[gmx-users] 3dc + GPU

Szilárd Páll pall.szilard at gmail.com
Thu Jul 10 11:55:15 CEST 2014


On Thu, Jul 10, 2014 at 11:10 AM, Ondrej Kroutil <okroutil at gmail.com> wrote:
> 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...

That's the help page which can be accessed using the "-h" option. The
man pages are also useful and if you have not heard of shell
completion you may want to try it: source GMXRC, type in the command,
press "TAB" and you get the available arguments.

Cheers,
--
Szilárd

> 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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>> >
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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
> --
> Gromacs Users mailing list
>
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