Respected Gromacs people's,
my query is my system very
slow? how can i improve the speed, its running like or equal to (25
minutes) "Intel Core I 7 processors" only.
Here i am given my entire system information,and i found my system 8 core
not taking job (GPU only running).
mdrun-gpu -device
"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=yes" -v -deffnm nvt
Non-supported GPU selected (#0, Tesla C2075), forced continuing.Note, that
the simulation can be slow or it migth even crash.
Pre-simulation ~15s memtest in progress...
Memory test completed without errors.
Back Off! I just backed up nvt.log to ./#nvt.log.1#
Getting Loaded...
Reading file nvt.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Back Off! I just backed up nvt.trr to ./#nvt.trr.1#
Back Off! I just backed up nvt.edr to ./#nvt.edr.1#
WARNING: OpenMM supports only Andersen thermostat with the
md/md-vv/md-vv-avek integrators.
WARNING: OpenMM provides contraints as a combination of SHAKE, SETTLE and
CCMA. Accuracy is based on the SHAKE tolerance set by the "shake_tol"
option.
WARNING: Non-supported GPU selected (#0, Tesla C2075), forced
continuing.Note, that the simulation can be slow or it migth even crash.
Pre-simulation ~15s memtest in progress...done, no errors detected
starting mdrun 'Protein in water'
50000 steps, 100.0 ps.
OpenMM run - timing based on wallclock.
NODE (s) Real (s) (%)
Time: 1319.043 1319.043 100.0
21:59
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 0.006 6.550 3.664
NVIDIA-SMI -l
+------------------------------------------------------+
| NVIDIA-SMI 3.295.59 Driver Version: 295.59
|
|-------------------------------+----------------------+----------------------+
| Nb. Name | Bus Id Disp. | Volatile ECC SB /
DB |
| Fan Temp Power Usage /Cap | Memory Usage | GPU Util. Compute
M. |
|===============================+======================+======================|
| 0. Tesla C2075 | 0000:01:00.0 On | 0
0 |
| 30% 75 C P0 150W / 225W | 8% 435MB / 5375MB | 95%
Default |
|-------------------------------+----------------------+----------------------|
| Compute processes: GPU
Memory |
| GPU PID Process name
Usage |
|=============================================================================|
| 0. 5889 mdrun-gpu
372MB |
+-----------------------------------------------------------------------------+
system:
top
top - 22:48:22 up 13 min, 4 users, load average: 0.19, 0.18, 0.09
Tasks: 308 total, 2 running, 304 sleeping, 2 stopped, 0 zombie
Cpu0 : 16.4%us, 1.7%sy, 0.0%ni, 81.9%id, 0.0%wa, 0.0%hi, 0.0%si,
0.0%st
Cpu1 : 5.4%us, 0.7%sy, 0.0%ni, 94.0%id, 0.0%wa, 0.0%hi, 0.0%si,
0.0%st
Cpu2 : 9.3%us, 0.7%sy, 0.0%ni, 90.0%id, 0.0%wa, 0.0%hi, 0.0%si,
0.0%st
Cpu3 : 0.0%us, 0.7%sy, 0.0%ni, 99.3%id, 0.0%wa, 0.0%hi, 0.0%si,
0.0%st
Cpu4 : 13.0%us, 0.7%sy, 0.0%ni, 86.4%id, 0.0%wa, 0.0%hi, 0.0%si,
0.0%st
Cpu5 : 1.0%us, 0.0%sy, 0.0%ni, 99.0%id, 0.0%wa, 0.0%hi, 0.0%si,
0.0%st
Cpu6 : 0.3%us, 0.3%sy, 0.0%ni, 99.3%id, 0.0%wa, 0.0%hi, 0.0%si,
0.0%st
Cpu7 : 0.0%us, 0.0%sy, 0.0%ni,100.0%id, 0.0%wa, 0.0%hi, 0.0%si,
0.0%st
Mem: 12188656k total, 1191628k used, 10997028k free, 34804k buffers
Swap: 0k total, 0k used, 0k free, 418428k cached
system?
protein + sol + NA total atom(nvt.gro)
158 residues 10742 2 34646
npt.mdp file
; Run parameters
integrator = md-vv ;
nsteps = 50000 ; 2 * 50000 = 100 ps
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 0.2 ps
nstvout = 100 ; save velocities every 0.2 ps
nstenergy = 100 ; save energies every 0.2 ps
nstlog = 100 ; update log file every 0.2 ps
; Bond parameters
continuation = yes ; Restarting after NVT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = System ; two coupling groups - more accurate
tau_t = 0.1 ; time constant, in ps
ref_t = 300 ; reference temperature, one for each group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
refcoord_scaling = com
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
