Hi,
My OS is Fedora 13 (64 bits) and I used gcc 4.4.4. I ran the program
you sent me. Bellow are the results of 5 runs. As you can see the
results are rougly the same
[ren...@scrat ~]$ ./time
2.09 2.102991
[ren...@scrat ~]$ ./time
2.09 2.102808
[ren...@scrat ~]$ ./time
2.09 2.104577
[
Hi,
On Fri, Oct 22, 2010 at 3:20 PM, Renato Freitas wrote:
>
>
> Do you think that the "NODE" and "Real" time difference could be
> attributed to some compilation problem in the mdrun-gpu. Despite I'm
> asking this I didn't get any error in the compilation.
>
It is very odd that these are differ
Hi Szilárd,
Thans for your explanation. Do you know if there will be a new
improvement of PME algorithms to take the full advantage of GPU video
cards?
Do you think that the "NODE" and "Real" time difference could be
attributed to some compilation problem in the mdrun-gpu. Despite I'm
asking this
Hi Roland,
In fact I get better performance values using different rcoulomb,
fourierspacing and the values of -npme suggested by g_tune_pme using
-nt=12.
The simulation using GPU was carried out using the dedicated machine,
no other programs was runnig, even the graphical interface was
stopped.
Hi Renato,
First of all, what you're seeing is pretty normal, especially that you
have a CPU that is crossing the border of insane :) Why is it normal?
The PME algorithms are just simply not very well not well suited for
current GPU architectures. With an ill-suited algorithm you won't be
able to
On Thu, Oct 21, 2010 at 5:53 PM, Renato Freitas wrote:
> Thanks Roland. I will do a newer test using the fourier spacing equal
> to 0.11.
I'd also suggest to look at g_tune_pme and run with different rcoulomb,
fourier_spacing. As long as the ratio is the same you get the same accuracy.
And you s
Thanks Roland. I will do a newer test using the fourier spacing equal
to 0.11. However, about the performance of GPU versus CPU (mpi) let me
try to explain it better:
The simulation using gromacs with GPU started and finished:
Started mdrun on node 0 Wed Oct 20 09:52:09 2010
Finished mdrun on nod
On Thu, Oct 21, 2010 at 3:18 PM, Renato Freitas wrote:
> Hi gromacs users,
>
> I have installed the lastest version of gromacs (4.5.1) in an i7 980X
> (6 cores or 12 with HT on; 3.3 GHz) with 12GB of RAM and compiled its
> mpi version. Also I compiled the GPU-accelerated
> version of gromacs. The
Hi gromacs users,
I have installed the lastest version of gromacs (4.5.1) in an i7 980X
(6 cores or 12 with HT on; 3.3 GHz) with 12GB of RAM and compiled its
mpi version. Also I compiled the GPU-accelerated
version of gromacs. Then I did a 2 ns simulation using a small system
(11042 atoms) to co
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