[gmx-users] GPU warnings
tevang3 at gmail.com
Tue Nov 6 00:03:27 CET 2012
I get these two warnings when I run the dhfr/GPU/dhfr-solv-PME.bench
benchmark with the following command line:
mdrun_intel_cuda5 -v -s topol.tpr -testverlet
"WARNING: Oversubscribing the available 0 logical CPU cores with 1
0 logical CPU cores? Isn't this bizarre? My CPU is Intel Core i7-3610QM
(2.3 GHz). Unlike Albert, I don't see any performance loss, I get 13.4
ns/day on a single core with 1 GPU and 13.2 ns/day with GROMACS v4.5.5 on 4
cores (8 threads) without the GPU. Yet, I don't see any performance gain
with more that 4 -nt threads.
mdrun_intel_cuda5 -v -nt 2 -s topol.tpr -testverlet : 15.4 ns/day
mdrun_intel_cuda5 -v -nt 3 -s topol.tpr -testverlet : 16.0 ns/day
mdrun_intel_cuda5 -v -nt 4 -s topol.tpr -testverlet : 16.3 ns/day
mdrun_intel_cuda5 -v -nt 6 -s topol.tpr -testverlet : 16.2 ns/day
mdrun_intel_cuda5 -v -nt 8 -s topol.tpr -testverlet : 15.4 ns/day
I have also attached my log file (from "mdrun_intel_cuda5 -v -s topol.tpr
-testverlet") in case you find it helpful.
On 5 November 2012 18:54, Szilárd Páll <szilard.pall at cbr.su.se> wrote:
> The first warning indicates that you are starting more threads than the
> hardware supports which would explain the poor performance.
> Could share a log file of the suspiciously slow run as well as the command
> line you used to start mdrun?
> On Sun, Nov 4, 2012 at 5:32 PM, Albert <mailmd2011 at gmail.com> wrote:
> > well, IC.
> > the performance is rather poor than GTX590..... 32ns/day vs 4 ns/day
> > probably that's also something related to the warnings?
> > THX
> > On 11/04/2012 01:59 PM, Justin Lemkul wrote:
> >> On 11/4/12 4:55 AM, Albert wrote:
> >>> hello:
> >>> I am running Gromacs 4.6 GPU on a workstation with two GTX 660 Ti (2
> >>> 1344
> >>> CUDA cores), and I got the following warnings:
> >>> thank you very much.
> >>> ---------------------------**messages----------------------**
> >>> -------------
> >>> WARNING: On node 0: oversubscribing the available 0 logical CPU cores
> >>> per node
> >>> with 2 MPI processes.
> >>> This will cause considerable performance loss!
> >>> 2 GPUs detected on host boreas:
> >>> #0: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC: no, stat:
> >>> compatible
> >>> #1: NVIDIA GeForce GTX 660 Ti, compute cap.: 3.0, ECC: no, stat:
> >>> compatible
> >>> 2 GPUs auto-selected to be used for this run: #0, #1
> >>> Using CUDA 8x8x8 non-bonded kernels
> >>> Making 1D domain decomposition 1 x 2 x 1
> >>> * WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *
> >>> We have just committed the new CPU detection code in this branch,
> >>> and will commit new SSE/AVX kernels in a few days. However, this
> >>> means that currently only the NxN kernels are accelerated!
> >>> In the mean time, you might want to avoid production runs in 4.6.
> >> I can't address the first warning, but the second is fairly obvious.
> >> You're not using an official release, you're using the development
> >> - let the user beware. The code is not yet production-ready.
> >> -Justin
> > --
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University of Athens
Faculty of Pharmacy
Department of Pharmaceutical Chemistry
157 71 Athens
email: tevang at pharm.uoa.gr
tevang3 at gmail.com
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