[gmx-users] GPU-C2075-simulation-solw or GPU only running -reg

[venkatesh s]

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



thank you

-- 
Regards,*
*S.VENKATESH,