I have a question concerning running gromacs in parallel. I have read over the
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:
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
On-line CPU(s) list: 0-11
Thread(s) per core: 2
Core(s) per socket: 6
NUMA node(s): 1
Vendor ID: AuthenticAMD
CPU family: 21
CPU MHz: 1400.000
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
My question is: how should I write my mdrun command run to utilize all the
possible cores and nodes?
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