[gmx-users] 3dc + GPU

[Ondrej Kroutil]

Dear Mark,
Thank for suggestion concerning switching between CPU and GPU. Second
option was the one I was looking for! Thank you.
And this reminds me I have one remark about new 5.0 version: in previous
versions, when I forgot what switch should I use for something I just typed
name of program with no options, pushed "enter" and it wrote me whole list
of available switches. I cannot see this in new version (if I compiled it
right).
What to put this back? Sure, it's not necessary but life was little bit
easier with this on-screen list. No searching in manual, web, and so on...

Thank you and if anybody has any suggestions or experience with 3dc and
GPU, please, share your ideas.

Ondrej



On Wed, Jul 9, 2014 at 8:49 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Jul 9, 2014 7:39 PM, "Ondrej Kroutil" <okroutil at gmail.com> wrote:
> >
> > Hi gromacs users and developers,
> > I have troubles with simulations of the system with surface (slab
> geometry)
> > using GPU and Verlet cut-off scheme.
> > When I run this simulation on CPU everything goes right and ions
> dissolved
> > in the water above the surface seems to behave normally. But when I
> switch
> > to GPU positively charged ions move in z-direction to the bottom of the
> > simulation box and negatively charged ions go to opposite side of the
> box.
> > I have had this problem with 4.6 version and now even with version 5.0.
> > Do you have any suggestion what can be wrong? Bad input parameters? Etc.
> > You can download tar file with input file, .tpr file (if you want to run
> it
> > on your system, output log and pictures of initial and final state)
> >
> >
>
> https://drive.google.com/file/d/0Byl8CD_rdzQOZVB2UGVHQzllMms/edit?usp=sharing
> >
> > Thank you very much and keep developing Gromacs, the best simulation
> > package ever!
> >
> > Ondřej
> >
> > Btw.: How can I set-up in gromacs-5.0 to run simulations only on CPU?
>
> No idea for the main issue, but cmake -DGMX_GPU=off or running as mdrun -nb
> CPU are different ways to do what you want.
>
> Mark
>
> > --
> > Ondřej Kroutil
> >         ,,              Faculty of Health and Social Studies
> >    ----"))'             University of South Bohemia
> >      OOO           Jirovcova 24, Ceske Budejovice
> >       OOO          The Czech Republic
> >         | OO         E-mail:  okroutil at gmail.com
> > >------    O         Mobile:  +420 736 537 190
> > --
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-- 
Ondřej Kroutil
        ,,              Faculty of Health and Social Studies
   ----"))'             University of South Bohemia
     OOO           Jirovcova 24, Ceske Budejovice
      OOO          The Czech Republic
        | OO         E-mail:  okroutil at gmail.com
>------    O         Mobile:  +420 736 537 190