[gmx-users] CPU running doesn't match command line

[Szilárd Páll]

Most of that copy-pasted info is not what I asked for and overall not
very useful. You have still not shown any log files (or details on the
hardware). Share the *relevant* stuff, please!
--
Szilárd


On Tue, Aug 16, 2016 at 5:07 PM, Albert <mailmd2011 at gmail.com> wrote:
> Hello:
>
> Here is my MDP file:
>
> define                  = -DREST_ON -DSTEP6_4
> integrator              = md
> dt                      = 0.002
> nsteps                  = 1000000
> nstlog                  = 1000
> nstxout                 = 0
> nstvout                 = 0
> nstfout                 = 0
> nstcalcenergy           = 100
> nstenergy               = 1000
> nstxout-compressed      = 10000
> ;
> cutoff-scheme           = Verlet
> nstlist                 = 20
> rlist                   = 1.0
> coulombtype             = pme
> rcoulomb                = 1.0
> vdwtype                 = Cut-off
> vdw-modifier            = Force-switch
> rvdw_switch             = 0.9
> rvdw                    = 1.0
> ;
> tcoupl                  = berendsen
> tc_grps                 = PROT   MEMB   SOL_ION
> tau_t                   = 1.0    1.0    1.0
> ref_t                   = 310   310   310
> ;
> pcoupl                  = berendsen
> pcoupltype              = semiisotropic
> tau_p                   = 5.0
> compressibility         = 4.5e-5  4.5e-5
> ref_p                   = 1.0     1.0
> ;
> constraints             = h-bonds
> constraint_algorithm    = LINCS
> continuation            = yes
> ;
> nstcomm                 = 100
> comm_mode               = linear
> comm_grps               = PROT   MEMB   SOL_ION
> ;
> refcoord_scaling        = com
>
>
> I compiled Gromacs with the following settings, using Intel MPI:
>
> env CC=mpicc CXX=mpicxx F77=mpif90 FC=mpif90 LDF90=mpif90
> CMAKE_PREFIX_PATH=/soft/gromacs/fftw-3.3.4:/soft/intel/impi/5.1.3.223 cmake
> .. -DBUILD_SHARED_LIB=OFF -DBUILD_TESTING=OFF
> -DCMAKE_INSTALL_PREFIX=/soft/gromacs/5.1.3_intel -DGMX_MPI=ON -DGMX_GPU=ON
> -DGMX_PREFER_STATIC_LIBS=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
>
>
> I tried it again with one of the job with options:
>
> -ntomp 8 -pin on -pinoffset 8
>
>
> The two submitted jobs can still only use 8 CPU and the speed is extremely
> slow (10ns/day)....when I remove option "-pin on" from one of the job, it
> fasten a lot (32ns/day) and 16 CPU were used..... If I only submit one job
> with option "-pin on", I can obtain 52ns/day..........
>
>
> thx a lot
>
>
> On 08/16/2016 04:59 PM, Szilárd Páll wrote:
>>
>> Hi,
>>
>> Without log and hw configs, I it's hard to tell what's happening.
>>
>> By turning off pinning the OS is free to move threads around and it
>> will try to ensure cores are utilized. However, by leaving threads
>> up-pinned you risk taking a significant performance hit. So I'd
>> recommend that you run with correct settings.
>>
>> If you start with "-ntomp 8 -pin on -pioffset 8" (and you indeed have
>> 16 cores no HT), you should be able to see in htop the first eight
>> cores empty while the last eight occupied.
>>
>> Cheers,
>> --
>> Szilárd
>
>
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