[gmx-users] GPU Not Being Utilized during mdrun
Vito Spadavecchio
spadavecchio at gmail.com
Fri Jul 15 04:35:16 CEST 2016
Szilard
You are correct; I misspoke. It appears that the GPU is doing *something*,
but I it would seem it is severely under performing (near the point where
its basically doing nothing).
the entire log, not just parts, in particular we want to see the
> header, perf table
>
xyz at Turing:~/Desktop/xyz_MD/APO_xyz$ gmx mdrun -deffnm md_0_2 -nb gpu
:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
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Dimitrios Karkoulis Peter Kasson Jiri Kraus Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
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GROMACS: gmx mdrun, VERSION 5.1.2
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Command line:
gmx mdrun -deffnm md_0_2 -nb gpu
Back Off! I just backed up md_0_2.log to ./#md_0_2.log.1#
Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU
Hardware detected:
CPU info:
Vendor: GenuineIntel
Brand: Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
SIMD instructions most likely to fit this hardware: AVX2_256
SIMD instructions selected at GROMACS compile time: AVX2_256
GPU info:
Number of GPUs detected: 1
#0: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC: no, stat:
compatible
Reading file md_0_2.tpr, VERSION 5.1.2 (single precision)
Changing nstlist from 10 to 40, rlist from 1 to 1.099
Using 1 MPI thread
Using 8 OpenMP threads
1 compatible GPU is present, with ID 0
1 GPU auto-selected for this run.
Mapping of GPU ID to the 1 PP rank in this node: 0
Back Off! I just backed up md_0_2.trr to ./#md_0_2.trr.1#
Back Off! I just backed up md_0_2.xtc to ./#md_0_2.xtc.1#
Back Off! I just backed up md_0_2.edr to ./#md_0_2.edr.1#
starting mdrun 'Protein in water'
500000 steps, 1000.0 ps.
- the output of nvidia-smi dmon executing *during* mdrun's execution
heres a snapshot:
# gpu pwr temp sm mem enc dec mclk pclk
> # Idx W C % % % % MHz MHz
> 0 117 51 56 3 0 0 4513 1847
> 0 115 52 54 3 0 0 4513 1847
> 0 117 52 47 3 0 0 4513 1847
> 0 101 52 52 3 0 0 4513 1848
> 0 119 53 54 3 0 0 4513 1847
> 0 115 53 54 3 0 0 4513 1848
> 0 106 54 54 3 0 0 4513 1848
> 0 118 54 54 3 0 0 4513 1849
> 0 94 54 52 3 0 0 4513 1848
> 0 110 55 52 3 0 0 4513 1849
> 0 116 55 53 3 0 0 4513 1854
> 0 126 55 51 3 0 0 4513 1854
> 0 119 56 51 3 0 0 4513 1855
> 0 116 56 52 3 0 0 4513 1855
> 0 116 56 53 3 0 0 4513 1855
> 0 120 57 53 3 0 0 4513 1855
> 0 113 57 54 3 0 0 4513 1855
>
and here's the tail of the performance in .log
Reading file md_0_2.tpr, VERSION 5.1.2 (single precision)
> Changing nstlist from 10 to 40, rlist from 1 to 1.099
> Using 1 MPI thread
> Using 8 OpenMP threads
> 1 compatible GPU is present, with ID 0
> 1 GPU auto-selected for this run.
> Mapping of GPU ID to the 1 PP rank in this node: 0
>
> Back Off! I just backed up md_0_2.trr to ./#md_0_2.trr.1#
> Back Off! I just backed up md_0_2.xtc to ./#md_0_2.xtc.1#
> Back Off! I just backed up md_0_2.edr to ./#md_0_2.edr.1#
> starting mdrun 'Protein in water'
> 500000 steps, 1000.0 ps.
> Writing final coordinates.
> Back Off! I just backed up md_0_2.gro to ./#md_0_2.gro.1#
> Core t (s) Wall t (s) (%)
> Time: 25285.344 3409.337 741.6
> 56:49
> (ns/day) (hour/ns)
> Performance: 25.342 0.947
> gcq#11: "She's Not Bad, She's Just Genetically Mean" (Captain Beefheart)
>
>
As we can see, there is *something* running on the GPU (process id: 30784),
but its never more than 135MiB of memory being used and only uses a very
small portion of the gpus power.
Any thoughts are greatly appreciated!
