1 > gpu3 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 64 --CUDASOAintegrate on +devices 4 2>&1 > gpu4 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 72 --CUDASOAintegrate on +devices 5 2>&1 > gpu5 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 80 --CUDASOAintegrate on +devices 6 2>&1 > gpu6 &
/opt/namd/bin/namd3 $BENCHMARK +p1 +pemap 88 --CUDASOAintegrate on +devices 7 2>&1 > gpu7
wait
./ns_per_day.py gpu0
./ns_per_day.py gpu1
./ns_per_day.py gpu2
./ns_per_day.py gpu3
./ns_per_day.py gpu4
./ns_per_day.py gpu5
./ns_per_day.py gpu6
./ns_per_day.py gpu7

Compute figure of merit (FOM)

From the completed Workloads list, select your completed NAMD3 job. Select the STDOUT tab to view stdout logs. The FOM for NAMD3 8-GPU workload is the sum of the eight Nanoseconds per day numbers.