[gmx-users] Running Gromacs in parallel

[Szilárd Páll]

First of all, use a more recent release. Secondly read the user guide
and check this paper:
http://onlinelibrary.wiley.com/doi/10.1002/jcc.24030/full
in particular the performance checklist on Figure 8!
--
Szilárd


On Tue, Sep 20, 2016 at 10:54 PM, Thanh Le <thanh.q.le at sjsu.edu> wrote:
> 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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