NAMD v.2.7b1

For details of the systems used, see the corresponding pages for NAMD v.2.6, or view the scripts included at the end of this page. The ApoA1 benchmark is as distributed by the NAMD developers. If you'd rather prefer cutting a long story short, see the timings (in ns/day) shown on the very last table of this page.

The following executables have been tested

  • Prebuilt NAMD_2.7b1_Linux-x86_64
  • Prebuilt NAMD_2.7b1_Linux-x86_64-TCP
  • From source UDP-ICC-SMP
  • From source MPI-SMP
  • For comparison, results from NAMD2.6 have also been included

For all executables (except MPI), a slurm script in the spirit of the following was used:

#!/bin/tcsh -f

/usr/local/namdtest/charmrun /usr/local/namdtest/namd2 +p16 +giga equi.namd >& LOG


There is one exception though: for jobs to be run on 4 (or less) cores full advantage of the SMP capabilities was achieved by submitting without charmrun:

#!/bin/tcsh -f

/usr/local/namdtest/namd2 +p4 equi.namd >& LOG


The MPI executable was the worst of all. It was so bad, that it will not be examined any further. The results from the TCP version were also systematically worse, so they will also be excluded. The results for the three remaining executables and the various systems are (in nanoseconds per day):

NAMD v.2.6 Prebuilt UDP Source UDP-SMP
100K atoms, _8 cores 0.78 0.87 1.00
100K atoms, 16 cores 1.23 1.35 1.64
100K atoms, 32 cores 1.69 1.72 2.00
60K atoms, _8 cores 1.24 1.42 1.68
60K atoms, 16 cores 1.91 2.00 2.60
60K atoms, 32 cores 2.59
25K atoms, _4 cores 1.70 1.94 2.53
25K atoms, _8 cores 2.38 2.85 4.10
25K atoms, 16 cores 4.04
1.6K atoms, _1 cores 11.50 14.10 13.50
1.6K atoms, _2 cores 11.80 13.80 20.60
1.6K atoms, _4 cores 47.60
0.9K atoms, _1 cores 22.20 26.70 25.90
0.9K atoms, _2 cores 21.20 25.60 40.00
0.9K atoms, _4 cores 79.00

For the udp-smp-icc executable, the results from the standard ApoA1 NAMD benchmark are:

Number of cores 1 2 4 8 16 32
Nanosecond per day 0.097 0.19 0.37 0.72 1.38 2.31
Days per nanosecond 10.325 5.257 2.730 1.380 0.723 0.433
Parallel Efficiency (%) - 98.2 94.5 93.5 89.2 74.5
Days/nsec for 100% efficiency 10.325 5.163 2.581 1.290 0.645 0.327

ApoA1 benchmark, Ideal (orange) vs. observed (green) scaling

Finally, running the udp-smp-icc NAMD executable with +max_dgram_size 5800 +os_buffer_size 400000 +LBPredictor +LBLoop +noAnytimeMigration +asynciooff +setcpuaffinity +LBSameCpus +giga gave the following measurements in nanoseconds per day (compare with tables shown above):

Number of nodes (cores) 1 (4) 2 (8) 4 (16) 8 (32)
ApoA1 benchmark 2.42
100K atoms 1.69 2.40
60K atoms 1.67 2.75 3.22
25K atoms 2.53 4.13 5.35 x
13.3K atoms 7.27 8.28 x x
1.6K atoms 47.6 x x x
0.9K atoms 79.0 x x x

In this table, vacant entries mean 'no measurement taken', crosses mean 'measurement taken and it was worse than that obtained with half the number of cores'.

Now the crucial question: should we be happy with these numbers ? The answer is, of course, “possibly” : 2.42 nsec/day for ApoA1 translates to approximately 0.071 seconds per step, which according to this page is 15% faster than what you would get from 128 cores on the SDSC IBM BlueGene/L. To make the comparison more meaningful (and up-to-date), we also compare with this HPC advisory dated January 2009. According to the data shown on page 9 of this PDF file, 2.42 nsec/day for the ApoA1 benchmark and 32 cores is slightly better than what you would have get from that cluster if you have 10 Gbit ethernet (and not much slower if you had infiband, running at ~2.8 nsec/day). Referring to the same slide, to get the same performance as norma does using simple gigabit, you would have to use (assuming linear scaling) somewhere between 12 and 16 nodes (corresponding to somewhere between 48 and 64 cores). In summary, and if we were hard pressed to reach a conclusion, we would have said that norma's performance appears to be satisfactory.

Further evidence for the satisfactory performance of the cluster comes with a direct comparison with the results shown in the NAMD performance page as follows: We have (unashamedly) copied the graph produced by the NAMD developers, and placed on it a white asterisk corresponding to norma's performance. The thus modified graph is the following:

 NAMD performance graph including Norma

which places norma half-way between the “NCSA Xeon/2.33 Infiband” and the “Indiana PPC970/2.5 Myrinet” clusters [but do keep in mind the important difference in NAMD version (2.6 vs. 2.7b1)].

For some further tests with this version of NAMD, see here.

NAMD script for 0.9K-atoms tests

NAMD script for 1.6K-atoms tests

NAMD script for 13.3K-atoms tests

NAMD script for 25K-atoms tests

NAMD script for 60K-atoms tests

NAMD script for 100K-atoms tests

about/benchmarks/namdv27b1.txt · Last modified: 2009/09/09 18:06 (external edit)