Hi,
Actually, if you don't want to run across the network, with those Westmere
processors you should be fine with running OpenMP across the two sockets,
i.e
mdrun -ntomp 24
or to run without HyperThreading (which can be sometimes faster) just use
mdrun -ntomp 12 -pin on
Now, when it comes to GPU
Hello Szilard
Many thanks for these very useful comments!
We run jobs on a single node of a small Apple cluster (no Infiniband
unfortunately). One node has two Intel(R) Xeon(R) X5650 Processors each
with 6 cores and 12 threads, so in total 12 cores and 24 threads.
I have compiled GROMACS 4.6.1 w
FYI: On your machine running OpenMP across two sockets will probably not be
very efficient. Depending on the input and at how high paralleliation are
you running, you could be better off with running multiple MPI ranks per
GPU. This is a bit of an unexplained feature due to it being complicated to
Hi Carsten
Thanks a lot for this tip. It worked!
George
> Hi,
>
> On Mar 11, 2013, at 10:50 AM, George Patargias wrote:
>
>> Hello
>>
>> Sorry for posting this again.
>>
>> I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration
>> (CUDA 5.0 lib) using the following SGE batch scri
Hi,
On Mar 11, 2013, at 10:50 AM, George Patargias wrote:
> Hello
>
> Sorry for posting this again.
>
> I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration
> (CUDA 5.0 lib) using the following SGE batch script.
>
> #!/bin/sh
> #$ -V
> #$ -S /bin/sh
> #$ -N test-gpus
> #$ -l
Hello
Sorry for posting this again.
I am trying to run GROMACS 4.6 compiled with MPI and GPU acceleration
(CUDA 5.0 lib) using the following SGE batch script.
#!/bin/sh
#$ -V
#$ -S /bin/sh
#$ -N test-gpus
#$ -l h="xgrid-node02"
#$ -pe mpi_fill_up 12
#$ -cwd
source /opt/NetUsers/pgkeka/gromacs-4
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