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...@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 > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
