[gmx-users] Running Gromacs in parallel
pall.szilard at gmail.com
Wed Sep 21 14:29:22 CEST 2016
First of all, use a more recent release. Secondly read the user guide
and check this paper:
in particular the performance checklist on Figure 8!
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?
> Thanh Le
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