[gmx-users] Running Gromacs in parallel

[jkrieger at mrc-lmb.cam.ac.uk]

Hi Thanh Le,

Assuming all the nodes are the same (9 nodes with 12 CPUs) then you could
try the following

mpirun -np 9 --map-by node mdrun -ntomp 12 ...
mpirun -np 18 mdrun -ntomp 6 ...
mpirun -np 54 mdrun -ntomp 2 ...

Which of these works best will depend on your setup.

Using the whole cluster for one job may not be the most efficient way. I
found on our cluster that once I reach 216 CPUs (equivalent settings from
the queuing system to -np 108 and -ntomp 2), I can't do better by adding
more nodes (where presumably communication becomes an issue). In addition
to running -multi or -multidir jobs, which takes the load off
communication a bit, it may also be worth having separate jobs and using
-pin on and -pinoffset.

Best wishes
James

> Hi everyone,
> I have a question concerning running gromacs in parallel. I have read over
> the
> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html
> <http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html>
> but I still dont quite understand how to run it efficiently.
> My gromacs version is 4.5.4
> The cluster I am using has CPUs total: 108 and 4 hosts up.
> The node iam using:
> Architecture:          x86_64
> CPU op-mode(s):        32-bit, 64-bit
> Byte Order:            Little Endian
> CPU(s):                12
> On-line CPU(s) list:   0-11
> Thread(s) per core:    2
> Core(s) per socket:    6
> Socket(s):             1
> NUMA node(s):          1
> Vendor ID:             AuthenticAMD
> CPU family:            21
> Model:                 2
> Stepping:              0
> CPU MHz:               1400.000
> BogoMIPS:              5200.57
> Virtualization:        AMD-V
> L1d cache:             16K
> L1i cache:             64K
> L2 cache:              2048K
> L3 cache:              6144K
> NUMA node0 CPU(s):     0-11
> MPI is already installed. I also have permission to use the cluster as
> much as I can.
> My question is: how should I write my mdrun command run to utilize all the
> possible cores and nodes?
> Thanks,
> Thanh Le
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