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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