Re: [gmx-users] Problems with REMD in Gromacs 4.6.3

2013-07-31 Thread Szilárd Páll
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

Re: [gmx-users] Problems with REMD in Gromacs 4.6.3

2013-07-19 Thread gigo
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

Re: [gmx-users] Problems with REMD in Gromacs 4.6.3

2013-07-17 Thread Mark Abraham
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

Re: [gmx-users] Problems with REMD in Gromacs 4.6.3

2013-07-17 Thread 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

Re: [gmx-users] Problems with REMD in Gromacs 4.6.3

2013-07-13 Thread Mark Abraham
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

Re: [gmx-users] Problems with REMD in Gromacs 4.6.3

2013-07-12 Thread gigo
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

Re: [gmx-users] Problems with REMD in Gromacs 4.6.3

2013-07-12 Thread Mark Abraham
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

Re: [gmx-users] Problems with REMD in Gromacs 4.6.3

2013-07-12 Thread gigo
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

Re: [gmx-users] Problems with REMD in Gromacs 4.6.3

2013-07-12 Thread Mark Abraham
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).