Hi all,
I have just compiled amber12 with gcc and mpi ( gcc-version ) on one of our
cluster and on a cray-system with pgi-compilers.
To test the speed and scaling of amber - I run a NPT calculation ( input
file below ) with 64852 atoms in the system which is composed of a ligand,
ions, explicit water and a protein:
1ns MD
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 0,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 5000000, dt = 0.002,
ntpr = 5000, ntwx = 5000, ntwr = 5000
/
but the scaling I get is not very good - so I was wondering what kind of
speeds to expect
On cluster 1 which has the following specifications:
Myrinet 10G network connects all nodes in a topology appropriate for
latency-sensitive parallel codes while also supporting I/O bandwidth for
data-intensive workloads. Each compute rack supports a total of 56 nodes
split among four IBM Blade Center H chassis. Additional racks are reserved
for storage, servers, and networking
I run the simulation for 5000 steps before it is terminated and I get the
following numbers with sander.MPI :
16 cpus: ns/day = 1.00
32 cpus: ns/day = 0.24
which suggest that I am doing something completely wrong and with pmemd:
16 cpus: ns/day = 0.21
32 cpus: ns/day = 0.21
On the cray I get the following
32 cpus: ns/day = 1.23
64 cpus: ns/day = 1.42
Any help to improve the speed cause when I see the benchmark numbers from
Ross Walker they are quite different and much better so any improvement
would be great.
Thanks and sorry for any lack of information
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Received on Sun Jul 14 2013 - 16:00:03 PDT
