As Mark said, please share the *entire* log file. Among other
important things, the result of PP-PME tuning is not included above.
However, I suspect that in this case scaling is strongly affected or
by the small size of the system you are simulating.
--
Szilárd
On Sun, Nov 10, 2013 at 5:28 AM,
Hi Mark and Szilard
Thanks for your both suggestions. They are very helpful.
Neither run had a PP-PME work distribution suitable for the hardware it
was
running on (and fixing that for each run requires opposite changes).
Adding
a GPU and hoping to see scaling requires that there be
On Sun, Nov 10, 2013 at 5:28 AM, Dwey Kauffman mpi...@gmail.com wrote:
Hi Szilard,
Thank you very much for your suggestions.
Actually, I was jumping to conclusions too early, as you mentioned AMD
cluster, I assumed you must have 12-16-core Opteron CPUs. If you
have an 8-core (desktop?)
Hi Szilard,
Thank you very much for your suggestions.
Actually, I was jumping to conclusions too early, as you mentioned AMD
cluster, I assumed you must have 12-16-core Opteron CPUs. If you
have an 8-core (desktop?) AMD CPU, than you may not need to run more
than one rank per GPU.
Yes, we do
First, there is no value in ascribing problems to the hardware if the
simulation setup is not yet balanced, or not large enough to provide enough
atoms and long enough rlist to saturate the GPUs, etc. Look at the log
files and see what complaints mdrun makes about things like PME load
balance, and
Let's not hijack James' thread as your hardware is different from his.
On Tue, Nov 5, 2013 at 11:00 PM, Dwey Kauffman mpi...@gmail.com wrote:
Hi Szilard,
Thanks for your suggestions. I am indeed aware of this page. In a 8-core
AMD with 1GPU, I am very happy about its performance. See
On Thu, Nov 7, 2013 at 6:34 AM, James Starlight jmsstarli...@gmail.com wrote:
I've gone to conclusion that simulation with 1 or 2 GPU simultaneously gave
me the same performance
mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test,
mdrun -ntmpi 2 -ntomp 6 -gpu_id 0 -v -deffnm
Hi Dwey,
On 05/11/13 22:00, Dwey Kauffman wrote:
Hi Szilard,
Thanks for your suggestions. I am indeed aware of this page. In a 8-core
AMD with 1GPU, I am very happy about its performance. See below. My
intention is to obtain a even better one because we have multiple nodes.
### 8 core
I've gone to conclusion that simulation with 1 or 2 GPU simultaneously gave
me the same performance
mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test,
mdrun -ntmpi 2 -ntomp 6 -gpu_id 0 -v -deffnm md_CaM_test,
Doest it be due to the small CPU cores or addition RAM ( this system has 32
: Re: [gmx-users] Gromacs-4.6 on two Titans GPUs
To: Discussion list for GROMACS users gmx-users@gromacs.org
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camnumasm5ht40ub+unppv7gmhqzxsb6psewma+hblv+gnb2...@mail.gmail.com
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On Tue, Nov 5, 2013 at 12:55 PM, James Starlight
mark.j.abra...@gmail.com
Subject: Re: [gmx-users] Gromacs-4.6 on two Titans GPUs
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
camnumasm5ht40ub+unppv7gmhqzxsb6psewma+hblv+gnb2...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
On Tue, Nov 5, 2013
Hi Szilard,
Thanks for your suggestions. I am indeed aware of this page. In a 8-core
AMD with 1GPU, I am very happy about its performance. See below. My
intention is to obtain a even better one because we have multiple nodes.
### 8 core AMD with 1 GPU,
Force evaluation time GPU/CPU: 4.006
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