Hello,
I am having some troubles efficiently running simulations in parallel on a
gpu-cluster. The cluster has 8 GPUs and 16 CPUs. Currently, the command that I
am using is:
mpirun -np 8 mdrun_mpi -multi 8 -nice 4 -s md -o md -c after_md -v -x frame
-pin on
Per-simulation, the performance
I'm confused by your description of the cluster as having 8 GPUs and 16
CPUs. The relevant parameters are the number of GPUs and CPU cores per
node. See the examples at
http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-features.html#running-multi-simulations
Mark
On Tue, Sep 1
Wed, Sep 16, 2015 at 4:41 PM Zimmerman, Maxwell
wrote:
> Hi Mark,
>
> Sorry for the confusion, what I meant to say was that each node on the
> cluster has 8 GPUs and 16 CPUs.
>
OK. Please note that "CPU" is ambiguous, so you should prefer not to use it
without clarificatio
Hi,
On Wed, Sep 16, 2015 at 5:46 PM Zimmerman, Maxwell
wrote:
> Hi Mark,
>
> Thank you for the feedback.
>
> To ensure that I am making a proper comparison, I tried running:
> mpirun -np 1 mdrun_mpi -ntomp 2 -gpu_id 0 -pin on
> and I still see the same pattern; running a sin
ct and unambiguous. There's 8 simulations, each
with 1 domain, so 8 PP ranks, and each is mapped to one of 8 GPUs *in this
node*. You've been reading "node" and thinking "simulation."
Mark
On Wed, Sep 16, 2015 at 9:23 PM Zimmerman, Maxwell
wrote:
> Hi Mark
...@maillist.sys.kth.se
on behalf of Mark Abraham
Sent: Thursday, September 17, 2015 12:18 PM
To: gmx-us...@gromacs.org; gromacs.org_gmx-users@maillist.sys.kth.se
Subject: Re: [gmx-users] Efficiently running multiple simulations
Hi,
On Thu, Sep 17, 2015 at 6:24 PM Zimmerman, Maxwell
wrote
