From: Gengbin Zheng (gzheng_at_ks.uiuc.edu)
Date: Sun May 30 2004 - 22:20:51 CDT
Hi,
from the benchmark time suggested, only 1 CPU were actually used in your
runs.
I think you have to consult the sysadmin about how to run a MPI program on
your system, and how to write a job script to allocate more than one
processor. (I don't think the problem was at NAMD side).
>From the name "prun", I guess you are using Quadics
interconnection. Normally you should say
prun -np 16 ./namd2 config
to start a parallel job.
Another possiblity is that your job script failed to ask for more than one
processor. You may want to print which and how many compute nodes were
allocated for you.
Gengbin
On Mon, 31 May 2004, Ioana Cozmuta wrote:
> 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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