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 -- Gromacs Users mailing list
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