On 7/14/16 10:35 PM, Vito Spadavecchio wrote:
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@Turing:~/Desktop/xyz_MD/APO_xyz$ gmx mdrun -deffnm md_0_2 -nb gpu
:-) GROMACS - gmx mdrun, VERSION 5.1.2 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par
Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Anca Hamuraru Vincent Hindriksen
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
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2015, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
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!
You cut out the part of the .log file that shows how mdrun actually spent its
time. This is perhaps the most valuable information. This is why Szilard asked
for you to share a complete .log file (upload it somewhere, post a URL) so we
can see all relevant details.
-Justin
On Thu, Jul 14, 2016 at 4:54 PM, Szilárd Páll <pall.szil...@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
<spadavecc...@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!
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--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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==================================================
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