[gmx-users] Running Gromacs in parallel

Thanh Le thanh.q.le at sjsu.edu
Tue Sep 20 22:54:52 CEST 2016

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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