On Thu, Jul 14, 2016 at 4:54 PM, Szilárd Páll <pall.szilard at gmail.com>
wrote:
> Hi,
>
> If mdrun claims it's using the GPU and you see no errors (and results
> look reasonable), the GPU is likely being used. That nvidia-smi is not
> showing it is admittedly strange. However, this truncated log output
> does not confirm much, e.g. it does not show the performance table and
> the final performance.
>
> Could you please run again and look at (and share if approapriate):
> - the entire log, not just parts, in particular we want to see the
> header, perf table
> - the output of nvidia-smi dmon executing *during* mdrun's execution
> (this monitors the device continuously)
>
> Cheers,
>
> --
> Szilárd
>
>
> On Thu, Jul 14, 2016 at 8:28 PM, Vito Spadavecchio
> <spadavecchio at gmail.com> wrote:
> > Hello
> >
> > After building GROMACS with GPU support and running some simple MD, I am
> > only getting ~20ns/day (which is what I would expect to get out of my
> > i7-6700k cpu only. My machine currently has a 1080 GTX in it, which
> should
> > even on moderately large systems, be getting ~100ns/day)
> >
> > I've tried launching a mdrun with with the following command:
> >
> > gmx mdrun -deffnm md_0_1 -gpu_id 0 -nb gpu
> >
> >
> >
> > With the following in my md.mdp file:
> >
> > ; Neighborsearching
> >
> > cutoff-scheme = Verlet
> >
> >
> >
> > The top of the log file for the mdrun notes:
> >
> > Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU
> >> Hardware detected:
> >> CPU info:
> >> Vendor: GenuineIntel
> >> Brand: Intel(R) Core(TM) i7-6700K CPU @ 4.00GHz
> >> SIMD instructions most likely to fit this hardware: AVX2_256
> >> SIMD instructions selected at GROMACS compile time: AVX2_256
> >> GPU info:
> >> Number of GPUs detected: 1
> >> #0: NVIDIA GeForce GTX 1080, compute cap.: 6.1, ECC: no, stat:
> >> compatible
> >> Reading file md_0_1.tpr, VERSION 5.1.2 (single precision)
> >> Changing nstlist from 10 to 40, rlist from 1 to 1.099
> >> Using 1 MPI thread
> >> Using 8 OpenMP threads
> >> 1 GPU user-selected for this run.
> >> Mapping of GPU ID to the 1 PP rank in this node: 0
> >>
> >
> > The output of *nvidia-smi *on my machine is:
> >
> > hu Jul 14 11:25:04 2016
> >>
> >>
> +-----------------------------------------------------------------------------+
> >> | NVIDIA-SMI 367.27 Driver Version: 367.27
> >> |
> >>
> >>
> |-------------------------------+----------------------+----------------------+
> >> | GPU Name Persistence-M| Bus-Id Disp.A | Volatile
> Uncorr.
> >> ECC |
> >> | Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | GPU-Util
> Compute
> >> M. |
> >>
> >>
> |===============================+======================+======================|
> >> | 0 GeForce GTX 1080 Off | 0000:01:00.0 On |
> >> N/A |
> >> | 30% 41C P8 7W / 180W | 730MiB / 8113MiB | 3%
> >> Default |
> >>
> >>
> +-------------------------------+----------------------+----------------------+
> >>
> >>
> >>
> >>
> +-----------------------------------------------------------------------------+
> >> | Processes: GPU
> >> Memory |
> >> | GPU PID Type Process name Usage
> >> |
> >>
> >>
> |=============================================================================|
> >> | 0 1035 G /usr/lib/xorg/Xorg
> >> 424MiB |
> >> | 0 2132 G compiz
> >> 103MiB |
> >> | 0 5296 G ...s-passed-by-fd --v8-snapshot-passed-by-fd
> >> 59MiB |
> >> | 0 14079 G ...s-passed-by-fd --v8-snapshot-passed-by-fd
> >> 31MiB |
> >> | 0 14234 G ...ing<BrotliEncoding --disable-features=Doc
> >> 108MiB |
> >>
> >>
> +-----------------------------------------------------------------------------+
> >
> >
> > and output of *nvcc --version* is:
> >
> > nvcc: NVIDIA (R) Cuda compiler driver
> >> Copyright (c) 2005-2015 NVIDIA Corporation
> >> Built on Tue_Aug_11_14:27:32_CDT_2015
> >> Cuda compilation tools, release 7.5, V7.5.17
> >
> >
> > Does anyone have any ideas what the problem might be?
> >
> > Thanks!
> > --
> > Gromacs Users mailing list
> >
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