[gmx-users] GPU-C2075-simulation-solw or GPU only running -reg
Justin Lemkul
jalemkul at vt.edu
Sun Oct 21 21:41:38 CEST 2012
On 10/21/12 3:38 PM, venkatesh s wrote:
> 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
>
>
Explicit solvent systems (especially those using PME) perform poorly on GPU.
Performance will be better in the next release, but for the 4.5.x series, only
implicit systems run very fast on GPU.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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