On Fri, Jul 19, 2013 at 6:59 PM, gigo wrote:
> Hi!
>
>
> On 2013-07-17 21:08, Mark Abraham wrote:
>>
>> You tried ppn3 (with and without --loadbalance)?
>
>
> I was testing on 8-replicas simulation.
>
> 1) Without --loadbalance and -np 8.
> Excerpts from the script:
> #PBS -l nodes=8:ppn=3
> seten
Hi!
On 2013-07-17 21:08, Mark Abraham wrote:
You tried ppn3 (with and without --loadbalance)?
I was testing on 8-replicas simulation.
1) Without --loadbalance and -np 8.
Excerpts from the script:
#PBS -l nodes=8:ppn=3
setenv OMP_NUM_THREADS 4
mpiexec mdrun_mpi -v -cpt 20 -multi 8 -ntomp 4 -re
You tried ppn3 (with and without --loadbalance)?
Mark
On Wed, Jul 17, 2013 at 6:30 PM, gigo wrote:
> On 2013-07-13 11:10, Mark Abraham wrote:
>>
>> On Sat, Jul 13, 2013 at 1:24 AM, gigo wrote:
>>>
>>> On 2013-07-12 20:00, Mark Abraham wrote:
On Fri, Jul 12, 2013 at 4:27 PM, gigo
On 2013-07-13 11:10, Mark Abraham wrote:
On Sat, Jul 13, 2013 at 1:24 AM, gigo wrote:
On 2013-07-12 20:00, Mark Abraham wrote:
On Fri, Jul 12, 2013 at 4:27 PM, gigo wrote:
Hi!
On 2013-07-12 11:15, Mark Abraham wrote:
What does --loadbalance do?
It balances the total number of proce
On Sat, Jul 13, 2013 at 1:24 AM, gigo wrote:
> On 2013-07-12 20:00, Mark Abraham wrote:
>>
>> On Fri, Jul 12, 2013 at 4:27 PM, gigo wrote:
>>>
>>> Hi!
>>>
>>> On 2013-07-12 11:15, Mark Abraham wrote:
What does --loadbalance do?
>>>
>>>
>>>
>>> It balances the total number of proces
On 2013-07-12 20:00, Mark Abraham wrote:
On Fri, Jul 12, 2013 at 4:27 PM, gigo wrote:
Hi!
On 2013-07-12 11:15, Mark Abraham wrote:
What does --loadbalance do?
It balances the total number of processes across all allocated nodes.
OK, but using it means you are hostage to its assumptions
On Fri, Jul 12, 2013 at 4:27 PM, gigo wrote:
> Hi!
>
> On 2013-07-12 11:15, Mark Abraham wrote:
>>
>> What does --loadbalance do?
>
>
> It balances the total number of processes across all allocated nodes.
OK, but using it means you are hostage to its assumptions about balance.
> The
> thing is
Hi!
On 2013-07-12 11:15, Mark Abraham wrote:
What does --loadbalance do?
It balances the total number of processes across all allocated nodes.
The thing is that mpiexec does not know that I want each replica to fork
to 4 OpenMP threads. Thus, without this option and without affinities
(in a
What does --loadbalance do? What do the .log files say about
OMP_NUM_THREADS, thread affinities, pinning, etc?
Mark
On Fri, Jul 12, 2013 at 3:46 AM, gigo wrote:
> Dear GMXers,
> With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were
> separate MPI jobs of course (OpenMPI 1.6.4).
Dear GMXers,
With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were
separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4
cores with OpenMP. There is Torque installed on the cluster build of
12-cores nodes, so I used the following script:
#!/bin/tcsh -f
#PBS -S
Dear GMXers,
With Gromacs 4.6.2 I was running REMD with 144 replicas. Replicas were
separate MPI jobs of course (OpenMPI 1.6.4). Each replica I run on 4
cores with OpenMP. There is Torque installed on the cluster build of
12-cores nodes, so I used the following script:
#!/bin/tcsh -f
#PBS -S
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