[gmx-users] FEP calculations on multiple nodes

Leandro Bortot leandro.obt at gmail.com
Thu Aug 24 17:34:16 CEST 2017 

Hello all,

     This may add something: I had Segmentation Fault using flat-bottom
restraints with GPUs before. I just assumed that this type of restraint was
not supported by GPUs and moved to a CPU-only system.
     Sadly it was some time ago and I don't have the files anymore.

Best,
Leandro


On Thu, Aug 24, 2017 at 5:13 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Thanks. Good lesson here - try simplifying until things work. That does
> suggest there is a bug in flat bottomed position restraints. Can you please
> upload a tpr with those restraints, along with a report at
> https://redmine.gromacs.org so we can reproduce and hopefully fix it?
>
> Mark
>
> On Thu, 24 Aug 2017 16:55 Vikas Dubey <vikasdubey055 at gmail.com> wrote:
>
> > Hi,
> >
> > I have just checked with normal restraints. it works fine. Simulation
> crash
> > with flat bottom restraints.
> >
> > On 24 August 2017 at 16:43, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
> >
> > > Hi,
> > >
> > > Does it work if you just have the normal position restraints, or just
> > have
> > > the flat-bottom restraints? In particular, I could image the latter are
> > not
> > > widely used and might have a bug.
> > >
> > > Mark
> > >
> > > On Thu, Aug 24, 2017 at 4:36 PM Vikas Dubey <vikasdubey055 at gmail.com>
> > > wrote:
> > >
> > > > Hi everyone,
> > > >
> > > > I have found out that positions restrains is the issue in my FEP
> > > > simulation.  As soon as I switch off position restraints it works
> > fine. I
> > > > have the following the restraint file for the ions in my system (I
> > don't
> > > > see any problems with it):
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > > *[ position_restraints ]; atom  type      fx      fy      fz    1
>  1
> > > 0
> > > > 0  1000     2     1  0  0  1000     3     1  0  0  1000     4     1
> > 0  0
> > > > 1000    5     1  0  0  1000     6     1  0  0  1000     8     1  0  0
> > > > 1000     9     1  0  0  1000    10     1  0  0  1000    11     1  0
> 0
> > > > 1000    12     1  0  0  1000    13     1  0  0  1000    14     1  0
> 0
> > > > 1000    15     1  0  0  1000    16     1  0  0  1000    17     1  0
> 0
> > > > 1000    18     1  0  0  1000    19     1  0  0  1000    20     1  0
> 0
> > > > 1000    21     1  1000  1000  1000;[ position_restraints ] ; flat
> > bottom
> > > > position restraints, here for potassium in site I;  type, g(8 for a
> > > > cylinder), r(nm), k    7      2    8      1  1000*
> > > >
> > > >
> > > > On 22 August 2017 at 14:18, Vikas Dubey <vikasdubey055 at gmail.com>
> > wrote:
> > > >
> > > > > Hi, I use the following script for my cluster. Also, I think
> problem
> > is
> > > > > calculation specific. I have run a quite a few normal simulations ,
> > it
> > > > > works fine :
> > > > >
> > > > >
> > > > > #SBATCH --job-name=2_1_0
> > > > > #SBATCH --mail-type=ALL
> > > > > #SBATCH --time=24:00:00
> > > > > #SBATCH --nodes=1
> > > > > #SBATCH --ntasks-per-node=1
> > > > > #SBATCH --ntasks-per-core=2
> > > > > #SBATCH --cpus-per-task=4
> > > > > #SBATCH --constraint=gpu
> > > > > #SBATCH --output out.txt
> > > > > #SBATCH --error  err.txt
> > > > > #========================================
> > > > > # load modules and run simulation
> > > > > module load daint-gpu
> > > > > module load GROMACS
> > > > > export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
> > > > > export CRAY_CUDA_MPS=1
> > > > >
> > > > > srun -n $SLURM_NTASKS --ntasks-per-node=$SLURM_NTASKS_PER_NODE -c
> > > > > $SLURM_CPUS_PER_TASK gmx_mpi mdrun -deffnm md_0
> > > > >
> > > > > On 22 August 2017 at 06:11, Nikhil Maroli <scinikhil at gmail.com>
> > wrote:
> > > > >
> > > > >> Okay, you might need to consider
> > > > >>
> > > > >> gmx mdrun -v -ntmpi XX -ntomp XX -deffnm XXXX  -gpu_id XXX
> > > > >>
> > > > >>
> > > > >>
> > > > >> http://manual.gromacs.org/documentation/5.1/user-guide/mdrun
> > > > >> -performance.html
> > > > >>
> > > > >> http://www.gromacs.org/Documentation/Errors#There_is_no_
> > > > >> domain_decomposition_for_n_nodes_that_is_compatible_with_the
> > > > >> _given_box_and_a_minimum_cell_size_of_x_nm
> > > > >> --
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