NAMD on HP-IA64 Linux

From: Ioana Cozmuta (ioana_cozmuta_at_hotmail.com)
Date: Sun May 30 2004 - 20:58:00 CDT

Hi NAMD developers and users,

I've built NAMD on - a HP machinewith 980 nodes, - each node consists of
dual Intel 1.5GHz Itanium-2 processors
- the system has distributed memory
- runs a version of Linux based on Red Hat Linux Advanced Server
- the processor allocation is scheduled with the LSF resource manager
- instead of mpirun the prun command is used to submit parallel jobs
(however when I built charm I used the mpi_intel libraries)

I've run both tests for charm and namd successfully. However my benchmark
data look weird (see below), like the processors would not be
connected/communicating between them (each job would be run on only 1
Processor).

Could this be caused by the fact that I am using prun instead of mpirun
(although I've forced the use of mpirun into an interactive session and I
got the same result as with using prun)? Could it be that NAMD does not
handle well distributed memory systems?
Could it be that the Benchmarking time calculations is calling some
functions that Linux might not have?

Any ideea/suggestion would be welcomed!

Thanks,
Ioana

PS. My benchmark system has ~120k atoms, uses a cutoff of 17.5 and PBC (unit
cell of ~100A)

16 CPU;s
Info: Benchmark time: 1 CPUs 6.01797 s/step 69.6524 days/ns 895144 kB memory
Info: Benchmark time: 1 CPUs 6.00938 s/step 69.553 days/ns 895144 kB memory
Info: Benchmark time: 1 CPUs 5.88953 s/step 68.1659 days/ns 903472 kB memory
Info: Benchmark time: 1 CPUs 5.88063 s/step 68.0628 days/ns 903472 kB memory
Info: Benchmark time: 1 CPUs 5.8768 s/step 68.0185 days/ns 903472 kB memory
Info: Benchmark time: 1 CPUs 5.86992 s/step 67.9389 days/ns 903472 kB memory
32 CPU's
Info: Benchmark time: 1 CPUs 6.07359 s/step 70.2962 days/ns 895160 kB memory
Info: Benchmark time: 1 CPUs 6.07609 s/step 70.3252 days/ns 895160 kB memory
Info: Benchmark time: 1 CPUs 5.93727 s/step 68.7184 days/ns 895160 kB memory
Info: Benchmark time: 1 CPUs 5.94625 s/step 68.8223 days/ns 895160 kB memory
Info: Benchmark time: 1 CPUs 5.92906 s/step 68.6234 days/ns 903488 kB memory
Info: Benchmark time: 1 CPUs 5.9318 s/step 68.6551 days/ns 903488 kB memory
48 CPU's
Info: Benchmark time: 1 CPUs 6.08336 s/step 70.4093 days/ns 895144 kB memory
Info: Benchmark time: 1 CPUs 6.08758 s/step 70.4581 days/ns 895144 kB memory
Info: Benchmark time: 1 CPUs 5.94773 s/step 68.8395 days/ns 895144 kB memory
Info: Benchmark time: 1 CPUs 5.95234 s/step 68.8929 days/ns 895144 kB memory
Info: Benchmark time: 1 CPUs 5.92961 s/step 68.6297 days/ns 911800 kB memory
Info: Benchmark time: 1 CPUs 5.93531 s/step 68.6957 days/ns 911800 kB memory
64 CPU's
Info: Benchmark time: 1 CPUs 6.07016 s/step 70.2564 days/ns 889712 kB memory
Info: Benchmark time: 1 CPUs 6.1032 s/step 70.6389 days/ns 889712 kB memory
Info: Benchmark time: 1 CPUs 5.94602 s/step 68.8196 days/ns 898040 kB memory
Info: Benchmark time: 1 CPUs 5.97289 s/step 69.1307 days/ns 898040 kB memory
Info: Benchmark time: 1 CPUs 5.94148 s/step 68.7672 days/ns 906368 kB memory
Info: Benchmark time: 1 CPUs 5.96578 s/step 69.0484 days/ns 906368 kB memory
96 CPU's
Info: Benchmark time: 1 CPUs 6.04344 s/step 69.9472 days/ns 892448 kB memory
Info: Benchmark time: 1 CPUs 6.05594 s/step 70.0919 days/ns 892448 kB memory
Info: Benchmark time: 1 CPUs 5.91297 s/step 68.4371 days/ns 900776 kB memory
Info: Benchmark time: 1 CPUs 5.92805 s/step 68.6117 days/ns 900776 kB memory
Info: Benchmark time: 1 CPUs 5.90109 s/step 68.2997 days/ns 909104 kB memory
Info: Benchmark time: 1 CPUs 5.91242 s/step 68.4308 days/ns 909104 kB memory

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