[gmx-users] Hyper-threading Gromacs 5.0.1

[Johnny Lu]

this mail list thread talks about it:
https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg06331.html


On Thu, Sep 11, 2014 at 9:45 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> The gromacs wiki also says that mixing mpi and openmp is bad on small
> computers.
>
> On Thu, Sep 11, 2014 at 9:44 AM, Johnny Lu <johnny.lu128 at gmail.com> wrote:
>
>> Ah. Thanks a lot.
>> As suggested by (
>> https://www.ibm.com/developerworks/community/blogs/brian/entry/linux_show_the_number_of_cpu_cores_on_your_system17?lang=en),
>>
>> $ cat /proc/cpuinfo | grep "physical id" | sort | uniq | wc -l
>> 2
>> $ cat /proc/cpuinfo | egrep "core id|physical id" | tr -d "\n" | sed
>> s/physical/\\nphysical/g | grep -v ^$ | sort | uniq | wc -l
>> 12
>>
>> There are 12 real cores.
>> Type "top" and then press 1 sometimes give double the number of real
>> cores, but sometimes doesn't double the number (tested on different
>> machines).
>>
>> How to run "an MPI  rank per core" ? By this way? "OMP_NUM_THREADS=12
>> mdrun" on a 12 core machine?
>>
>> I tried openmp threads instead of mpi thread because gromacs wiki says
>> openmp threads are faster than mpi based parallelization.
>>
>> from the gromacs wiki (
>> http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multi-level_parallelization.3a_MPI_and_OpenMP
>> ):
>>
>> In GROMACS 4.6 compiled with thread-MPI, OpenMP-only parallelization is
>> the default with Verlet scheme when using up to 8 cores on AMD platforms
>> and up to 12 and 16 cores on Intel Nehalem and Sandy Bridge, respectively.
>> Note that even running across two CPUs (in different sockets) on Intel
>> platforms OpenMP mutithreading is, in the majority of the cases,
>> significantly faster than MPI-based parallelization.
>>
>> ...
>>
>> Assuming that there are N cores available, the following commands are
>> equivalent:
>>
>> mdrun -ntomp N -ntmpi 1
>> OMP_NUM_THREADS=N mdrun
>> mdrun #assuming that N <= 8 on AMD or N <= 12/16 on Intel Nehalem/Sandy Bridge
>>
>>
>>
>>
>