1. The performance of NAMD on a large Power4 system
Joachim Hein
EPCC, The University of Edinburgh

2. Measurement based load balancing
NAMD measures its performance for the first 200 steps
Redistributes the work load to optimise the performance
Performance benefit for larger number of processors
Benchmark time: Better estimate for production jobs from short jobs
NAMD on Power4
11 May 2019

3. Measurement based load balancing
NAMD on Power4
11 May 2019

4. Loadbalance Example: All but one CPUs in a narrow Window 128 CPUs
96769 atoms
32000 iters
All but one CPUs in a narrow Window
Effect of “slow” guy negligible
NAMD on Power4
11 May 2019

5. Tune it! MP_EAGER_LIMIT
Environment variable MP_EAGER_LIMIT changes the behaviour of MPI
Messages smaller than MP_EAGER_LIMIT are send instantaneous
Messages larger than MP_EAGER_LIMIT are send using “hand-shake”
Default value is small and not optimal for NAMD
Tune it!
NAMD on Power4
11 May 2019

6. MP_EAGER_LIMIT
NAMD on Power4
11 May 2019

7. Sample loadleveler script
shell = /bin/ksh
job_type = parallel
network.MPI = csss,shared,us
account_no = z001
output = namd_run.$(schedd_host)_$(jobid).out
error = namd_run.$(schedd_host)_$(jobid).err
wall_clock_limit = 00:30:00
node = 1
tasks_per_node = 8
queue
export MP_SHARED_MEMORY=yes
export MP_EAGER_LIMIT=65536
poe path/namd2 inputfile
Communication: shared memory
Setting MP_EAGER_LIMIT
Set path & inputfile
NAMD on Power4
11 May 2019

8. Benchmark Joint Amber Charm (JAC) Benchmark Apo A-1 benchmark
Dihydrofolate reductase in water, atoms
Apo A-1 benchmark
Apolipoprotein A-1, atoms
TCR peptide-MHC
96796 atoms
F1-ATP synthase
F1 subunit of ATP synthase, atoms
NAMD on Power4
11 May 2019

9. The HPCx system Presently: Future (Summer 2004)
40 IBM p690 Regata H frames
32 POWER4 processors per frame (1.3 GHz)
Frames subdivided into LPARs of 8 processors
8 GB of main memory per LPAR
IBM SP Switch2 (Colony) network
2 switch adapters per LPAR
Dual plane
Future (Summer 2004)
Upgrade to p690+ frames (1.7 GHz)
LPARs of 32 processors
IBM HPS (Federation) network
NAMD on Power4
11 May 2019

10. Time per step for 32 processors
Benchmark
NAMD 2.4
NAMD 2.5
Comment
dhf reductase
23558 atoms
0.051s
0.032s
Too small for 32 cpus
APO A-1
92224 atoms
0.28s
0.19s
TCR MHC
96796 atoms
0.30s
0.21s
F1-ATP
atoms
0.58s
NAMD 2.5 substantially faster than NAMD 2.4
NAMD on Power4
11 May 2019

11. Large number of processors
NAMD on Power4
11 May 2019

12. Further Reading Full technical report: The performance of NAMD on HPCx
Joachim Hein
NAMD on Power4
11 May 2019