That should never happen. If mdrun is compiled with GPU support and
GPUs are detected, the detection stats should always get printed.
Can you reliably reproduce the issue?
--
Szilárd
On Fri, Aug 2, 2013 at 9:50 AM, Jernej Zidar wrote:
> Hi there.
> Lately I've been running simulations using G
Hi there.
Lately I've been running simulations using GPUs on a computer node.
I noticed that though the GPUs are always in use sometimes I don't get
this message in the output:
Using 4 MPI threads
Using 2 OpenMP threads per tMPI thread
4 GPUs detected:
#0: NVIDIA Tesla C2070, compute cap.: 2.0
On Mon, Jun 24, 2013 at 4:43 PM, Szilárd Páll wrote:
> On Sat, Jun 22, 2013 at 5:55 PM, Mirco Wahab
> wrote:
>> On 22.06.2013 17:31, Mare Libero wrote:
>>>
>>> I am assembling a GPU workstation to run MD simulations, and I was
>>> wondering if anyone has any recommendation regarding the GPU/CPU
>
Thanks Mirco, good info, your numbers look quite consistent. The only
complicating factor is that your CPUs are overclocked by different
amounts, which changes the relative performances somewhat compared to
non-overclocked parts.
However, let me list some prices to show that the top-of-the line AM
On Sat, Jun 22, 2013 at 5:55 PM, Mirco Wahab
wrote:
> On 22.06.2013 17:31, Mare Libero wrote:
>>
>> I am assembling a GPU workstation to run MD simulations, and I was
>> wondering if anyone has any recommendation regarding the GPU/CPU
>> combination.
>> From what I can see, the GTX690 could be th
I strongly suggest that you consider the single-chip GTX cards instead
of a dual-chip one; from the point of view of price/performance you'll
probably get the most from a 680 or 780.
You could ask why, so here are the reasons:
- The current parallelization scheme requires domain-decomposition to
u
On 22.06.2013 22:18, Mare Libero wrote:
The vendor I contacted was pushing for one of the
high end i7 processors with hyper-threading. But from what I can read,
most of the MD software don't make any use of it. So, using a the
multi-cores AMD (like your FX-8350) can be a cheaper and more
advanta
On 22.06.2013 17:31, Mare Libero wrote:
I am assembling a GPU workstation to run MD simulations, and I was wondering if
anyone has any recommendation regarding the GPU/CPU combination.
From what I can see, the GTX690 could be the best bang for my buck in terms of
number of cores, memory, clock
Hello,
I am assembling a GPU workstation to run MD simulations, and I was wondering if
anyone has any recommendation regarding the GPU/CPU combination.
From what I can see, the GTX690 could be the best bang for my buck in terms of
number of cores, memory, clock rate. But being a dual GPU card,
Can you re-compile with debugging symbols and obtain a full backtrace?
-Justin
On 11/21/12 11:58 AM, Emanuele Coccia wrote:
4.1.1 installed from binaries.
2012/11/21 Justin Lemkul
On 11/21/12 11:11 AM, Emanuele Coccia wrote:
Running your benchmark for the first time (dhfr-impl-1nm.benc
4.1.1 installed from binaries.
2012/11/21 Justin Lemkul
>
>
> On 11/21/12 11:11 AM, Emanuele Coccia wrote:
>
>> Running your benchmark for the first time (dhfr-impl-1nm.bench) I have the
>> following message:
>>
>>
>> *Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single
>> precision
On 11/21/12 11:11 AM, Emanuele Coccia wrote:
Running your benchmark for the first time (dhfr-impl-1nm.bench) I have the
following message:
*Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)
*
*
*
*WARNING: OpenMM does not support leap-frog, will use velocity-verlet
i
Running your benchmark for the first time (dhfr-impl-1nm.bench) I have the
following message:
*Reading file topol.tpr, VERSION 4.5.1-dev-20100917-b1d66 (single precision)
*
*
*
*WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.*
*
*
*
*
*WARNING: OpenMM supports onl
On 11/21/12 10:43 AM, Emanuele Coccia wrote:
Dear Support,
I have installed the version 4.5.5 of Gromacs, I have also installede
mdrun-gpu. I have a GeForce GTX 670 and CUDA toolkit 4.0; is this
environment compatible with Gromacs-GPU?
Likely. Are you having some issue getting mdrun to w
Hi,
First I thought that there might be a memory leak which could have
caused this if you ran for really long time. However, I've just ran
the very same benchmark (dhfr with PME) for one hour, monitored the
memory usage and I couldn't see any change whatsoever (see the plot
attached).
I've attach
Hi,
I have Gromacs-GPU version 4.5.5 and GTX 580.
I ran dhfr-solv-PME benchmark test (see below) and my run was killed after
couple of hours exhausting all the computer memory, including the swap (2G + 4G
swap).
Has anyone encountered this problem? What is wrong?
Thanks, Efrat
> mdrun-gpu -dev
Hi,
I have Gromacs- GPU version 4.5.5 and GTX 580.
I run dhfr-solv-PME benchmark test (see below) and my run is killed after
couple of hours when it exhausts all the computer memory, including the swap
(2G + 4G swap).
Has anyone encountered this problem? What do I do wrong?
Thanks, Efrat
--
gm
Hi all,
The NAIS Centre in Edinburgh is holding a Workshop on State-of-the-Art
Algorithms for Molecular Dynamics on May 2-4.
The days before this workshop, April 30-May 2, I and David Hardy from NAMD will
organize a tutorial on the use of GPUs and parallel computing. Here, among
other things,
Hi Matt,
> Thanks- gromacs 4.5.5 is working with my NVidia card with the "force
> option". I found one weirdness - if I check the card temperature
> (using NVIDIA's configuration tool in X11) it seems like this messes
> up the MR and all the trajectories after that point have no atoms in
> VMD.
Szilárd,
Thanks- gromacs 4.5.5 is working with my NVidia card with the "force
option". I found one weirdness - if I check the card temperature
(using NVIDIA's configuration tool in X11) it seems like this messes
up the MR and all the trajectories after that point have no atoms in
VMD. So, that'
Hi Matt,
Yes, you should use the "force-device=yes" option, the patch which was
meant to update the list of compatible GPUs didn't make it for 4.5.5.
Cheers,
--
Szilárd
On Sun, Oct 23, 2011 at 10:24 PM, Matt Larson wrote:
> I am having an error trying to use a compiled mdrun-gpu on my GPU set
I am having an error trying to use a compiled mdrun-gpu on my GPU setup here:
Fatal error:
The selected GPU (#0, GeForce GTX 580) is not supported by Gromacs!
Most probably you have a low-end GPU which would not perform well, or
new hardware that has not been tested with the current release. If y
Hi all!
I am trying to run the dppc example located in
ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz, with the gpu
version of gromacs, when I run it I get
WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.
---
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